[RESOLVED] Import dicom raising No such file or directory error

gilinaggar · May 5, 2026, 5:18pm

Description:

Hi,

I have already used create study successfully, and now want to use import_dicom**:**

qunex_container import_dicom \
>     --sessionsfolder="${STUDY_FOLDER}/sessions"\
>     --sessions="${SESSIONS}" \
>     --masterinbox="${RAW_DATA}" \
>     --dockeropt="-v ${BIND_FOLDER}:${BIND_FOLDER}"\
>     --archive="leave" \
>     --container="${QUNEX_CONTAINER}"\
>     --overwrite=yes

I keep getting this error:

---> QuNex will run the command over 1 sessions. It will utilize:

    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: 041
bash: /home/docker/volumes/hcppipelines/gili/couples_study/processing/logs/batchlogs/qunex_container_command_2026-05-05_20.06.52.064927.sh: No such file or directory

When I go to the batchlogs folders manually to check, the file which is reported nonexistent does exist.

What am I doing wrong to cause this?

Thank you!

demsarjure · May 5, 2026, 6:19pm

Hi gilinaggar,

Welcome to the QuNex forum!

The most likely culprit is that you need to spefically give the system inside the QuNex container access to the location (folder). Try this:

qunex_container import_dicom \
  --sessionsfolder="${STUDY_FOLDER}/sessions"\
  --sessions="${SESSIONS}" \
  --masterinbox="${RAW_DATA}" \
  --bind="/home/docker/volumes/hcppipelines/gili:/home/docker/volumes/hcppipelines/gili" \
  --archive="leave" \
  --container="${QUNEX_CONTAINER}"\
  --overwrite=yes

I already see that you are doing some binding with --dockeropt, that should work as well, but a more elegant way is to use the --bind parameter. If needed also add ${BIND_FOLDER}:${BIND_FOLDER} to the bind parameter, just add a comma between multiple binds.

Let me know how it goes.

gilinaggar · May 11, 2026, 1:01pm

Hey Jure,

Thank you so much for the help! This worked and I moved on with the preprocessing.

When trying to run hcp_icafix I ran into a problem which I assume had to do with the way tasks are defined in my mapping and batch file, will greatly appreciate your help.

My code:

export QUNEX_CONTAINER=“qunexcontainer:0.99.2d_edited”
qunex_container hcp_icafix 
–sessionsfolder=“${STUDY_FOLDER}/sessions” 
–batchfile=“${STUDY_FOLDER}/processing/batch.txt” 
–sessions=“${SESSIONS}”
-hcp_icafix_bolds=“rsfMRI,tfMRI_EmotionalNBack,tfMRI_social_dialogue_video_AP,tfMRI_social_dynamic_video_AP,tfMRI_neutral_nature_video_AP,tfMRI_neutral_painting_video_AP”
–bind=“/home/docker/volumes/hcppipelines/gilinaggar:/home/docker/volumes/hcppipelines/gilinaggar”
–container=“${QUNEX_CONTAINER}” \ 
–parsessions=3 
–hcp_filename=userdefined

the error I got:

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

Session id: 041 

[started on Monday, 11. May 2026 08:32:44]

Running HCP ICAFix pipeline [HCPStyleData] ...



Comparing bolds with those specifed via parameters

     ... all bolds specified via hcp_icafix_bolds are present



Single-run HCP ICAFix on 6 bolds



Processing 2 ICAFix elements in parallel



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

---> Processing BOLD image 6

     ... ERROR: bold image [/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp/041/MNINonLinear/Results/6/6.nii.gz] missing!

---> ERROR: something missing, skipping this BOLD!



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

---> Processing BOLD image 1

     ... ERROR: bold image [/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp/041/MNINonLinear/Results/1/1.nii.gz] missing!

---> ERROR: something missing, skipping this BOLD!



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

---> Processing BOLD image 5

     ... ERROR: bold image [/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp/041/MNINonLinear/Results/5/5.nii.gz] missing!

---> ERROR: something missing, skipping this BOLD!



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

---> Processing BOLD image 4

     ... ERROR: bold image [/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp/041/MNINonLinear/Results/4/4.nii.gz] missing!

---> ERROR: something missing, skipping this BOLD!



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

---> Processing BOLD image 2

     ... ERROR: bold image [/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp/041/MNINonLinear/Results/2/2.nii.gz] missing!

