[RESOLVED] Hcp_freesurfer fails with AttributeError

Description:
Hi, I am running into an issue running hcp_freesurfer in QuNex 0.90.6 within a Singularity container. hcp_pre_freesurfer ran perfectly, but I’m having trouble figuring out why when hcp_freesurfer is submitted with the same options it fails with AttributeError: ‘module’ object has no attribute ‘ExternalFailed’ (see logs below). Thanks in advance for the help troubleshooting this!

Call:

# ran from singularity container qunex_suite-0.90.6 on UCLA hoffman2 cluster
qunex hcp_freesurfer \
     --sessions=/u/project/cbearden/data/22q/qunex_studyfolder/processing/22q_trio_batch_Q_0001_09242012.txt \
     --sessionsfolder=/u/project/cbearden/data/22q/qunex_studyfolder/sessions \
     --parsessions=1 \
     --overwrite=no

Logs:
This is the error printed to the terminal:


/u/local/Modules/4.7.0/gcc-4.8.5/init/bash: line 37: /usr/bin/tclsh: No such file or directory
........................ Running QuNex v0.90.6 ........................ 



Using /u/project/cbearden/data/22q/qunex_studyfolder/processing/22q_trio_batch_Q_0001_09242012.txt for input.


--- Full QuNex call for command: hcp_freesurfer 

gmri hcp_freesurfer --sessions="/u/project/cbearden/data/22q/qunex_studyfolder/processing/22q_trio_batch_Q_0001_09242012.txt" --sessionsfolder="/u/projec
t/cbearden/data/22q/qunex_studyfolder/sessions" --parsessions="1" --overwrite="no" 

--------------------------------------------------------- 


WARNING: Parameter qx_cifti_tail was not specified. Its value was imputed from parameter hcp_cifti_tail and set to '_Atlas'!
WARNING: Parameter qx_nifti_tail was not specified. Its value was imputed from parameter hcp_nifti_tail and set to ''!
WARNING: Parameter cifti_tail was not specified. Its value was imputed from parameter qx_cifti_tail and set to '_Atlas'!
WARNING: Parameter nifti_tail was not specified. Its value was imputed from parameter qx_nifti_tail and set to ''!
# Generated by QuNex 0.90.6 on 2021-06-14_14.34.1623706496
#
=================================================================
gmri hcp_freesurfer \
  --sessionsfolder="/u/project/cbearden/data/22q/qunex_studyfolder/sessions" \
  --parsessions="1" \
  --overwrite="no" \
  --sessions="/u/project/cbearden/data/22q/qunex_studyfolder/processing/22q_trio_batch_Q_0001_09242012.txt" \
=================================================================

Starting multiprocessing sessions in /u/project/cbearden/data/22q/qunex_studyfolder/processing/22q_trio_batch_Q_0001_09242012.txt with a pool of 1 concur
rent processes

---- Running local

Starting processing of sessions Q_0001_09242012 at Monday, 14. June 2021 14:34:56
--------------------==== QuNex failed! ====--------------------

ERROR: Execution of command `hcp_freesurfer` failed!
       Please check documentation for the command (`qunex ?hcp_freesurfer`)!

The call received was:
(please note that when run through scheduler, all possible parameters,
even non relevant ones are passed)

qunex hcp_freesurfer \
    --sessions=/u/project/cbearden/data/22q/qunex_studyfolder/processing/22q_trio_batch_Q_0001_09242012.txt \
    --sessionsfolder=/u/project/cbearden/data/22q/qunex_studyfolder/sessions \
    --parsessions=1 \
    --overwrite=no

--------------------------------------------------------------
Here's the error as caught by python:

Traceback (most recent call last):
  File "/opt/qunex/python/qx_utilities/gmri", line 499, in <module>
    main()
  File "/opt/qunex/python/qx_utilities/gmri", line 467, in main
    runCommand(comm, opts)
  File "/opt/qunex/python/qx_utilities/gmri", line 164, in runCommand
    gp.run(command, args)
  File "/opt/qunex/python/qx_utilities/general/process.py", line 716, in run
    r, status = procResponse(pending_actions(session, soptions, overwrite, c + 1))
  File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 1260, in hcp_freesurfer
    except (ge.ExternalFailed, pc.NoSourceFolder), errormessage:
AttributeError: 'module' object has no attribute 'ExternalFailed' 


no logs were generated in logs/comlogs/ and the contents of log/runlogs/Log-hcp_freesurfer-2021-06-14_14.34.1623706496.log are below:

# Generated by QuNex 0.90.6 on 2021-06-14_14.34.1623706496
#
=================================================================
gmri hcp_freesurfer \
  --sessionsfolder="/u/project/cbearden/data/22q/qunex_studyfolder/sessions" \
  --parsessions="1" \
  --overwrite="no" \
  --sessions="/u/project/cbearden/data/22q/qunex_studyfolder/processing/22q_trio_batch_Q_0001_09242012.txt" \
=================================================================

Starting multiprocessing sessions in /u/project/cbearden/data/22q/qunex_studyfolder/processing/22q_trio_batch_Q_0001_09242012.txt with a pool of 1 concurrent processes

1 Like

Hi cschleifer,

Welcome to the QuNex forums! Due to a bug in our code you are not seeing a proper error report, instead of AttributeError: 'module' object has no attribute 'ExternalFailed' QuNex should write details about what went wrong. This bug makes my work a bit harder. I will first fix the code so the error will be printed out properly.

Is there a way for me to get access to the problematic study perhaps? That way I can quickly find out what is going on. It seems like an issue with input parameters. Could you please attach the batch file ("/u/project/cbearden/data/22q/qunex_studyfolder/processing/22q_trio_batch_Q_0001_09242012.txt") to this forum post, so I can inspect.

Cheers, Jure

Hi Jure,
Thank you for your help with this! Batch file is copied below, let me know if there is any other info I can provide

# Generated by QuNex 0.90.6 on 2021-06-14_11.43.1623696203
#
# Sessions folder: /u/project/cbearden/data/22q/qunex_studyfolder/sessions
# Source files: ['session_hcp.txt']
# Parameter file: /u/project/cbearden/data/22q/qunex_studyfolder/sessions/specs/22q_trio_params.txt
#
# SPDX-FileCopyrightText: 2021 QuNex development team <https://qunex.yale.edu/>
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
# Generated by QuNex
# Suitable for version 0.90.2 and above
#
# ===============================================================================
# == Batch example preprocessing options for singleband non-HCP-compliant data ==
# == Edited by C. Schleifer, June 2021 for Bearden Lab 22q Trio data           ==
# == For all supported batch parameter options run > qunex -o                  ==
# ===============================================================================

# -------------------------> General HCP settings

_hcp_Pipeline           : ${HCPPIPEDIR}
_hcp_folderstructure    : hcpls
_hcp_filename           : standard
_hcp_processing_mode    : LegacyStyleData

# ---> Pre FreeSurfer

_hcp_suffix             :
_hcp_brainsize          : 150
_hcp_t2                 : NONE
_hcp_t1samplespacing    : NONE
_hcp_t2samplespacing    : NONE
_hcp_unwarpdir          : NONE
_hcp_gdcoeffs           : NONE
_hcp_avgrdcmethod       : NONE
_hcp_topupconfig        : NONE
_hcp_printcom           : 
_hcp_sephaseneg         : NONE
_hcp_sephasepos         : NONE
_hcp_seechospacing      : NONE
_hcp_seunwarpdir        : NONE
_hcp_biascorrect_t1w    : YES

# ---> FreeSurfer

_hcp_freesurfer_home    : ${FREESURFER_HOME}

# ---> Post FreeSurfer

_hcp_regname            : MSMSulc
_hcp_grayordinatesres   : 2
_hcp_hiresmesh          : 164
_hcp_lowresmesh         : 32
 
# ---> Diffusion preprocessing (qunex hcpd)

_hcp_dwi_echospacing    : NONE

  
# ---> fMRI Volume

#_hcp_bold_echospacing   : NONE
_hcp_bold_dcmethod      : NONE
_hcp_bold_topupconfig   : 
_hcp_bold_sephaseneg    :
_hcp_bold_sephasepos    :
_hcp_bold_sbref         : NONE
_hcp_bold_echodiff      : NONE
_hcp_bold_unwarpdir     : NONE
_hcp_bold_res           : 2
_hcp_bold_gdcoeffs      : NONE
_hcp_bold_doslicetime   : TRUE
_hcp_bold_slicetimerparams : --odd
 
# ---> fMRI Surface
 
_hcp_bold_smoothFWHM    : 2



# ===================================================
# == Settings for further preprocessing & analyses ==
# ===================================================
#
# map_hcp_data
# create_bold_brain_masks
# compute_bold_stats
# create_stats_report
# extract_nuisance_signal
# preprocess_bold
# preprocess_conc
#
# ===================================================

# ---> CIFTI mapping naming variable (qunex map_hcp_data & qunex create_bold_brain_masks)

_hcp_cifti_tail     : _Atlas


# ---> Movement scrubbing settings (qunex compute_bold_stats & qunex create_stats_report)

_mov_dvars          : 3.0
_mov_dvarsme        : 1.6
_mov_fd             : 0.5
_mov_radius         : 50.0
_mov_scrub          : yes
_mov_fidl           : udvarsme
_mov_plot           : mov_report
_mov_post           : udvarsme
_mov_before         : 1
_mov_after          : 2
_mov_bad            : udvarsme
_mov_mreport        : movement_report.txt
_mov_preport        : movement_report_post.txt
_mov_sreport        : movement_scrubbing_report.txt
_mov_pdf            : movement_plots
_mov_pref           : 


# ---> Nuisance signal (qunex extract_nuisance_signal)

_shrinknsroi        : true


# ---> Smoothing parameters

_surface_smooth     : 4
_volume_smooth      : 4
_voxel_smooth       : 2
_smooth_mask        : nonzero
_dilate_mask        : ${TemplateFolder}/atlases/mni_templates/MNI152_T1_2mm_brain_mask.nii.gz


# ---> BOLD processing (qunex preprocess_bold & preprocess_conc)

_image_source       : hcp
_image_target       : cifti
_bold_preprocess    : resting
_TR                 : 2
_omit               : 5
_pignore            : hipass=linear|regress=ignore|lopass=linear
_log                : keep
_glm_matrix         : both
_glm_residuals      : save

---
id: Q_0001_09242012
subject: Q_0001
dicom: /u/project/cbearden/data/22q/qunex_studyfolder/sessions/Q_0001_09242012/dicom
raw_data: /u/project/cbearden/data/22q/qunex_studyfolder/sessions/Q_0001_09242012/nii
data: /u/project/cbearden/data/22q/qunex_studyfolder/sessions/Q_0001_09242012/4dfp
hcp: /u/project/cbearden/data/22q/qunex_studyfolder/sessions/Q_0001_09242012/hcp

hcpready: true
11  :                 :scout-trufi localizer 3-plane [1/3] i00001
12  :                 :scout-trufi localizer 3-plane [2/3] i00002
13  :                 :scout-trufi localizer 3-plane [3/3] i00003
21  :                 :scout-trufi localizer 3-plane [1/3] i00001
22  :                 :scout-trufi localizer 3-plane [2/3] i00002
23  :                 :scout-trufi localizer 3-plane [3/3] i00003
31  : T1w             :ADNI_MPRAGE
41  : DWI:dir64       :DTI 64dir
51  :                 :Matched Bandwidth HiRes
61  : bold1:resting   :BOLD - RESTING
71  : bold2:stopsignal:BOLD - STOPSIGNAL
81  : bold3:scap      :BOLD - SCAP

I would add that I just received this same error, when attempting to run through the quickstart turnkey steps while using Qunex as a Singularity container.

1 Like

Hi droediger!

If I understand correctly you just tried to run the QuNex quick start as is. Where all components (data, batch file, mapping file) are the same as in the guide?

