Dear Jure and QuNex Experts:
I have been trying to run dwi_legacy but was not able to. I unfortunately couldn’t figure out what was the problem at all.
Below is the exact command I ran:
qunex_container dwi_legacy \
--sessionsfolder="${WORK_DIR}/${STUDY_NAME}/sessions" \
--sessions="${SESSIONS}" \
--function='dwi_legacy' \
--PEdir='1' \
--echospacing='0.69' \
--TE='2.46'\
--unwarpdir='x-' \
--diffdatasuffix='DWI_dir98_99_AP' \
--usefieldmap='no' \
--scanner='siemens' \
--overwrite='yes' \
--container="${QUNEX_CONTAINER}" \
--nv;
And below is the error messages that I got:
--> QuNex will run the command over 1 sessions. It will utilize:
Scheduled jobs: 1
Maximum sessions run in parallel for a job: 1.
Maximum elements run in parallel for a session: 1.
Up to 1 processes will be utilized for a job.
Job #1 will run sessions: 010A
/home/ehui/tmpxg4uy14t
singularity exec --cleanenv --nv /hdd/qunex/qunexcontainer/qunex_suite-0.93.6.sif bash /home/ehui/tmpxg4uy14t
ehui@ehui:~/qunex$ --> unsetting the following environment variables: PATH MATLABPATH PYTHONPATH QUNEXVer TOOLS QUNEXREPO QUNEXPATH QUNEXLIBRARY QUNEXLIBRARYETC TemplateFolder FSL_FIXDIR FREESURFERDIR FREESURFER_HOME FREESURFER_SCHEDULER FreeSurferSchedulerDIR WORKBENCHDIR DCMNIIDIR DICMNIIDIR MATLABDIR MATLABBINDIR OCTAVEDIR OCTAVEPKGDIR OCTAVEBINDIR RDIR HCPWBDIR AFNIDIR PYLIBDIR FSLDIR FSLGPUDIR PALMDIR QUNEXMCOMMAND HCPPIPEDIR CARET7DIR GRADUNWARPDIR HCPPIPEDIR_Templates HCPPIPEDIR_Bin HCPPIPEDIR_Config HCPPIPEDIR_PreFS HCPPIPEDIR_FS HCPPIPEDIR_PostFS HCPPIPEDIR_fMRISurf HCPPIPEDIR_fMRIVol HCPPIPEDIR_tfMRI HCPPIPEDIR_dMRI HCPPIPEDIR_dMRITract HCPPIPEDIR_Global HCPPIPEDIR_tfMRIAnalysis HCPCIFTIRWDIR MSMBin HCPPIPEDIR_dMRITractFull HCPPIPEDIR_dMRILegacy AutoPtxFolder FSLGPUScripts FSLGPUBinary EDDYCUDADIR USEOCTAVE QUNEXENV CONDADIR MSMBINDIR MSMCONFIGDIR R_LIBS FSL_FIX_CIFTIRW FSFAST_HOME SUBJECTS_DIR MINC_BIN_DIR MNI_DIR MINC_LIB_DIR MNI_DATAPATH FSF_OUTPUT_FORMAT
Generated by QuNex
------------------------------------------------------------------------
Version: 0.93.6
User: ehui
System: ehui
OS: RedHat Linux #141~18.04.1-Ubuntu SMP Thu Aug 11 20:15:56 UTC 2022
------------------------------------------------------------------------
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\___███\ \______/ ║ \__| \__| \_______\__/ \__|
\___| ║
DEVELOPED & MAINTAINED BY:
Anticevic Lab, Yale University
Mind & Brain Lab, University of Ljubljana
Murray Lab, Yale University
COPYRIGHT & LICENSE NOTICE:
Use of this software is subject to the terms and conditions defined in
'LICENSE.md' which is a part of the QuNex Suite source code package:
https://bitbucket.org/oriadev/qunex/src/master/LICENSE.md
---> Setting up Octave
........................ Running QuNex v0.93.6 ........................
NOTE: Processing without FieldMap (TE option not needed)
Running dwi_legacy with the following parameters:
--------------------------------------------------------------
Study Folder: /home/ehui/qunex/cimt
Sessions Folder: /home/ehui/qunex/cimt/sessions
Sessions: 010A
Study Log Folder:
Scanner: siemens
Using FieldMap: no
Echo Spacing: 0.69
Phase Encoding Direction: 1
TE value for Fieldmap: 2.46
EPI Unwarp Direction: x-
Diffusion Data Suffix Name: DWI_dir98_99_AP
Overwrite prior run: yes
--- Full QuNex call for command: dwi_legacy
/opt/qunex/bash/qx_utilities/dwi_legacy.sh --sessionsfolder=/home/ehui/qunex/cimt/sessions --session=010A --scanner=siemens --usefieldmap=no --PEdir=1 --echospacing=0.69 --TE=2.46 --unwarpdir=x- --diffdatasuffix=DWI_dir98_99_AP --overwrite=yes
--------------------------------------------------------------
--------------------------------------------------------------
Running dwi_legacy locally on ehui
Command log: /home/ehui/qunex/cimt/processing/logs/runlogs/Log-dwi_legacy_2022-10-07_09.18.50.162679.log
Command output: /home/ehui/qunex/cimt/processing/logs/comlogs/tmp_dwi_legacy_010A_2022-10-07_09.18.50.162679.log
--------------------------------------------------------------
This function runs the DWI preprocessing using the FUGUE method for legacy data
that are not TOPUP compatible.
It explicitly assumes the the Human Connectome Project folder structure for
preprocessing.