---> ERROR: something missing, skipping this BOLD!



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

---> Processing BOLD image 3

     ... ERROR: bold image [/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp/041/MNINonLinear/Results/3/3.nii.gz] missing!

---> ERROR: something missing, skipping this BOLD!



HCP ICAFix completed on Monday, 11. May 2026 08:32:44

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





===> Final report for command hcp_icafix

... 041 ---> HCP ICAFix: 6, 1, 5, 4, 2, 3 not ready

===> Not all tasks completed fully!

My mapping file:

#  HCP mapping file
#  ----------------

T1w_MPRAGE_RL           => T1w
T2w_SPC_RL              => T2w
SpinEchoFieldMap_AP     => SE-FM-AP
SpinEchoFieldMap_PA     => SE-FM-PA
rsfMRI_AP_SBRef  => boldref:rest:filename(rsfMRI_SBRef)
rsfMRI_AP        => bold:rest:filename(rsfMRI)
tfMRI_EmotionalNBack_AP     => bold:emot_nback1:filename(tfMRI_EmotionalNBack)
tfMRI_EmotionalNBack_AP_SBRef     => boldref:emot_nbackref1:filename(tfMRI_EmotionalNBack_SBRef)
tfMRI_social_dialogue_video_AP     => bold:social_dia1:filename(tfMRI_social_dialogue_video_AP)
tfMRI_social_dialogue_video_AP_SBRef     => boldref:social_diaref1:filename(tfMRI_social_dialogue_video_AP_SBRef)
tfMRI_social_dynamic_video_AP     => bold:social_dyn1:filename(tfMRI_social_dynamic_video_AP)
tfMRI_social_dynamic_video_AP_SBRef     => boldref:social_dynref1:filename(tfMRI_social_dynamic_video_AP_SBRef)
tfMRI_neutral_nature_video_AP     => bold:neutral_nat1:filename(tfMRI_neutral_nature_video_AP)
tfMRI_neutral_nature_video_AP_SBRef     => boldref:neutral_natref1:filename(tfMRI_neutral_nature_video_AP_SBRef)
tfMRI_neutral_painting_video_AP     => bold:neutral_pain1:filename(tfMRI_neutral_painting_video_AP)
tfMRI_neutral_painting_video_AP_SBRef     => boldref:neutral_painref1:filename(tfMRI_neutral_painting_video_AP_SBRef)
dMRI_MB4_185dirs_d15D45_AP_SBRef        => DWI:dir185_AP_SBRef
dMRI_MB4_185dirs_d15D45_AP        => DWI:dir185_AP
dMRI_MB4_6dirs_d15D45_PA_SBRef        => DWI:dir6_PA_SBRef
dMRI_MB4_6dirs_d15D45_PA        => DWI:dir6_PA

My batch file:

# Generated by QuNex 1.3.0 [QIO] on 2026-05-06_08.32.18.266886

#

# Sessions folder: /home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions

# Source files: ['session_hcp.txt']

# Parameter file: /home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/specs/couples_study_batch_file.txt

#

# Generated by QuNex 0.98.1 on 2024-02-05_10.23.19.657180

#

# Sessions folder: /home/docker/volumes/hcppipelines/asaf_decoy_mouse/decoy/sessions

# Source files: ['session_hcp.txt']

# Parameter file: /home/docker/volumes/hcppipelines/asaf_decoy_mouse/decoy/sessions/specs/batch.txt

#

# Generated by QuNex 0.98.1 on 2023-07-31_10.00.04.704860

#

# Sessions folder: /Users/elaine/qunex/decoy/sessions

# Source files: ['session_hcp.txt']

# Parameter file: /Users/elaine/qunex/decoy_data/decoy_batch_file.txt

#

# -------------------------------------------------

# -- Qu|Nex Environment Preprocessing Parameters --

# -------------------------------------------------



# -------------------------------------

# ---> HCP Pipelines general parameters

# -------------------------------------

_hcp_Pipeline            : ${HCPPIPEDIR}

_parsessions             : 1

_parelements             : 2



# -------------------------------------

# ---> Pre FreeSurfer parameters

# -------------------------------------

_hcp_suffix             :

_hcp_brainsize          : 150

_hcp_t2                 : t2

_hcp_fmap               : NONE

_hcp_t1samplespacing    : 0.0000098 # taken from Shachar's pipeline scripts (run_PreFreeSurfer_HCP.sh)