Cheers, Jure

Correct. I just followed all the steps in the QuickStart guide (without a scheduler). Everything ran normally for me, including prefreesurfer, until this error came up in hcp_freesurfer.

Great to know, thanks! I will try to reproduce the error by doing the same, this should help me fix this.

Unfortunately I was unable to reproduce the error, hcp_freesurfer started running without any issues on my end. Below is the command that I used:

# study name
export STUDY_NAME="quickstart"
export WORK_DIR="${HOME}/qunex"
export QUNEX_CONTAINER=/Singularity/qunex_suite-0.90.6.sif
export RAW_DATA="${WORK_DIR}/data"
export INPUT_BATCH_FILE="${RAW_DATA}/HCPA001_batch.txt"
export INPUT_MAPPING_FILE="${RAW_DATA}/HCPA001_mapping.txt"
export SESSIONS="HCPA001"
export RUNTURNKEY_TYPE="local"
export RUNTURNKEY_STEPS="hcp_freesurfer"

qunex_container run_turnkey \
  --rawdatainput="${RAW_DATA}" \
  --batchfile="${INPUT_BATCH_FILE}" \
  --mappingfile="${INPUT_MAPPING_FILE}" \
  --workingdir="${WORK_DIR}" \
  --projectname="${STUDY_NAME}" \
  --path="${WORK_DIR}/${STUDY_NAME}" \
  --sessions="${SESSIONS}" \
  --sessionids="${SESSIONS}" \
  --sessionsfoldername="sessions" \
  --turnkeytype="${RUNTURNKEY_TYPE}" \
  --container="${QUNEX_CONTAINER}" \
  --turnkeysteps="${RUNTURNKEY_STEPS}" \
  --overwritestep="yes"

Could you please upload the comlog of the successful hcp_pre_freesurfer, so I can check if that one finished OK. Thanks!

When I try to upload here I get “Sorry, new users can not upload attachments”. I copy/pasted below.

PREFREESURFER

(base) roedi004@ln0004 [~/qunex/quickstart/processing/logs/comlogs] % cat done_hcp_pre_freesurfer_HCPA001_2021-06-16_00.07.1623820053.log 
# Generated by QuNex 0.90.6 on 2021-06-16_00.07.1623820053
#
------------------------------------------------------------
Running external command via QuNex:
/opt/HCP/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh
     --path="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp"
     --subject="HCPA001"
     --t1="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/T1w/HCPA001_T1w_MPR1.nii.gz"
     --t2="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/T2w/HCPA001_T2w_SPC1.nii.gz"
     --t1template="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz"
     --t1templatebrain="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz"
     --t1template2mm="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz"
     --t2template="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz"
     --t2templatebrain="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz"
     --t2template2mm="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz"
     --templatemask="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz"
     --template2mmmask="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz"
     --brainsize="150"
     --fnirtconfig="/opt/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf"
     --SEPhaseNeg="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz"
     --SEPhasePos="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz"
     --seechospacing="0.000580009"
     --seunwarpdir="y"
     --t1samplespacing="0.0000071"
     --t2samplespacing="0.0000021"
     --unwarpdir="z"
     --gdcoeffs="NONE"
     --avgrdcmethod="TOPUP"
     --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf"
     --processing-mode="HCPStyleData"

Test file: 
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/MNINonLinear/T1w_restore_brain.nii.gz
------------------------------------------------------------

========================================
  DIRECTORY: /opt/HCP/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: v4.3.0
========================================
Wed Jun 16 00:07:33 CDT 2021:PreFreeSurferPipeline.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Wed Jun 16 00:07:33 CDT 2021:PreFreeSurferPipeline.sh: FSLDIR: /opt/fsl/fsl
Wed Jun 16 00:07:33 CDT 2021:PreFreeSurferPipeline.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Wed Jun 16 00:07:33 CDT 2021:PreFreeSurferPipeline.sh: Platform Information Follows: 
Linux cn2001 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Wed Jun 16 00:07:33 CDT 2021:PreFreeSurferPipeline.sh: Parsing Command Line Options
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: Finished Parsing Command Line Options
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: StudyFolder: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: Subject: HCPA001
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T1wInputImages: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/T1w/HCPA001_T1w_MPR1.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T2wInputImages: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/T2w/HCPA001_T2w_SPC1.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T1wTemplate: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T1wTemplateBrain: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T1wTemplate2mm: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T2wTemplate: /opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T2wTemplateBrain: /opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T2wTemplate2mm: /opt/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: TemplateMask: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: Template2mmMask: /opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: BrainSize: 150
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: FNIRTConfig: /opt/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: MagnitudeInputName: 
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: PhaseInputName: 
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: GEB0InputName: 
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: TE: 
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodeNegative: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: SpinEchoPhaseEncodePositive: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: SEEchoSpacing: 0.000580009
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: SEUnwarpDir: y
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T1wSampleSpacing: 0.0000071
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T2wSampleSpacing: 0.0000021
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: UnwarpDir: z
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: GradientDistortionCoeffs: NONE
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: AvgrdcSTRING: TOPUP
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: TopupConfig: /opt/HCP/HCPpipelines/global/config/b02b0.cnf
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: BiasFieldSmoothingSigma: 
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: UseJacobian: true
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T1wBiasCorrect: 
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: CustomBrain: NONE
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: ProcessingMode: HCPStyleData
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T1wFolder: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: T2wFolder: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T2w
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: AtlasSpaceFolder: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/MNINonLinear
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: mkdir -p /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/xfms/
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: mkdir -p /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T2w/xfms/
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: mkdir -p /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/MNINonLinear/xfms/
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: POSIXLY_CORRECT=
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: Processing Modality: T1w
Wed Jun 16 00:07:36 CDT 2021:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION
Wed Jun 16 00:07:43 CDT 2021:PreFreeSurferPipeline.sh: Not Averaging T1w Images
Wed Jun 16 00:07:43 CDT 2021:PreFreeSurferPipeline.sh: ONLY ONE IMAGE FOUND: COPYING
Wed Jun 16 00:07:44 CDT 2021:PreFreeSurferPipeline.sh: Aligning T1w image to /opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz to create native volume space
Wed Jun 16 00:07:44 CDT 2021:PreFreeSurferPipeline.sh: mkdir -p /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/ACPCAlignment
Wed Jun 16 00:07:44 CDT 2021:ACPCAlignment.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Wed Jun 16 00:07:44 CDT 2021:ACPCAlignment.sh: FSLDIR: /opt/fsl/fsl
Wed Jun 16 00:07:45 CDT 2021:ACPCAlignment.sh: START
Final FOV is: 
0.000000 208.000000 0.000000 300.000000 70.000000 188.000000 

Wed Jun 16 00:09:38 CDT 2021:ACPCAlignment.sh: END
Wed Jun 16 00:09:38 CDT 2021:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking
Wed Jun 16 00:09:38 CDT 2021:PreFreeSurferPipeline.sh: mkdir -p /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/BrainExtraction_FNIRTbased
Wed Jun 16 00:09:38 CDT 2021:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Wed Jun 16 00:09:38 CDT 2021:BrainExtraction_FNIRTbased.sh: FSLDIR: /opt/fsl/fsl
Wed Jun 16 00:09:38 CDT 2021:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /opt/HCP/HCPpipelines/global/templates
Wed Jun 16 00:09:39 CDT 2021:BrainExtraction_FNIRTbased.sh: START: BrainExtraction_FNIRT
Wed Jun 16 00:24:55 CDT 2021:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT
Wed Jun 16 00:24:55 CDT 2021:PreFreeSurferPipeline.sh: Processing Modality: T2w
Wed Jun 16 00:24:55 CDT 2021:PreFreeSurferPipeline.sh: NOT PERFORMING GRADIENT DISTORTION CORRECTION
Wed Jun 16 00:24:56 CDT 2021:PreFreeSurferPipeline.sh: Not Averaging T2w Images
Wed Jun 16 00:24:56 CDT 2021:PreFreeSurferPipeline.sh: ONLY ONE IMAGE FOUND: COPYING
Wed Jun 16 00:24:57 CDT 2021:PreFreeSurferPipeline.sh: Aligning T2w image to /opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz to create native volume space
Wed Jun 16 00:24:57 CDT 2021:PreFreeSurferPipeline.sh: mkdir -p /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T2w/ACPCAlignment
Wed Jun 16 00:24:57 CDT 2021:ACPCAlignment.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Wed Jun 16 00:24:57 CDT 2021:ACPCAlignment.sh: FSLDIR: /opt/fsl/fsl
Wed Jun 16 00:24:58 CDT 2021:ACPCAlignment.sh: START
Final FOV is: 
0.000000 208.000000 0.000000 300.000000 71.000000 188.000000 