DWI data needs to be in the following folder::
<study_folder>/<session>/hcp/<session>/T1w/Diffusion
T1w data needs to be in the following folder::
<study_folder>/<case>/hcp/<case>/T1w
Note:
- If PreFreeSurfer component of the HCP Pipelines was run the function will
make use of the T1w data [Results will be better due to superior brain
stripping].
- If PreFreeSurfer component of the HCP Pipelines was NOT run the function will
start from raw T1w data [Results may be less optimal].
- If you are this function interactively you need to be on a GPU-enabled node
or send it to a GPU-enabled queue.
INPUTS
======
--sessionsfolder Path to study data folder
--sessions Comma separated list of sessions to run
--scanner Name of scanner manufacturer (siemens or ge supported)
--echospacing EPI Echo Spacing for data [in msec]; e.g. 0.69
--PEdir Use 1 for Left-Right Phase Encoding, 2 for
Anterior-Posterior
--unwarpdir Direction for EPI image unwarping; e.g. x or x- for LR/RL,
y or y- for AP/PA; may been to try out both -/+ combinations
--usefieldmap Whether to use the standard field map (yes / no). If set
to <yes> then the parameter --TE becomes mandatory
--diffdatasuffix Name of the DWI image; e.g. if the data is called
<SessionID>_DWI_dir91_LR.nii.gz - you would enter
DWI_dir91_LR
--overwrite Delete prior run for a given session (yes / no)
FIELDMAP-SPECFIC INPUT
----------------------
--TE This is the echo time difference of the fieldmap sequence
- find this out form the operator - defaults are *usually*
2.46ms on SIEMENS
EXAMPLE USE
===========
Examples using Siemens FieldMap (needs GPU-enabled node).
Run directly via::
/opt/qunex/bash/qx_utilities/DWIPreprocPipelineLegacy.sh \
--<parameter1> --<parameter2> --<parameter3> ... --<parameterN>
NOTE: --scheduler is not available via direct script call.
Run via::
qunex dwi_legacy --<parameter1> --<parameter2> ... --<parameterN>
NOTE: scheduler is available via qunex call.
--scheduler A string for the cluster scheduler (e.g. LSF, PBS or SLURM)
followed by relevant options
For SLURM scheduler the string would look like this via the qunex call::
--scheduler='SLURM,jobname=<name_of_job>,time=<job_duration>,ntasks=<number_of_tasks>,cpus-per-task=<cpu_number>,mem-per-cpu=<memory>,partition=<queue_to_send_job_to>'
::
qunex dwi_legacy \
--sessionsfolder='<folder_with_sessions>' \
--sessions='<comma_separarated_list_of_cases>' \
--function='dwi_legacy' \
--PEdir='1' \
--echospacing='0.69' \
--TE='2.46' \
--unwarpdir='x-' \
--diffdatasuffix='DWI_dir91_LR' \
--usefieldmap='yes' \
--scanner='siemens' \
--overwrite='yes'
Example with flagged parameters for submission to the scheduler using Siemens
FieldMap (needs GPU-enabled queue)::
qunex dwi_legacy \
--sessionsfolder='<folder_with_sessions>' \
--sessions='<comma_separarated_list_of_cases>' \
--function='dwi_legacy' \
--PEdir='1' \
--echospacing='0.69' \
--TE='2.46' \
--unwarpdir='x-' \
--diffdatasuffix='DWI_dir91_LR' \
--scheduler='<name_of_scheduler_and_options>' \
--usefieldmap='yes' \
--scanner='siemens' \
--overwrite='yes' \
Example with flagged parameters for submission to the scheduler using GE data
without FieldMap (needs GPU-enabled queue)::
qunex dwi_legacy \
--sessionsfolder='<folder_with_sessions>' \
--sessions='<comma_separarated_list_of_cases>' \
--diffdatasuffix='DWI_dir91_LR' \
--scheduler='<name_of_scheduler_and_options>' \
--usefieldmap='no' \
--PEdir='1' \
--echospacing='0.69' \
--unwarpdir='x-' \
--scanner='ge' \
--overwrite='yes' \
===> ERROR during dwi_legacy. Check final QuNex error log output:
/home/ehui/qunex/cimt/processing/logs/comlogs/error_dwi_legacy_010A_2022-10-07_09.18.50.162679.log
▄▄▄▄▄▄▄ || ▄▄ ▄▄
▓▓ ▓ || ▓▓▓▄ ▓▓ ▓▓▓▓▓ ▄▓▓▓▓ ▓ ▄▓ ▄▓▓▓ ▓▓▓▄
▓▓ ▓ ▓ ▓ ▓ || ▓▓ ▐▓▓▓ ▄▄▄▄ ▀▓▓ ▓▓▀ ▓▓ ▓ ▓▓ ▓▓ ▓▓ ▄▓▓▄ ▓ ▓▓
▓▓▄▄▓▄▓ ▓▓ ▓ || ▓▓ ▓▓ ▓▄▄▓ ▓▄ ▓▓▀▀ ▓▓▓▓▓ ▓▌ ▓▓ ▀▓▓ ▓ ▓▓
▓▄▄ ▓▓▄▄▓ || ▓▓ ▓ ▓▄▄ ▄▓▓ ▓▓▄ ▓ ▓▀ ▓ ▓ ▓▓▓▀▀ ▓▓▓▓ ▓▓▓▀
||
I did put the data under ${sessionsfolder}/${sessions}/hcp/${sessions}/T1w/Diffusion like so:
010A_DWI_dir98_99_AP.nii.gz
QC
bvals
bvecs
eddylogs
Your help would be greatly appreciated. Thank you very much!
Best,
Ed