Wed Jun 16 00:26:54 CDT 2021:ACPCAlignment.sh: END
Wed Jun 16 00:26:55 CDT 2021:PreFreeSurferPipeline.sh: Performing Brain Extraction using FNIRT-based Masking
Wed Jun 16 00:26:55 CDT 2021:PreFreeSurferPipeline.sh: mkdir -p /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T2w/BrainExtraction_FNIRTbased
Wed Jun 16 00:26:55 CDT 2021:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Wed Jun 16 00:26:55 CDT 2021:BrainExtraction_FNIRTbased.sh: FSLDIR: /opt/fsl/fsl
Wed Jun 16 00:26:55 CDT 2021:BrainExtraction_FNIRTbased.sh: HCPPIPEDIR_Templates: /opt/HCP/HCPpipelines/global/templates
Wed Jun 16 00:26:55 CDT 2021:BrainExtraction_FNIRTbased.sh: START: BrainExtraction_FNIRT
Wed Jun 16 00:41:23 CDT 2021:BrainExtraction_FNIRTbased.sh: END: BrainExtraction_FNIRT
Wed Jun 16 00:41:23 CDT 2021:PreFreeSurferPipeline.sh: Performing TOPUP Readout Distortion Correction
Wed Jun 16 00:41:23 CDT 2021:PreFreeSurferPipeline.sh: mkdir -p /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T2w/T2wToT1wDistortionCorrectAndReg
Wed Jun 16 00:41:23 CDT 2021:T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Wed Jun 16 00:41:23 CDT 2021:T2wToT1wDistortionCorrectAndReg.sh: FSLDIR: /opt/fsl/fsl
Wed Jun 16 00:41:23 CDT 2021:T2wToT1wDistortionCorrectAndReg.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Wed Jun 16 00:41:25 CDT 2021:T2wToT1wDistortionCorrectAndReg.sh: START
TopupPreprocessingAll.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
TopupPreprocessingAll.sh: FSLDIR: /opt/fsl/fsl
TopupPreprocessingAll.sh: HCPPIPEDIR_Global: /opt/HCP/HCPpipelines/global/scripts
Wed Jun 16 00:41:25 CDT 2021:TopupPreprocessingAll.sh: START: Topup Field Map Generation and Gradient Unwarping
SSD = 1196.32	n = 88400	Reg = 0	Cost = 1196.32
SSD = 798.614	n = 88400	Reg = 56.9924	Cost = 855.607
SSD = 662.918	n = 88296	Reg = 99.713	Cost = 762.631
SSD = 627.94	n = 88125	Reg = 118.7	Cost = 746.64
SSD = 618.877	n = 88055	Reg = 124.886	Cost = 743.763
SSD = 616.689	n = 88023	Reg = 126.595	Cost = 743.285
***Going to next resolution level***
SSD = 977.868	n = 88023	Reg = 57.1253	Cost = 1034.99
SSD = 760.575	n = 88216	Reg = 106.062	Cost = 866.637
SSD = 691.843	n = 88400	Reg = 141.443	Cost = 833.286
SSD = 671.038	n = 88400	Reg = 154.506	Cost = 825.544
SSD = 663.7	n = 88400	Reg = 159.293	Cost = 822.993
SSD = 660.594	n = 88400	Reg = 161.359	Cost = 821.953
***Going to next resolution level***
SSD = 1445.73	n = 88400	Reg = 35.3318	Cost = 1481.06
SSD = 1140.03	n = 88400	Reg = 102.836	Cost = 1242.87
SSD = 1035.07	n = 88400	Reg = 146.037	Cost = 1181.11
SSD = 999.501	n = 88400	Reg = 163.136	Cost = 1162.64
SSD = 983.721	n = 88400	Reg = 169.866	Cost = 1153.59
SSD = 974.719	n = 88400	Reg = 173.194	Cost = 1147.91
***Going to next resolution level***
SSD = 1453.24	n = 88400	Reg = 47.5658	Cost = 1500.81
SSD = 1069.51	n = 88400	Reg = 71.7109	Cost = 1141.23
SSD = 953.937	n = 88400	Reg = 105.643	Cost = 1059.58
SSD = 919.988	n = 88400	Reg = 120.414	Cost = 1040.4
SSD = 905.566	n = 88400	Reg = 126.428	Cost = 1031.99
SSD = 896.987	n = 88400	Reg = 129.625	Cost = 1026.61
***Going to next resolution level***
SSD = 897.134	n = 88400	Reg = 43.2244	Cost = 940.358
SSD = 850.027	n = 88400	Reg = 59.7443	Cost = 909.771
SSD = 826.284	n = 88400	Reg = 70.6749	Cost = 896.959
SSD = 817.342	n = 88400	Reg = 74.9143	Cost = 892.257
SSD = 813.245	n = 88400	Reg = 76.5635	Cost = 889.808
SSD = 810.758	n = 88400	Reg = 77.3701	Cost = 888.128
***Going to next resolution level***
SSD = 1702.06	n = 739294	Reg = 182.876	Cost = 1884.94
SSD = 1658.62	n = 739294	Reg = 178.164	Cost = 1836.79
SSD = 1599.84	n = 739294	Reg = 171.827	Cost = 1771.67
SSD = 1521.14	n = 739294	Reg = 163.44	Cost = 1684.58
SSD = 1424.29	n = 739294	Reg = 153.48	Cost = 1577.77
SSD = 1349.67	n = 739294	Reg = 146.508	Cost = 1496.18
SSD = 1289.58	n = 739294	Reg = 141.194	Cost = 1430.77
SSD = 1226.34	n = 739294	Reg = 136.627	Cost = 1362.96
SSD = 1154.37	n = 739294	Reg = 133.645	Cost = 1288.01
SSD = 1106.71	n = 739294	Reg = 133.591	Cost = 1240.3
SSD = 1076.97	n = 739294	Reg = 134.175	Cost = 1211.14
***Going to next resolution level***
SSD = 1635.3	n = 739294	Reg = 36.117	Cost = 1671.42
SSD = 1610.25	n = 739294	Reg = 35.5803	Cost = 1645.83
SSD = 1573.53	n = 739294	Reg = 34.8112	Cost = 1608.35
SSD = 1517.06	n = 739294	Reg = 33.6702	Cost = 1550.73
SSD = 1438.81	n = 739294	Reg = 32.2064	Cost = 1471.02
SSD = 1392.34	n = 739294	Reg = 31.4712	Cost = 1423.81
SSD = 1295.82	n = 739294	Reg = 30.0852	Cost = 1325.91
SSD = 1216.16	n = 739294	Reg = 29.3626	Cost = 1245.52
SSD = 1147.76	n = 739294	Reg = 29.3315	Cost = 1177.09
SSD = 1095.13	n = 739294	Reg = 30.0121	Cost = 1125.14
SSD = 1057.64	n = 739294	Reg = 31.1054	Cost = 1088.74
***Going to next resolution level***
SSD = 1057.87	n = 739294	Reg = 0.311122	Cost = 1058.18
SSD = 1051.78	n = 739294	Reg = 0.309215	Cost = 1052.09
SSD = 1044.34	n = 739294	Reg = 0.306809	Cost = 1044.65
SSD = 1031.39	n = 739294	Reg = 0.302658	Cost = 1031.69
SSD = 1012.48	n = 739294	Reg = 0.296969	Cost = 1012.77
SSD = 993.873	n = 739294	Reg = 0.292316	Cost = 994.165
SSD = 982.359	n = 739294	Reg = 0.289789	Cost = 982.649
SSD = 954.275	n = 739294	Reg = 0.285718	Cost = 954.561
SSD = 938.931	n = 739294	Reg = 0.285454	Cost = 939.216
SSD = 912.199	n = 739294	Reg = 0.290286	Cost = 912.489
SSD = 888.584	n = 739294	Reg = 0.299746	Cost = 888.884
SSD = 865.734	n = 739294	Reg = 0.317869	Cost = 866.052
SSD = 841.446	n = 739294	Reg = 0.345575	Cost = 841.792
SSD = 826.897	n = 739294	Reg = 0.370955	Cost = 827.268
SSD = 815.007	n = 739294	Reg = 0.391801	Cost = 815.399
SSD = 801.588	n = 739294	Reg = 0.41613	Cost = 802.005
SSD = 792.82	n = 739294	Reg = 0.434102	Cost = 793.254
SSD = 785.168	n = 739294	Reg = 0.447639	Cost = 785.615
SSD = 775.192	n = 739294	Reg = 0.463825	Cost = 775.656
SSD = 768.664	n = 739294	Reg = 0.47446	Cost = 769.139
SSD = 759.746	n = 739294	Reg = 0.487179	Cost = 760.233
***Going to next resolution level***
SSD = 759.746	n = 739294	Reg = 0.00974359	Cost = 759.756
SSD = 757.684	n = 739294	Reg = 0.00971125	Cost = 757.694
SSD = 755.043	n = 739294	Reg = 0.00966449	Cost = 755.053
SSD = 750.397	n = 739294	Reg = 0.00957671	Cost = 750.407
SSD = 743.019	n = 739294	Reg = 0.0094324	Cost = 743.028
SSD = 736.614	n = 739294	Reg = 0.00929566	Cost = 736.623
SSD = 729.196	n = 739294	Reg = 0.00913957	Cost = 729.205
SSD = 718.629	n = 739294	Reg = 0.00889958	Cost = 718.638
SSD = 709.088	n = 739294	Reg = 0.00866397	Cost = 709.097
SSD = 701.188	n = 739294	Reg = 0.00844548	Cost = 701.196
SSD = 694.962	n = 739294	Reg = 0.00825682	Cost = 694.97
SSD = 688.995	n = 739294	Reg = 0.00806673	Cost = 689.003
SSD = 684.579	n = 739294	Reg = 0.00793687	Cost = 684.587
SSD = 680.353	n = 739294	Reg = 0.00783304	Cost = 680.361
SSD = 677.477	n = 739294	Reg = 0.00778715	Cost = 677.485
SSD = 675.376	n = 739294	Reg = 0.00777417	Cost = 675.384
SSD = 672.634	n = 739294	Reg = 0.00779116	Cost = 672.642
SSD = 671.172	n = 739294	Reg = 0.00782169	Cost = 671.18
SSD = 668.707	n = 739294	Reg = 0.00789957	Cost = 668.715
SSD = 666.167	n = 739294	Reg = 0.00800021	Cost = 666.175
SSD = 663.258	n = 739294	Reg = 0.00814093	Cost = 663.266
SSD = 658.625	n = 739294	Reg = 0.00840197	Cost = 658.633
SSD = 655.466	n = 739294	Reg = 0.00860128	Cost = 655.475
SSD = 650.922	n = 739294	Reg = 0.0089153	Cost = 650.931
SSD = 646.778	n = 739294	Reg = 0.00922999	Cost = 646.788
SSD = 643.567	n = 739294	Reg = 0.00948493	Cost = 643.576
SSD = 639.631	n = 739294	Reg = 0.0098023	Cost = 639.641
SSD = 636.758	n = 739294	Reg = 0.0100317	Cost = 636.768
SSD = 633.158	n = 739294	Reg = 0.0103444	Cost = 633.168
SSD = 630.29	n = 739294	Reg = 0.0105938	Cost = 630.3
SSD = 626.75	n = 739294	Reg = 0.0108969	Cost = 626.761
SSD = 622.417	n = 739294	Reg = 0.0113055	Cost = 622.428
SSD = 619.941	n = 739294	Reg = 0.0115386	Cost = 619.952
SSD = 615.83	n = 739294	Reg = 0.0119124	Cost = 615.842
SSD = 612.552	n = 739294	Reg = 0.0122048	Cost = 612.564
SSD = 610.007	n = 739294	Reg = 0.0124427	Cost = 610.019
SSD = 607.419	n = 739294	Reg = 0.0126831	Cost = 607.432
SSD = 605.202	n = 739294	Reg = 0.01289	Cost = 605.215
SSD = 603.278	n = 739294	Reg = 0.0130499	Cost = 603.291
SSD = 601.163	n = 739294	Reg = 0.0132227	Cost = 601.176
SSD = 599.254	n = 739294	Reg = 0.0133814	Cost = 599.267
SSD = 597.475	n = 739294	Reg = 0.0135187	Cost = 597.489
SSD = 595.523	n = 739294	Reg = 0.0136563	Cost = 595.537
SSD = 593.505	n = 739294	Reg = 0.0138015	Cost = 593.519
SSD = 591.714	n = 739294	Reg = 0.0139278	Cost = 591.728
SSD = 590.196	n = 739294	Reg = 0.0140175	Cost = 590.21
SSD = 588.113	n = 739294	Reg = 0.0141362	Cost = 588.127
SSD = 586.525	n = 739294	Reg = 0.0142333	Cost = 586.539
SSD = 585.506	n = 739294	Reg = 0.0142886	Cost = 585.52
SSD = 583.713	n = 739294	Reg = 0.0143818	Cost = 583.727
SSD = 582.213	n = 739294	Reg = 0.0144539	Cost = 582.227
Wed Jun 16 00:53:50 CDT 2021:TopupPreprocessingAll.sh: END: Topup Field Map Generation and Gradient Unwarping
Running FAST segmentation
FLIRT pre-alignment
Running BBR
0.204121 0.999993 0.002351 -0.002906 0.000000 -0.002357 0.999995 -0.001953 0.000000 0.002902 0.001960 0.999994 0.000000 -0.003567 -1.022259 0.857348 1.000000 
Wed Jun 16 01:15:56 CDT 2021:T2wToT1wDistortionCorrectAndReg.sh: END
Wed Jun 16 01:15:56 CDT 2021:PreFreeSurferPipeline.sh: Performing Bias Field Correction using sqrt(T1w x T2w)
Wed Jun 16 01:15:56 CDT 2021:PreFreeSurferPipeline.sh: mkdir -p /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/BiasFieldCorrection_sqrtT1wXT2w
Wed Jun 16 01:15:56 CDT 2021:BiasFieldCorrection_sqrtT1wXT2w.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Wed Jun 16 01:15:56 CDT 2021:BiasFieldCorrection_sqrtT1wXT2w.sh: FSLDIR: /opt/fsl/fsl
Wed Jun 16 01:15:56 CDT 2021:BiasFieldCorrection_sqrtT1wXT2w.sh: CARET7DIR: /opt/workbench/workbench/bin_rh_linux64
Wed Jun 16 01:15:57 CDT 2021:BiasFieldCorrection_sqrtT1wXT2w.sh: START: BiasFieldCorrection
0.270981
0.965339
.8298485
Wed Jun 16 01:18:36 CDT 2021:BiasFieldCorrection_sqrtT1wXT2w.sh: END: BiasFieldCorrection
Wed Jun 16 01:18:36 CDT 2021:PreFreeSurferPipeline.sh: Creating one-step resampled version of {T1w,T2w}_acpc_dc outputs
Wed Jun 16 01:23:47 CDT 2021:PreFreeSurferPipeline.sh: Performing Atlas Registration to MNI152 (FLIRT and FNIRT)
Wed Jun 16 01:23:47 CDT 2021:AtlasRegistrationToMNI152_FLIRTandFNIRT.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Wed Jun 16 01:23:47 CDT 2021:AtlasRegistrationToMNI152_FLIRTandFNIRT.sh: FSLDIR: /opt/fsl/fsl
Wed Jun 16 01:23:48 CDT 2021:AtlasRegistrationToMNI152_FLIRTandFNIRT.sh: START: AtlasRegistration to MNI152
Wed Jun 16 01:50:57 CDT 2021:AtlasRegistrationToMNI152_FLIRTandFNIRT.sh: END: AtlasRegistration to MNI152
Wed Jun 16 01:50:57 CDT 2021:PreFreeSurferPipeline.sh: Completed!


===> Successful completion of task

All looks good in the log you pasted. Did you try the run_turnkey example from above? If that does not work then you can try running only hcp_freesurfer:

# set study path
STUDY_FOLDER=...

# set singularity location
CONTAINER=...

qunex_container hcp_freesurfer \
	--sessions=${STUDY_FOLDER}/processing/HCPA001_batch.txt \
	--sessionsfolder=${STUDY_FOLDER}/sessions \
	--overwrite=yes \
	--container=${CONTAINER}

Both through run_turnkey and running the command manually work on my end, which makes this hard to debug … Let me know how it goes.

I’ll try the exact command you used above now. It’s running so far, but I believe it didn’t fail right away last time. I neglected to note/notice that in my case logs were generated. Here’s the turnkey log from when I originally saw the error. I will also post the hcp_freesurfer error log and the recon-all log that’s buried in the HCP output shortly.

 ===> RUNNING RunTurnkey step ~~~ HCP Pipelines - hcp_pre_freesurfer. 


 ........................ Running QuNex v0.90.6 ........................ 



Using /home/wozniakj/roedi004/qunex/quickstart/processing/HCPA001_batch.txt for input.


--- Full QuNex call for command: hcp_pre_freesurfer 

gmri hcp_pre_freesurfer --sessionsfolder="/home/wozniakj/roedi004/qunex/quickstart/sessions" --sessions="/home/wozniakj/roedi004/qunex/quickstart/processing/HCPA001_batch.txt" --overwrite="no" --logfolder="/home/wozniakj/roedi004/qunex/quickstart/processing/logs" --sessionids="HCPA001" 

--------------------------------------------------------- 


WARNING: Parameter qx_cifti_tail was not specified. Its value was imputed from parameter hcp_cifti_tail and set to '_Atlas'!
WARNING: Parameter qx_nifti_tail was not specified. Its value was imputed from parameter hcp_nifti_tail and set to ''!
WARNING: Parameter cifti_tail was not specified. Its value was imputed from parameter qx_cifti_tail and set to '_Atlas'!
WARNING: Parameter nifti_tail was not specified. Its value was imputed from parameter qx_nifti_tail and set to ''!
# Generated by QuNex 0.90.6 on 2021-06-16_00.07.1623820053
#
=================================================================
gmri hcp_pre_freesurfer \
  --sessionids="HCPA001" \
  --sessionsfolder="/home/wozniakj/roedi004/qunex/quickstart/sessions" \
  --sessions="/home/wozniakj/roedi004/qunex/quickstart/processing/HCPA001_batch.txt" \
  --overwrite="no" \
  --logfolder="/home/wozniakj/roedi004/qunex/quickstart/processing/logs" \
=================================================================

Starting multiprocessing sessions in /home/wozniakj/roedi004/qunex/quickstart/processing/HCPA001_batch.txt with a pool of 16 concurrent processes

---- Running local

Adding processing of session HCPA001 to the pool at Wednesday, 16. June 2021 00:07:33
# Generated by QuNex 0.90.6 on 2021-06-16_00.07.1623820053
#
------------------------------------------------------------
Running external command via QuNex:
/opt/HCP/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh
     --path="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp"
     --subject="HCPA001"
     --t1="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/T1w/HCPA001_T1w_MPR1.nii.gz"
     --t2="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/T2w/HCPA001_T2w_SPC1.nii.gz"
     --t1template="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz"
     --t1templatebrain="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz"
     --t1template2mm="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz"
     --t2template="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz"
     --t2templatebrain="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz"
     --t2template2mm="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz"
     --templatemask="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz"
     --template2mmmask="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz"
     --brainsize="150"
     --fnirtconfig="/opt/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf"
     --SEPhaseNeg="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz"
     --SEPhasePos="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz"
     --seechospacing="0.000580009"
     --seunwarpdir="y"
     --t1samplespacing="0.0000071"
     --t2samplespacing="0.0000021"
     --unwarpdir="z"
     --gdcoeffs="NONE"
     --avgrdcmethod="TOPUP"
     --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf"
     --processing-mode="HCPStyleData"

Test file: 
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/MNINonLinear/T1w_restore_brain.nii.gz
------------------------------------------------------------
You can follow command's progress in:
/home/wozniakj/roedi004/qunex/quickstart/processing/logs/comlogs/tmp_hcp_pre_freesurfer_HCPA001_2021-06-16_00.07.1623820053.log
------------------------------------------------------------

------------------------------------------------------------
Session id: HCPA001 
[started on Wednesday, 16. June 2021 00:07:33]
Running HCP PreFreeSurfer Pipeline [HCPStyleData] ...

---> T1w image file present.
---> T2w image file present.
---> TOPUP Correction, Spin-Echo pair 1 specified
---> Spin-Echo pair of images present. [SpinEchoFieldMap1]
---> TOPUP configuration file present.

------------------------------------------------------------
Running HCP Pipelines command via QuNex:

/opt/HCP/HCPpipelines/PreFreeSurfer/PreFreeSurferPipeline.sh 
    --path="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp" 
    --subject="HCPA001" 
    --t1="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/T1w/HCPA001_T1w_MPR1.nii.gz" 
    --t2="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/T2w/HCPA001_T2w_SPC1.nii.gz" 
    --t1template="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm.nii.gz" 
    --t1templatebrain="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain.nii.gz" 
    --t1template2mm="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm.nii.gz" 
    --t2template="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm.nii.gz" 
    --t2templatebrain="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_0.7mm_brain.nii.gz" 
    --t2template2mm="/opt/HCP/HCPpipelines/global/templates/MNI152_T2_2mm.nii.gz" 
    --templatemask="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_0.7mm_brain_mask.nii.gz" 
    --template2mmmask="/opt/HCP/HCPpipelines/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz" 
    --brainsize="150" 
    --fnirtconfig="/opt/HCP/HCPpipelines/global/config/T1_2_MNI152_2mm.cnf" 
    --SEPhaseNeg="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_AP_SB_SE.nii.gz" 
    --SEPhasePos="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/unprocessed/SpinEchoFieldMap1/HCPA001_BOLD_PA_SB_SE.nii.gz" 
    --seechospacing="0.000580009" 
    --seunwarpdir="y" 
    --t1samplespacing="0.0000071" 
    --t2samplespacing="0.0000021" 
    --unwarpdir="z" 
    --gdcoeffs="NONE" 
    --avgrdcmethod="TOPUP" 
    --topupconfig="/opt/HCP/HCPpipelines/global/config/b02b0.cnf" 
    --processing-mode="HCPStyleData"
------------------------------------------------------------


Running HCP PreFS
---> hcp_pre_freesurfer test file [T1w_restore_brain.nii.gz] present
---> logfile: /home/wozniakj/roedi004/qunex/quickstart/processing/logs/comlogs/done_hcp_pre_freesurfer_HCPA001_2021-06-16_00.07.1623820053.log
HCP PreFS completed on Wednesday, 16. June 2021 01:50:57
------------------------------------------------------------


===> Final report for command hcp_pre_freesurfer
... HCPA001 ---> hcp_pre_freesurfer done
===> Successful completion of all tasks

 ===> RUNNING RunTurnkey step ~~~ HCP Pipelines step - hcp_freesurfer. 


 ........................ Running QuNex v0.90.6 ........................ 



Using /home/wozniakj/roedi004/qunex/quickstart/processing/HCPA001_batch.txt for input.


--- Full QuNex call for command: hcp_freesurfer 

gmri hcp_freesurfer --sessionsfolder="/home/wozniakj/roedi004/qunex/quickstart/sessions" --sessions="/home/wozniakj/roedi004/qunex/quickstart/processing/HCPA001_batch.txt" --overwrite="no" --logfolder="/home/wozniakj/roedi004/qunex/quickstart/processing/logs" --sessionids="HCPA001" 

--------------------------------------------------------- 


WARNING: Parameter qx_cifti_tail was not specified. Its value was imputed from parameter hcp_cifti_tail and set to '_Atlas'!
WARNING: Parameter qx_nifti_tail was not specified. Its value was imputed from parameter hcp_nifti_tail and set to ''!
WARNING: Parameter cifti_tail was not specified. Its value was imputed from parameter qx_cifti_tail and set to '_Atlas'!
WARNING: Parameter nifti_tail was not specified. Its value was imputed from parameter qx_nifti_tail and set to ''!
# Generated by QuNex 0.90.6 on 2021-06-16_01.51.1623826263
#
=================================================================
gmri hcp_freesurfer \
  --sessionids="HCPA001" \
  --sessionsfolder="/home/wozniakj/roedi004/qunex/quickstart/sessions" \
  --sessions="/home/wozniakj/roedi004/qunex/quickstart/processing/HCPA001_batch.txt" \
  --overwrite="no" \
  --logfolder="/home/wozniakj/roedi004/qunex/quickstart/processing/logs" \
=================================================================

Starting multiprocessing sessions in /home/wozniakj/roedi004/qunex/quickstart/processing/HCPA001_batch.txt with a pool of 16 concurrent processes

---- Running local

Adding processing of session HCPA001 to the pool at Wednesday, 16. June 2021 01:51:03
# Generated by QuNex 0.90.6 on 2021-06-16_01.51.1623826263
#
------------------------------------------------------------
Running external command via QuNex:
/opt/HCP/HCPpipelines/FreeSurfer/FreeSurferPipeline.sh
     --subjectDIR="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w"
     --subject="HCPA001"
     --processing-mode="HCPStyleData"
     --t1="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore.nii.gz"
     --t1brain="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz"
     --t2="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz"

Test file: 
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/label/BA_exvivo.thresh.ctab
------------------------------------------------------------
You can follow command's progress in:
/home/wozniakj/roedi004/qunex/quickstart/processing/logs/comlogs/tmp_hcp_freesurfer_HCPA001_2021-06-16_01.51.1623826263.log
------------------------------------------------------------

--------------------==== QuNex failed! ====--------------------

ERROR: Execution of command `hcp_freesurfer` failed!
       Please check documentation for the command (`qunex ?hcp_freesurfer`)!

The call received was: 
(please note that when run through scheduler, all possible parameters, 
even non relevant ones are passed) 

qunex hcp_freesurfer \
    --sessionsfolder=/home/wozniakj/roedi004/qunex/quickstart/sessions \
    --sessions=/home/wozniakj/roedi004/qunex/quickstart/processing/HCPA001_batch.txt \
    --overwrite=no \
    --logfolder=/home/wozniakj/roedi004/qunex/quickstart/processing/logs \
    --sessionids=HCPA001 

--------------------------------------------------------------
Here's the error as caught by python:

Traceback (most recent call last):
  File "/opt/qunex/python/qx_utilities/gmri", line 499, in <module>
    main()
  File "/opt/qunex/python/qx_utilities/gmri", line 467, in main
    runCommand(comm, opts)
  File "/opt/qunex/python/qx_utilities/gmri", line 164, in runCommand
    gp.run(command, args)
  File "/opt/qunex/python/qx_utilities/general/process.py", line 749, in run
    result = future.result()
  File "/opt/env/qunex/lib/python2.7/site-packages/concurrent/futures/_base.py", line 455, in result
    return self.__get_result()
  File "/opt/env/qunex/lib/python2.7/site-packages/concurrent/futures/_base.py", line 414, in __get_result
    raise exception_type, self._exception, self._traceback
AttributeError: 'module' object has no attribute 'ExternalFailed'

error_hcp_freesurfer_HCPA001_2021-06-16_01.51.1623826263.log

# Generated by QuNex 0.90.6 on 2021-06-16_01.51.1623826263
#
------------------------------------------------------------
Running external command via QuNex:
/opt/HCP/HCPpipelines/FreeSurfer/FreeSurferPipeline.sh
     --subjectDIR="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w"
     --subject="HCPA001"
     --processing-mode="HCPStyleData"
     --t1="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore.nii.gz"
     --t1brain="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz"
     --t2="/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz"

Test file: 
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/label/BA_exvivo.thresh.ctab
------------------------------------------------------------

========================================
  DIRECTORY: /opt/HCP/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: v4.3.0
========================================
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: HCPPIPEDIR: /opt/HCP/HCPpipelines
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: FREESURFER_HOME: /opt/freesurfer/freesurfer-6.0
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: Platform Information Follows: 
Linux cn2001 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
which: no recon-all.v6.hires in (/opt/qunex/qx_library/etc/fsl_gpu_binaries/probtrackx_gpu_cuda_9.1:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/bin:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/lib:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu:/usr/local/cuda/bin:/opt/HCP/HCPpipelines/global/matlab/:/opt/fsl/fix:/opt/qunex/qx_library/etc/fsl_gpu_binaries/eddy_cuda:/opt/qunex/qx_library/etc/fsl_gpu_binaries:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended:/opt/qunex/bash/qx_utilities:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense:/opt/qunex/bash/qx_utilities/diffusion_tractography/scripts:/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts:/opt/HCP/HCPpipelines/global/scripts:/opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts:/opt/HCP/HCPpipelines/tfMRI/scripts:/opt/HCP/HCPpipelines/fMRIVolume/scripts:/opt/HCP/HCPpipelines/fMRISurface/scripts:/opt/HCP/HCPpipelines/PostFreeSurfer/scripts:/opt/HCP/HCPpipelines/FreeSurfer/scripts:/opt/HCP/HCPpipelines/PreFreeSurfer/scripts:/opt/HCP/HCPpipelines/global/config:/opt/HCP/HCPpipelines/global/binaries:/opt/HCP/HCPpipelines/global/templates:/opt/gradunwarp/gradunwarp/gradunwarp/core:/opt/workbench/workbench/bin_rh_linux64:/opt/HCP/HCPpipelines:/opt/HCP/HCPpipelines/MSMConfig:/opt/qunex/python/qx_utilities/templates/:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/R/R:/opt/matlab/bin:/opt/octave/octave/bin:/opt/dcm2niix/dcm2niix:/opt/dcm2niix/dcm2niix/build/bin:/opt/afni/afni:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/freesurfer/FreeSurferScheduler:/opt/fsl/fsl/bin:/opt/freesurfer/freesurfer-6.0/bin:/panfs/roc/msisoft/freesurfer/5.3.0/fsfast/bin:/opt/freesurfer/freesurfer-6.0/tktools:/opt/fsl/fsl/bin:/panfs/roc/msisoft/freesurfer/5.3.0/mni/bin:/opt/freesurfer/freesurfer-6.0:/opt/fsl/fsl/bin:/usr/local/bin:/opt/qunex/lib:/opt/qunex/bin:/opt/bin:/opt/lib/bin:/opt/lib/lib/:/opt/olib:/opt/qunex/python/qx_utilities:/opt/env/qunex/bin:/opt/miniconda/condabin:/opt/miniconda/bin:/opt:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/bin)
which: no conf2hires in (/opt/qunex/qx_library/etc/fsl_gpu_binaries/probtrackx_gpu_cuda_9.1:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/bin:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/lib:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu:/usr/local/cuda/bin:/opt/HCP/HCPpipelines/global/matlab/:/opt/fsl/fix:/opt/qunex/qx_library/etc/fsl_gpu_binaries/eddy_cuda:/opt/qunex/qx_library/etc/fsl_gpu_binaries:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended:/opt/qunex/bash/qx_utilities:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense:/opt/qunex/bash/qx_utilities/diffusion_tractography/scripts:/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts:/opt/HCP/HCPpipelines/global/scripts:/opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts:/opt/HCP/HCPpipelines/tfMRI/scripts:/opt/HCP/HCPpipelines/fMRIVolume/scripts:/opt/HCP/HCPpipelines/fMRISurface/scripts:/opt/HCP/HCPpipelines/PostFreeSurfer/scripts:/opt/HCP/HCPpipelines/FreeSurfer/scripts:/opt/HCP/HCPpipelines/PreFreeSurfer/scripts:/opt/HCP/HCPpipelines/global/config:/opt/HCP/HCPpipelines/global/binaries:/opt/HCP/HCPpipelines/global/templates:/opt/gradunwarp/gradunwarp/gradunwarp/core:/opt/workbench/workbench/bin_rh_linux64:/opt/HCP/HCPpipelines:/opt/HCP/HCPpipelines/MSMConfig:/opt/qunex/python/qx_utilities/templates/:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/R/R:/opt/matlab/bin:/opt/octave/octave/bin:/opt/dcm2niix/dcm2niix:/opt/dcm2niix/dcm2niix/build/bin:/opt/afni/afni:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/freesurfer/FreeSurferScheduler:/opt/fsl/fsl/bin:/opt/freesurfer/freesurfer-6.0/bin:/panfs/roc/msisoft/freesurfer/5.3.0/fsfast/bin:/opt/freesurfer/freesurfer-6.0/tktools:/opt/fsl/fsl/bin:/panfs/roc/msisoft/freesurfer/5.3.0/mni/bin:/opt/freesurfer/freesurfer-6.0:/opt/fsl/fsl/bin:/usr/local/bin:/opt/qunex/lib:/opt/qunex/bin:/opt/bin:/opt/lib/bin:/opt/lib/lib/:/opt/olib:/opt/qunex/python/qx_utilities:/opt/env/qunex/bin:/opt/miniconda/condabin:/opt/miniconda/bin:/opt:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/bin)
which: no longmc in (/opt/qunex/qx_library/etc/fsl_gpu_binaries/probtrackx_gpu_cuda_9.1:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/bin:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/lib:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu:/usr/local/cuda/bin:/opt/HCP/HCPpipelines/global/matlab/:/opt/fsl/fix:/opt/qunex/qx_library/etc/fsl_gpu_binaries/eddy_cuda:/opt/qunex/qx_library/etc/fsl_gpu_binaries:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended:/opt/qunex/bash/qx_utilities:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense:/opt/qunex/bash/qx_utilities/diffusion_tractography/scripts:/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts:/opt/HCP/HCPpipelines/global/scripts:/opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts:/opt/HCP/HCPpipelines/tfMRI/scripts:/opt/HCP/HCPpipelines/fMRIVolume/scripts:/opt/HCP/HCPpipelines/fMRISurface/scripts:/opt/HCP/HCPpipelines/PostFreeSurfer/scripts:/opt/HCP/HCPpipelines/FreeSurfer/scripts:/opt/HCP/HCPpipelines/PreFreeSurfer/scripts:/opt/HCP/HCPpipelines/global/config:/opt/HCP/HCPpipelines/global/binaries:/opt/HCP/HCPpipelines/global/templates:/opt/gradunwarp/gradunwarp/gradunwarp/core:/opt/workbench/workbench/bin_rh_linux64:/opt/HCP/HCPpipelines:/opt/HCP/HCPpipelines/MSMConfig:/opt/qunex/python/qx_utilities/templates/:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/R/R:/opt/matlab/bin:/opt/octave/octave/bin:/opt/dcm2niix/dcm2niix:/opt/dcm2niix/dcm2niix/build/bin:/opt/afni/afni:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/freesurfer/FreeSurferScheduler:/opt/fsl/fsl/bin:/opt/freesurfer/freesurfer-6.0/bin:/panfs/roc/msisoft/freesurfer/5.3.0/fsfast/bin:/opt/freesurfer/freesurfer-6.0/tktools:/opt/fsl/fsl/bin:/panfs/roc/msisoft/freesurfer/5.3.0/mni/bin:/opt/freesurfer/freesurfer-6.0:/opt/fsl/fsl/bin:/usr/local/bin:/opt/qunex/lib:/opt/qunex/bin:/opt/bin:/opt/lib/bin:/opt/lib/lib/:/opt/olib:/opt/qunex/python/qx_utilities:/opt/env/qunex/bin:/opt/miniconda/condabin:/opt/miniconda/bin:/opt:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/bin)
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: We were not able to locate one of the following required tools:
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: recon-all.v6.hires, conf2hires, or longmc
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: 
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: To be able to run this script using the standard versions of these tools,
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: we added /opt/HCP/HCPpipelines/FreeSurfer/custom to the beginning of the PATH.
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: 
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: If you intended to use some other version of these tools, please configure
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: your PATH before invoking this script, such that the tools you intended to
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: use can be found on the PATH.
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: 
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: WARNING: PATH set to: /opt/HCP/HCPpipelines/FreeSurfer/custom:/opt/qunex/qx_library/etc/fsl_gpu_binaries/probtrackx_gpu_cuda_9.1:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/bin:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/lib:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu:/usr/local/cuda/bin:/opt/HCP/HCPpipelines/global/matlab/:/opt/fsl/fix:/opt/qunex/qx_library/etc/fsl_gpu_binaries/eddy_cuda:/opt/qunex/qx_library/etc/fsl_gpu_binaries:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended:/opt/qunex/bash/qx_utilities:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense:/opt/qunex/bash/qx_utilities/diffusion_tractography/scripts:/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts:/opt/HCP/HCPpipelines/global/scripts:/opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts:/opt/HCP/HCPpipelines/tfMRI/scripts:/opt/HCP/HCPpipelines/fMRIVolume/scripts:/opt/HCP/HCPpipelines/fMRISurface/scripts:/opt/HCP/HCPpipelines/PostFreeSurfer/scripts:/opt/HCP/HCPpipelines/FreeSurfer/scripts:/opt/HCP/HCPpipelines/PreFreeSurfer/scripts:/opt/HCP/HCPpipelines/global/config:/opt/HCP/HCPpipelines/global/binaries:/opt/HCP/HCPpipelines/global/templates:/opt/gradunwarp/gradunwarp/gradunwarp/core:/opt/workbench/workbench/bin_rh_linux64:/opt/HCP/HCPpipelines:/opt/HCP/HCPpipelines/MSMConfig:/opt/qunex/python/qx_utilities/templates/:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/R/R:/opt/matlab/bin:/opt/octave/octave/bin:/opt/dcm2niix/dcm2niix:/opt/dcm2niix/dcm2niix/build/bin:/opt/afni/afni:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/freesurfer/FreeSurferScheduler:/opt/fsl/fsl/bin:/opt/freesurfer/freesurfer-6.0/bin:/panfs/roc/msisoft/freesurfer/5.3.0/fsfast/bin:/opt/freesurfer/freesurfer-6.0/tktools:/opt/fsl/fsl/bin:/panfs/roc/msisoft/freesurfer/5.3.0/mni/bin:/opt/freesurfer/freesurfer-6.0:/opt/fsl/fsl/bin:/usr/local/bin:/opt/qunex/lib:/opt/qunex/bin:/opt/bin:/opt/lib/bin:/opt/lib/lib/:/opt/olib:/opt/qunex/python/qx_utilities:/opt/env/qunex/bin:/opt/miniconda/condabin:/opt/miniconda/bin:/opt:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/bin
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: Showing HCP Pipelines version
========================================
  DIRECTORY: /opt/HCP/HCPpipelines
    PRODUCT: HCP Pipeline Scripts
    VERSION: v4.3.0
========================================
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: Showing recon-all.v6.hires version
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: /opt/HCP/HCPpipelines/FreeSurfer/custom/recon-all.v6.hires
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Wed Jun 16 01:51:03 CDT 2021:FreeSurferPipeline.sh: Showing tkregister version
/opt/freesurfer/freesurfer-6.0/tktools/tkregister
stable6
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Showing mri_concatenate_lta version
/opt/freesurfer/freesurfer-6.0/bin/mri_concatenate_lta
stable6
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Showing mri_surf2surf version
/opt/freesurfer/freesurfer-6.0/bin/mri_surf2surf
stable6
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Showing fslmaths location
/opt/fsl/fsl/bin/fslmaths
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: INFO: Determined that FreeSurfer full version string is: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: INFO: Determined that FreeSurfer version is: 6.0.0
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Using named parameters
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Subject Directory: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Subject: HCPA001
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: T1w Image: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore.nii.gz
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: T1w Brain: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Include -conf2hires flag in recon-all: TRUE
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: ProcessingMode: HCPStyleData
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Starting main functionality
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Retrieve positional parameters
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: SubjectDIR: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: SubjectID: HCPA001
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: T1wImage: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore.nii.gz
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: T1wImageBrain: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: T2wImage: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: recon_all_seed: 
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: flair: FALSE
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: existing_subject: FALSE
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: extra_reconall_args: 
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: conf2hires: TRUE
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Figure out the number of cores to use.
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: num_cores: 8
Wed Jun 16 01:51:04 CDT 2021:FreeSurferPipeline.sh: Thresholding T1w image to eliminate negative voxel values
Wed Jun 16 01:51:05 CDT 2021:FreeSurferPipeline.sh: ...This produces a new file named: /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz
Wed Jun 16 01:51:08 CDT 2021:FreeSurferPipeline.sh: Call custom recon-all: recon-all.v6.hires
Wed Jun 16 01:51:08 CDT 2021:FreeSurferPipeline.sh: ...recon_all_cmd: recon-all.v6.hires -subjid HCPA001 -sd /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w -all -i /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz -emregmask /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz -T2 /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz -T2pial -openmp 8 -conf2hires
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w
Actual FREESURFER_HOME /opt/freesurfer/freesurfer-6.0
Linux cn2001 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
nu_correct: Command not found.
'/opt/HCP/HCPpipelines/FreeSurfer/custom/recon-all.v6.hires' -> '/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/scripts/recon-all.local-copy'
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001

 mri_convert /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/001.mgz 

mri_convert.bin /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_zero_threshold.nii.gz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/001.mgz...
#--------------------------------------------
#@# T2/FLAIR Input Wed Jun 16 01:51:21 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001

 mri_convert --no_scale 1 /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/T2raw.mgz 

mri_convert.bin --no_scale 1 /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/T2raw.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz...
TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Wed Jun 16 01:51:26 CDT 2021
Found 1 runs
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/001.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz 

/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001

 mri_convert /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz --conform 

mri_convert.bin /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz...

 mri_add_xform_to_header -c /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/transforms/talairach.xfm /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz 

INFO: extension is mgz

 mri_vol2vol --mov /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz --targ /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz --regheader --interp nearest --o /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/extern.emreg.mask.mgz 

movvol /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz
targvol /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz
outvol /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/extern.emreg.mask.mgz
invert 0
tal    0
talres 2
regheader 1
noresample 0
interp  nearest (0)
precision  float (3)
Gdiag_no  -1
Synth      0
SynthSeed  1624253354

Computing registration based on scanner-to-scanner

Final tkRAS-to-tkRAS Matrix is:
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00001;
 0.00000   0.00000   0.00000   1.00000;


Vox2Vox Matrix is:
 1.42857   0.00000   0.00000  -52.85715;
 0.00000   0.00000   1.42857  -27.35713;
 0.00000  -1.42857   0.00000   312.85715;
 0.00000   0.00000   0.00000   1.00000;

Resampling
Output registration matrix is identity

mri_vol2vol done
#--------------------------------------------
#@# Talairach Wed Jun 16 01:51:42 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri

 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 

/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
/opt/freesurfer/freesurfer-6.0/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux cn2001 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Wed Jun 16 01:51:42 CDT 2021
nu_correct: Command not found.
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.1763204
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1763204/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.1763204/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1763204/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Wed Jun 16 01:51:45 CDT 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.1763204/nu0.mnc ./tmp.mri_nu_correct.mni.1763204/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.1763204/0/ -iterations 1000 -distance 50
nu_correct: Command not found.
ERROR: nu_correct
Linux cn2001 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s HCPA001 exited with ERRORS at Wed Jun 16 01:51:45 CDT 2021

For more details, see the log file /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Wed Jun 16 01:51:45 CDT 2021:FreeSurferPipeline.sh: While running '/opt/HCP/HCPpipelines/FreeSurfer/FreeSurferPipeline.sh --subjectDIR=/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w --subject=HCPA001 --processing-mode=HCPStyleData --t1=/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore.nii.gz --t1brain=/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz --t2=/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz':
Wed Jun 16 01:51:45 CDT 2021:FreeSurferPipeline.sh: ERROR: recon-all command failed with return_code: 1
Wed Jun 16 01:51:45 CDT 2021:FreeSurferPipeline.sh: ERROR: recon-all command failed with return_code: 1
Wed Jun 16 01:51:45 CDT 2021:FreeSurferPipeline.sh: ABORTING
(base) roedi004@ln0004 [~/qunex/quickstart/processing/logs/comlogs] % 

EDIT: I’m a new user so I’ve hit the reply limit. Your comment below is correct. I’m now running on a high memory node and am not having any issues. That said, my issue may have been different from the one faced by the original poster.

recon-all.log (just the end due to character limit)

 mri_convert --no_scale 1 /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/T2raw.mgz 

mri_convert.bin --no_scale 1 /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/T2raw.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz...
TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Wed Jun 16 09:59:20 CDT 2021
Found 1 runs
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.

 cp /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/001.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz 

/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001

 mri_convert /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz --conform 

mri_convert.bin /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz...

 mri_add_xform_to_header -c /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/transforms/talairach.xfm /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz 

INFO: extension is mgz

 mri_vol2vol --mov /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz --targ /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz --regheader --interp nearest --o /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/extern.emreg.mask.mgz 

movvol /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz
targvol /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz
outvol /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/extern.emreg.mask.mgz
invert 0
tal    0
talres 2
regheader 1
noresample 0
interp  nearest (0)
precision  float (3)
Gdiag_no  -1
Synth      0
SynthSeed  1624712569

Computing registration based on scanner-to-scanner

Final tkRAS-to-tkRAS Matrix is:
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000  -0.00001;
 0.00000   0.00000   0.00000   1.00000;


Vox2Vox Matrix is:
 1.42857   0.00000   0.00000  -52.85715;
 0.00000   0.00000   1.42857  -27.35713;
 0.00000  -1.42857   0.00000   312.85715;
 0.00000   0.00000   0.00000   1.00000;

Resampling
Output registration matrix is identity

mri_vol2vol done
#--------------------------------------------
#@# Talairach Wed Jun 16 09:59:33 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri

 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 

/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
/opt/freesurfer/freesurfer-6.0/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux ln0004 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Wed Jun 16 09:59:33 CDT 2021
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.520195
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.520195/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.520195/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.520195/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Wed Jun 16 09:59:35 CDT 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.520195/nu0.mnc ./tmp.mri_nu_correct.mni.520195/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.520195/0/ -iterations 1000 -distance 50
[roedi004@ln0004:/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/] [2021-06-16 09:59:35] running:
  /opt/freesurfer/freesurfer-6.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.520195/0/ ./tmp.mri_nu_correct.mni.520195/nu0.mnc ./tmp.mri_nu_correct.mni.520195/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 25 
CV of field change: 0.000996372
 
 
 
mri_convert ./tmp.mri_nu_correct.mni.520195/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.520195/nu1.mnc orig_nu.mgz --like orig.mgz --conform 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.520195/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
writing to orig_nu.mgz...
 
 
Wed Jun 16 10:00:29 CDT 2021
mri_nu_correct.mni done

 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

talairach_avi log file is transforms/talairach_avi.log...
Started at Wed Jun 16 10:00:29 CDT 2021
Ended   at Wed Jun 16 10:01:02 CDT 2021
talairach_avi done

 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

#--------------------------------------------
#@# Talairach Failure Detection Wed Jun 16 10:01:04 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7258, pval=0.6675 >= threshold=0.0050)

 awk -f /opt/freesurfer/freesurfer-6.0/bin/extract_talairach_avi_QA.awk /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/transforms/talairach_avi.log 


 tal_QC_AZS /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/transforms/talairach_avi.log 

TalAviQA: 0.96889
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Wed Jun 16 10:01:04 CDT 2021

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 

/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
/opt/freesurfer/freesurfer-6.0/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux ln0004 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Wed Jun 16 10:01:04 CDT 2021
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.521075
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.521075/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.521075/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.521075/nu0.mnc...
 
--------------------------------------------------------
Iteration 1 Wed Jun 16 10:01:10 CDT 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.521075/nu0.mnc ./tmp.mri_nu_correct.mni.521075/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.521075/0/
[roedi004@ln0004:/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/] [2021-06-16 10:01:10] running:
  /opt/freesurfer/freesurfer-6.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.521075/0/ ./tmp.mri_nu_correct.mni.521075/nu0.mnc ./tmp.mri_nu_correct.mni.521075/nu1.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 18 
CV of field change: 0.000972136
 
 
--------------------------------------------------------
Iteration 2 Wed Jun 16 10:01:57 CDT 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.521075/nu1.mnc ./tmp.mri_nu_correct.mni.521075/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.521075/1/
[roedi004@ln0004:/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/] [2021-06-16 10:01:57] running:
  /opt/freesurfer/freesurfer-6.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.521075/1/ ./tmp.mri_nu_correct.mni.521075/nu1.mnc ./tmp.mri_nu_correct.mni.521075/nu2.imp

Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 7 
CV of field change: 0.000992815
 
 
 
mri_binarize --i ./tmp.mri_nu_correct.mni.521075/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.521075/ones.mgz

$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.521075/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.521075/ones.mgz 
sysname  Linux
hostname ln0004
machine  x86_64
user     roedi004

input      ./tmp.mri_nu_correct.mni.521075/nu2.mnc
frame      0
nErode3d   0
nErode2d   0
output     ./tmp.mri_nu_correct.mni.521075/ones.mgz
Binarizing based on threshold
min        -1
max        +infinity
binval        1
binvalnot     0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777216 voxels in final mask
Count: 16777216 16777216.000000 16777216 100.000000
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.521075/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.521075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.521075/input.mean.dat

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.521075/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.521075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.521075/input.mean.dat 
sysname  Linux
hostname ln0004
machine  x86_64
user     roedi004
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.521075/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.521075/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.521075/ones.mgz --i ./tmp.mri_nu_correct.mni.521075/nu2.mnc --sum ./tmp.mri_nu_correct.mni.521075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.521075/output.mean.dat

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.521075/ones.mgz --i ./tmp.mri_nu_correct.mni.521075/nu2.mnc --sum ./tmp.mri_nu_correct.mni.521075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.521075/output.mean.dat 
sysname  Linux
hostname ln0004
machine  x86_64
user     roedi004
UseRobust  0
Loading ./tmp.mri_nu_correct.mni.521075/ones.mgz
Loading ./tmp.mri_nu_correct.mni.521075/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to ./tmp.mri_nu_correct.mni.521075/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.521075/nu2.mnc ./tmp.mri_nu_correct.mni.521075/nu2.mnc mul .92391690360540490099
Saving result to './tmp.mri_nu_correct.mni.521075/nu2.mnc' (type = MINC )                       [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.521075/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.521075/nu2.mnc nu.mgz --like orig.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.521075/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 7 seconds.
mapping (36, 199) to ( 3, 110)
 
 
Wed Jun 16 10:03:07 CDT 2021
mri_nu_correct.mni done

 mri_add_xform_to_header -c /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/transforms/talairach.xfm nu.mgz nu.mgz 

INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Wed Jun 16 10:03:08 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri

 mri_normalize -g 1 -mprage nu.mgz T1.mgz 

using max gradient = 1.000
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading from nu.mgz...
normalizing image...
talairach transform
 1.25969  -0.00441  -0.00714  -0.54750;
 0.02505   1.18646   0.10081   1.56232;
 0.04489  -0.07770   1.36300  -2.36977;
 0.00000   0.00000   0.00000   1.00000;
processing without aseg, no1d=0
MRInormInit(): 
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize(): 
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...

Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 65 (65), valley at 31 (31)
csf peak at 33, setting threshold to 54
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 66 (66), valley at 31 (31)
csf peak at 34, setting threshold to 55
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 58 seconds.
#--------------------------------------------
#@# Skull Stripping Wed Jun 16 10:05:06 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri

 mri_em_register -mask extern.emreg.mask.mgz nu.mgz /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_externmask.lta 

using MR volume extern.emreg.mask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 8 == 
reading 1 input volumes...
logging results to talairach_with_externmask.log
reading '/opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7 
total sample mean = 78.5 (494 zeros)
************************************************
spacing=8, using 2252 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2252, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=29.1
skull bounding box = (66, 90, 49) --> (187, 199, 204)
using (106, 126, 127) as brain centroid...
mean wm in atlas = 107, using box (91,113,108) --> (120, 139,146) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 105 +- 4.5
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -4.858
************************************************
First Search limited to translation only.
************************************************
max log p =    -4.535702 @ (-9.091, -27.273, -27.273)
max log p =    -4.357319 @ (4.545, 4.545, 13.636)
max log p =    -4.256121 @ (2.273, -2.273, -2.273)
max log p =    -4.247165 @ (-1.136, 1.136, 3.409)
max log p =    -4.236141 @ (1.705, -1.705, -3.977)
max log p =    -4.226527 @ (0.284, 0.284, -1.989)
Found translation: (-1.4, -25.3, -18.5): log p = -4.227
****************************************
Nine parameter search.  iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.726, old_max_log_p =-4.227 (thresh=-4.2)
 1.15000   0.00000   0.00000  -20.64408;
 0.00000   1.22567  -0.14032  -33.02412;
 0.00000   0.16136   1.06580  -49.94852;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.668, old_max_log_p =-3.726 (thresh=-3.7)
 1.15000   0.00000   0.00000  -20.64408;
 0.00000   1.31760  -0.15084  -44.44769;
 0.00000   0.16136   1.06580  -49.94852;
 0.00000   0.00000   0.00000   1.00000;
****************************************
Nine parameter search.  iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.668, old_max_log_p =-3.668 (thresh=-3.7)
 1.15000   0.00000   0.00000  -20.64408;
 0.00000   1.31760  -0.15084  -44.44769;
 0.00000   0.16136   1.06580  -49.94852;
 0.00000   0.00000   0.00000   1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search.  iteration 3 nscales = 1 ...
****************************************
Terminated
Linux ln0004 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s HCPA001 exited with ERRORS at Wed Jun 16 10:13:01 CDT 2021

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

It seems like something terminates the process that is running hcp_freesurfer. This can happen if you do not have or do not reserve (when scheduling) enough resources when running. By resources I mostly mean memory and time.

1 Like

Hi Jure,
For me hcp_freesurfer fails right away when trying to run interactively on a node with 32G RAM and 24hrs allocated. Do you know what other parameters might be causing the process to terminate? Thanks!

Yes, cshleifer these are two separate issues. I am glad we resolved one though. I am still working on your issue, but the problem is that I am unable to reproduce it which makes it hard to debug. I will let you know once I make some progress.

@cschleifer

Could you please run qunex_envstatus from inside the Singularity container and paste the exact output here? The issue may stem from the way Singularity interprets the shell environment variables and you may have a system-wide FreeSurfer install that is not the one inside the container and this is conflicting.

Hi Alan,
Looks like that was the problem, thank you! My bashrc was setting up a different FreeSurfer path. If I remove that then hcp_freesurfer starts properly in the container.

Here is the original output of qunex_envstatus:

-------------------------------------------------------------- 
 QuNex Environment Status Report 
-------------------------------------------------------------- 



   OS Version 
---------------------------------------------- 

               NAME="CentOS Linux"
               VERSION="7 (Core)"
               ID="centos"
               ID_LIKE="rhel fedora"
               VERSION_ID="7"
               PRETTY_NAME="CentOS Linux 7 (Core)"
               ANSI_COLOR="0;31"
               CPE_NAME="cpe:/o:centos:centos:7"
               HOME_URL="https://www.centos.org/"
               BUG_REPORT_URL="https://bugs.centos.org/"
               
               CENTOS_MANTISBT_PROJECT="CentOS-7"
               CENTOS_MANTISBT_PROJECT_VERSION="7"
               REDHAT_SUPPORT_PRODUCT="centos"
               REDHAT_SUPPORT_PRODUCT_VERSION="7"

   QuNex General Environment Variables 
---------------------------------------------- 

                 QuNexVer : 0.90.6
                    TOOLS : /opt
                QUNEXREPO : qunex
                QUNEXPATH : /opt/qunex
                 QUNEXENV : /opt/env/qunex
           TemplateFolder : /opt/qunex/qx_library/data/
            QUNEXMCOMMAND : octave -q --no-init-file --eval

   Core Dependencies Environment Variables 
---------------------------------------------- 

                 CONDADIR : /opt/miniconda
                   FSLDIR : /u/project/cbearden/data/scripts/tools/fsl-6.0.4
                FSLGPUDIR : /opt/fsl/fsl/bin
            FSLGPUScripts : /opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu
             FSLGPUBinary : /opt/qunex/qx_library/etc/fsl_gpu_binaries
               FSL_FIXDIR : /opt/fsl/fix
          FREESURFER_HOME : /u/project/cbearden/data/scripts/tools/freesurfer
     FREESURFER_SCHEDULER : /opt/freesurfer/FreeSurferScheduler
             WORKBENCHDIR : /opt/workbench/workbench/bin_rh_linux64
                CARET7DIR : /opt/workbench/workbench/bin_rh_linux64
                  AFNIDIR : /opt/afni/afni
                DCMNIIDIR : /opt/dcm2niix/dcm2niix
               DICMNIIDIR : /opt/dicm2nii/dicm2nii
                OCTAVEDIR : /opt/octave/octave
             OCTAVEPKGDIR : /opt/octave/octavepkg
             OCTAVEBINDIR : /opt/octave/octave/bin
                     RDIR : /opt/R/R
                  PALMDIR : /opt/palm/palm-o

   HCP Pipelines Environment Variables 
---------------------------------------------- 

               HCPPIPEDIR : /u/project/cbearden/data/scripts/tools/HCPpipelines-4.1.3
            GRADUNWARPDIR : /opt/gradunwarp/gradunwarp
     HCPPIPEDIR_Templates : /opt/HCP/HCPpipelines/global/templates
           HCPPIPEDIR_Bin : /opt/HCP/HCPpipelines/global/binaries
        HCPPIPEDIR_Config : /opt/HCP/HCPpipelines/global/config
         HCPPIPEDIR_PreFS : /opt/HCP/HCPpipelines/PreFreeSurfer/scripts
            HCPPIPEDIR_FS : /opt/HCP/HCPpipelines/FreeSurfer/scripts
        HCPPIPEDIR_PostFS : /opt/HCP/HCPpipelines/PostFreeSurfer/scripts
      HCPPIPEDIR_fMRISurf : /opt/HCP/HCPpipelines/fMRISurface/scripts
       HCPPIPEDIR_fMRIVol : /opt/HCP/HCPpipelines/fMRIVolume/scripts
         HCPPIPEDIR_tfMRI : /opt/HCP/HCPpipelines/tfMRI/scripts
          HCPPIPEDIR_dMRI : /opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts
     HCPPIPEDIR_dMRITract : /opt/qunex/bash/qx_utilities/diffusion_tractography/scripts
        HCPPIPEDIR_Global : /opt/HCP/HCPpipelines/global/scripts
 HCPPIPEDIR_tfMRIAnalysis : /opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts
                MSMBINDIR : /opt/MSM_HOCR_v3/Centos
  HCPPIPEDIR_dMRITractFull : /opt/qunex/bash/qx_utilities/diffusion_tractography_dense
    HCPPIPEDIR_dMRILegacy : /opt/qunex/bash/qx_utilities
            AutoPtxFolder : /opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended
              EDDYCUDADIR : /opt/qunex/qx_library/etc/fsl_gpu_binaries/eddy_cuda


   Binary / Executable Locations and Versions 
---------------------------------------------- 

        HCPpipelines : v4.1.3
fatal: Not a git repository: '/u/project/cbearden/data/scripts/tools/HCPpipelines-4.1.3/.git'
    HCPpipelines TAG : 
fatal: Not a git repository: '/u/project/cbearden/data/scripts/tools/HCPpipelines-4.1.3/.git'
 HCPpipelines commit : 

         FSL Binary  : /u/project/cbearden/data/scripts/tools/fsl-6.0.4/bin/fsl
         FSL Version : 6.0.4:ddd0a010

  FreeSurfer Binary  : /u/project/cbearden/data/scripts/tools/freesurfer/bin/freesurfer
/u/local/Modules/4.7.0/gcc-4.8.5/init/bash: line 37: /usr/bin/tclsh: No such file or directory
  FreeSurfer Version :   freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551

    dcm2niix Binary  : /opt/dcm2niix/dcm2niix/dcm2niix
    dcm2niix Version : Chris Rorden's dcm2niiX version v1.0.20190720  (JP2:OpenJPEG) GCC4.8.5 (64-bit Linux)

      Octave Binary  : /opt/octave/octave/bin/octave
warning: function ./pathdef.m shadows a core library function
      Octave Version : 4.4.1

           R Binary  : /usr/local/bin/R
           R Version : R version 3.6.1 (2019-07-05) -- "Action of the Toes"

           R required packages : ggplot2

           R Package : ggplot2  ‘3.3.3’

        PALM Binary  : /opt/palm/palm-o/palm.m
        PALM Version : Feb/2021 alpha118

  wb_command Binary  : /opt/workbench/workbench/bin_rh_linux64/wb_command
/u/local/Modules/4.7.0/gcc-4.8.5/init/bash: line 37: /usr/bin/tclsh: No such file or directory
  wb_command Version : Version: 1.5.0

  Full Environment Paths 
---------------------------------------------- 

  PATH : /u/project/cbearden/data/scripts/tools/fsl-6.0.4/bin:/u/project/cbearden/data/scripts/tools/freesurfer/bin:/u/project/cbearden/data/scripts/tools/freesurfer/fsfast/bin:/u/project/cbearden/data/scripts/tools/freesurfer/tktools:/opt/fsl/fsl/bin:/u/project/cbearden/data/scripts/tools/freesurfer/mni/bin:/opt/qunex/qx_library/etc/fsl_gpu_binaries/probtrackx_gpu_cuda_9.1:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/bin:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/lib:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu:/usr/local/cuda/bin:/opt/HCP/HCPpipelines/global/matlab/:/opt/fsl/fix:/opt/qunex/qx_library/etc/fsl_gpu_binaries/eddy_cuda:/opt/qunex/qx_library/etc/fsl_gpu_binaries:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended:/opt/qunex/bash/qx_utilities:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense:/opt/qunex/bash/qx_utilities/diffusion_tractography/scripts:/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts:/opt/HCP/HCPpipelines/global/scripts:/opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts:/opt/HCP/HCPpipelines/tfMRI/scripts:/opt/HCP/HCPpipelines/fMRIVolume/scripts:/opt/HCP/HCPpipelines/fMRISurface/scripts:/opt/HCP/HCPpipelines/PostFreeSurfer/scripts:/opt/HCP/HCPpipelines/FreeSurfer/scripts:/opt/HCP/HCPpipelines/PreFreeSurfer/scripts:/opt/HCP/HCPpipelines/global/config:/opt/HCP/HCPpipelines/global/binaries:/opt/HCP/HCPpipelines/global/templates:/opt/gradunwarp/gradunwarp/gradunwarp/core:/opt/workbench/workbench/bin_rh_linux64:/opt/HCP/HCPpipelines:/opt/HCP/HCPpipelines/MSMConfig:/opt/qunex/python/qx_utilities/templates/:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/R/R:/opt/matlab/bin:/opt/octave/octave/bin:/opt/dcm2niix/dcm2niix:/opt/dcm2niix/dcm2niix/build/bin:/opt/afni/afni:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/freesurfer/FreeSurferScheduler:/opt/fsl/fsl/bin:/opt/freesurfer/freesurfer-6.0/bin:/u/project/cbearden/data/scripts/tools/freesurfer/fsfast/bin:/opt/freesurfer/freesurfer-6.0/tktools:/opt/fsl/fsl/bin:/u/project/cbearden/data/scripts/tools/freesurfer/mni/bin:/opt/freesurfer/freesurfer-6.0:/opt/fsl/fsl/bin:/usr/local/bin:/opt/qunex/lib:/opt/qunex/bin:/opt/bin:/opt/lib/bin:/opt/lib/lib/:/opt/olib:/opt/qunex/python/qx_utilities:/opt/env/qunex/bin:/opt/miniconda/condabin:/opt/miniconda/bin:/opt:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/bin:/u/project/cbearden/data/scripts/tools/workbench/bin_rh_linux64:/u/home/s/schleife/abin

  MATLABPATH : /opt/qunex/matlab/qx_utilities/general:/opt/qunex/matlab/qx_mri/stats:/opt/qunex/matlab/qx_mri/img:/opt/qunex/matlab/qx_mri/general:/opt/qunex/matlab/qx_mri/fc:/opt/HCP/HCPpipelines/global/matlab/:/opt/fsl/fix:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/dicm2nii/dicm2nii:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/fsl/fsl:/opt/fsl/fsl/bin:


=================== QuNex environment set successfully! ==================== 

And here is qunex_envstatus with the correct environment variables after removing the conflicting lines from my bashrc:

-------------------------------------------------------------- 
 QuNex Environment Status Report 
-------------------------------------------------------------- 



   OS Version 
---------------------------------------------- 

               NAME="CentOS Linux"
               VERSION="7 (Core)"
               ID="centos"
               ID_LIKE="rhel fedora"
               VERSION_ID="7"
               PRETTY_NAME="CentOS Linux 7 (Core)"
               ANSI_COLOR="0;31"
               CPE_NAME="cpe:/o:centos:centos:7"
               HOME_URL="https://www.centos.org/"
               BUG_REPORT_URL="https://bugs.centos.org/"
               
               CENTOS_MANTISBT_PROJECT="CentOS-7"
               CENTOS_MANTISBT_PROJECT_VERSION="7"
               REDHAT_SUPPORT_PRODUCT="centos"
               REDHAT_SUPPORT_PRODUCT_VERSION="7"

   QuNex General Environment Variables 
---------------------------------------------- 

                 QuNexVer : 0.90.6
                    TOOLS : /opt
                QUNEXREPO : qunex
                QUNEXPATH : /opt/qunex
                 QUNEXENV : /opt/env/qunex
           TemplateFolder : /opt/qunex/qx_library/data/
            QUNEXMCOMMAND : octave -q --no-init-file --eval

   Core Dependencies Environment Variables 
---------------------------------------------- 

                 CONDADIR : /opt/miniconda
                   FSLDIR : /opt/fsl/fsl
                FSLGPUDIR : /opt/fsl/fsl/bin
            FSLGPUScripts : /opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu
             FSLGPUBinary : /opt/qunex/qx_library/etc/fsl_gpu_binaries
               FSL_FIXDIR : /opt/fsl/fix
          FREESURFER_HOME : /opt/freesurfer/freesurfer-6.0
     FREESURFER_SCHEDULER : /opt/freesurfer/FreeSurferScheduler
             WORKBENCHDIR : /opt/workbench/workbench/bin_rh_linux64
                CARET7DIR : /opt/workbench/workbench/bin_rh_linux64
                  AFNIDIR : /opt/afni/afni
                DCMNIIDIR : /opt/dcm2niix/dcm2niix
               DICMNIIDIR : /opt/dicm2nii/dicm2nii
                OCTAVEDIR : /opt/octave/octave
             OCTAVEPKGDIR : /opt/octave/octavepkg
             OCTAVEBINDIR : /opt/octave/octave/bin
                     RDIR : /opt/R/R
                  PALMDIR : /opt/palm/palm-o

   HCP Pipelines Environment Variables 
---------------------------------------------- 

               HCPPIPEDIR : /opt/HCP/HCPpipelines
            GRADUNWARPDIR : /opt/gradunwarp/gradunwarp
     HCPPIPEDIR_Templates : /opt/HCP/HCPpipelines/global/templates
           HCPPIPEDIR_Bin : /opt/HCP/HCPpipelines/global/binaries
        HCPPIPEDIR_Config : /opt/HCP/HCPpipelines/global/config
         HCPPIPEDIR_PreFS : /opt/HCP/HCPpipelines/PreFreeSurfer/scripts
            HCPPIPEDIR_FS : /opt/HCP/HCPpipelines/FreeSurfer/scripts
        HCPPIPEDIR_PostFS : /opt/HCP/HCPpipelines/PostFreeSurfer/scripts
      HCPPIPEDIR_fMRISurf : /opt/HCP/HCPpipelines/fMRISurface/scripts
       HCPPIPEDIR_fMRIVol : /opt/HCP/HCPpipelines/fMRIVolume/scripts
         HCPPIPEDIR_tfMRI : /opt/HCP/HCPpipelines/tfMRI/scripts
          HCPPIPEDIR_dMRI : /opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts
     HCPPIPEDIR_dMRITract : /opt/qunex/bash/qx_utilities/diffusion_tractography/scripts
        HCPPIPEDIR_Global : /opt/HCP/HCPpipelines/global/scripts
 HCPPIPEDIR_tfMRIAnalysis : /opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts
                MSMBINDIR : /opt/MSM_HOCR_v3/Centos
  HCPPIPEDIR_dMRITractFull : /opt/qunex/bash/qx_utilities/diffusion_tractography_dense
    HCPPIPEDIR_dMRILegacy : /opt/qunex/bash/qx_utilities
            AutoPtxFolder : /opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended
              EDDYCUDADIR : /opt/qunex/qx_library/etc/fsl_gpu_binaries/eddy_cuda


   Binary / Executable Locations and Versions 
---------------------------------------------- 

        HCPpipelines : v4.3.0
    HCPpipelines TAG : v4.3.0
 HCPpipelines commit : 716e9f48f02bc9914d4618bb32a88988381d199e

         FSL Binary  : /opt/fsl/fsl/bin/fsl
         FSL Version : 6.0.4:ddd0a010

  FreeSurfer Binary  : /opt/freesurfer/freesurfer-6.0/bin/freesurfer
/u/local/Modules/4.7.0/gcc-4.8.5/init/bash: line 37: /usr/bin/tclsh: No such file or directory
  FreeSurfer Version :   freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

    dcm2niix Binary  : /opt/dcm2niix/dcm2niix/dcm2niix
    dcm2niix Version : Chris Rorden's dcm2niiX version v1.0.20190720  (JP2:OpenJPEG) GCC4.8.5 (64-bit Linux)

      Octave Binary  : /opt/octave/octave/bin/octave
warning: function ./pathdef.m shadows a core library function
      Octave Version : 4.4.1

           R Binary  : /usr/local/bin/R
           R Version : R version 3.6.1 (2019-07-05) -- "Action of the Toes"

           R required packages : ggplot2
Error: cannot allocate vector of size 8.7 Gb
Execution halted
           R Package : ggplot2 

        PALM Binary  : /opt/palm/palm-o/palm.m
        PALM Version : Feb/2021 alpha118

  wb_command Binary  : /opt/workbench/workbench/bin_rh_linux64/wb_command
/u/local/Modules/4.7.0/gcc-4.8.5/init/bash: line 37: /usr/bin/tclsh: No such file or directory
  wb_command Version : Version: 1.5.0

  Full Environment Paths 
---------------------------------------------- 

  PATH : /opt/qunex/qx_library/etc/fsl_gpu_binaries/probtrackx_gpu_cuda_9.1:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/bin:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu/lib:/opt/qunex/qx_library/etc/fsl_gpu_binaries/bedpostx_gpu_cuda_9.1/bedpostx_gpu:/usr/local/cuda/bin:/opt/HCP/HCPpipelines/global/matlab/:/opt/fsl/fix:/opt/qunex/qx_library/etc/fsl_gpu_binaries/eddy_cuda:/opt/qunex/qx_library/etc/fsl_gpu_binaries:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/fsl_gpu:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense/autoptx_hcp_extended:/opt/qunex/bash/qx_utilities:/opt/qunex/bash/qx_utilities/diffusion_tractography_dense:/opt/qunex/bash/qx_utilities/diffusion_tractography/scripts:/opt/HCP/HCPpipelines/TaskfMRIAnalysis/scripts:/opt/HCP/HCPpipelines/global/scripts:/opt/HCP/HCPpipelines/DiffusionPreprocessing/scripts:/opt/HCP/HCPpipelines/tfMRI/scripts:/opt/HCP/HCPpipelines/fMRIVolume/scripts:/opt/HCP/HCPpipelines/fMRISurface/scripts:/opt/HCP/HCPpipelines/PostFreeSurfer/scripts:/opt/HCP/HCPpipelines/FreeSurfer/scripts:/opt/HCP/HCPpipelines/PreFreeSurfer/scripts:/opt/HCP/HCPpipelines/global/config:/opt/HCP/HCPpipelines/global/binaries:/opt/HCP/HCPpipelines/global/templates:/opt/gradunwarp/gradunwarp/gradunwarp/core:/opt/workbench/workbench/bin_rh_linux64:/opt/HCP/HCPpipelines:/opt/HCP/HCPpipelines/MSMConfig:/opt/qunex/python/qx_utilities/templates/:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/R/R:/opt/matlab/bin:/opt/octave/octave/bin:/opt/dcm2niix/dcm2niix:/opt/dcm2niix/dcm2niix/build/bin:/opt/afni/afni:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/freesurfer/FreeSurferScheduler:/opt/fsl/fsl/bin:/opt/freesurfer/freesurfer-6.0/bin:/opt/freesurfer/freesurfer-6.0/fsfast/bin:/opt/freesurfer/freesurfer-6.0/tktools:/opt/fsl/fsl/bin:/opt/freesurfer/freesurfer-6.0/mni/bin:/opt/freesurfer/freesurfer-6.0:/opt/fsl/fsl/bin:/usr/local/bin:/opt/qunex/lib:/opt/qunex/bin:/opt/bin:/opt/lib/bin:/opt/lib/lib/:/opt/olib:/opt/qunex/python/qx_utilities:/opt/env/qunex/bin:/opt/miniconda/condabin:/opt/miniconda/bin:/opt:/usr/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/bin:/u/project/cbearden/data/scripts/tools/workbench/bin_rh_linux64:/u/home/s/schleife/abin

  MATLABPATH : /opt/qunex/matlab/qx_utilities/general:/opt/qunex/matlab/qx_mri/stats:/opt/qunex/matlab/qx_mri/img:/opt/qunex/matlab/qx_mri/general:/opt/qunex/matlab/qx_mri/fc:/opt/HCP/HCPpipelines/global/matlab/:/opt/fsl/fix:/opt/qunex/qx_library/data/:/opt/qunex/qx_library/data/atlases/hcp:/opt/dicm2nii/dicm2nii:/opt/palm/palm-o:/opt/workbench/workbench/bin_rh_linux64:/opt/fsl/fsl:/opt/fsl/fsl/bin:


=================== QuNex environment set successfully! ==================== 

Thank you @alan.anticevic and @demsarjure for your help with this!

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