_hcp_t2samplespacing    : 0.0000026 # taken from Shachar's pipeline scripts (run_PreFreeSurfer_HCP.sh)

_hcp_unwarpdir          : y

_hcp_avgrdcmethod       : TOPUP

_hcp_topupconfig        : b02b0.cnf

_hcp_printcom           :

_hcp_sephaseneg         : AP

_hcp_sephasepos         : PA

_hcp_seechospacing      : 0.000575072

_hcp_seunwarpdir        : y





# -------------------------------------

# ---> FreeSurfer parameters

# -------------------------------------

_hcp_freesurfer_home    : ${FREESURFER_HOME}





# -------------------------------------

# ---> Post FreeSurfer parameters

# -------------------------------------

_hcp_regname            : MSMSulc

_hcp_grayordinatesres   : 2

_hcp_hiresmesh          : 164

_hcp_lowresmesh         : 32





# -------------------------------------

# ---> Diffusion preprocessing - N/A

# -------------------------------------

_hcp_dwi_echospacing    : 0.689998

_hcp_dwi_PEdir          : 2





# -------------------------------------

# ---> fMRI Volume parameters

# -------------------------------------

_hcp_bold_echospacing   : 0.000575072

_hcp_bold_echodiff      : NONE

_hcp_bold_dcmethod      : TOPUP

_hcp_bold_topupconfig   : b02b0.cnf

_hcp_bold_sbref         : use

_hcp_bold_sephaseneg    : AP

_hcp_bold_sephasepos    : PA

_hcp_bold_unwarpdir     : y-

_hcp_bold_res           : 2

_hcp_bold_gdcoeffs      : NONE

_hcp_bold_doslicetime   : FALSE

_hcp_bold_seimg         : independent

_hcp_bold_movref        : independent

_hcp_bold_prefix        :





# -------------------------------------

# ---> fMRI Surface parameters

# -------------------------------------

_hcp_bold_smoothFWHM    : 2





# -------------------------------------

# ---> Further BOLD analyses parameters

# -------------------------------------

_image_source       : hcp

_image_target       : cifti

_bolds              : emot_nback1,rest,social_dyn1,social_dia1,neutral_nat1,neutral_pain1

_TR                 : 0.75

_omit               : 0

_pignore            : hipass=linear|regress=spline|lopass=linear

_log                : keep

_glm_matrix         : both

_glm_residuals      : save



   # # ==========  _bold_actions  ==============

   #

   # m ... Motion scrubbing.

   # s ... Spatial smooting.

   # h ... High-pass filtering.

   # r ... Regression (nuisance and/or task) with an optional number 0, 1, or 2

   #       specifying the type of regression to use (see REGRESSION below).

   # c ... Saving of resulting beta coefficients (allways to follow 'r').

   # l ... Low-pass filtering.

   #

   # =========================================



_bold_actions       : shrcl





# -------------------------------------

# ---> BOLD de-noising parameters

# -------------------------------------

_bold_nuisance      : m,V,WM,WB

_event_file         :

_nprocess           : 0

_bold_prefix        :

_event_string       :

_event_file         :

_boldname           : bold

_shrinknsroi        : true





# -------------------------------------

# ---> CIFTI mapping naming variable

# -------------------------------------

_hcp_cifti_tail      : _Atlas





# -------------------------------------

# ---> Smoothing parameters

# -------------------------------------

_surface_smooth      : 2

_volume_smooth       : 2

_voxel_smooth        : 1

_smooth_mask         : nonzero

_dilate_mask         : ${TOOLS}/${QUNEXREPO}/library/data/atlases/MNITemplates/MNI152_T1_2mm_brain_mask.nii.gz





# -------------------------------------

# ---> Movement scrubbing parameters

# -------------------------------------

_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:        0

_mov_after:         0

_mov_bad:           udvarsme

_mov_mreport:       movement_report.txt

_mov_preport:       movement_report_post.txt

_mov_sreport:       movement_scrubbing_report.txt

_mov_pdf:           movement_plots

---



---





---

# Generated by QuNex 1.3.0 [QIO] on 2026-05-06_08.24.08.227133

#

session: 041

subject: 041



dicom: /home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/dicom

raw_data: /home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/nii

data: /home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/4dfp

hcp: /home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp


   


hcpready: true



11  :                :localizer_3D_2 (9X5X5) [1/3] i00001: TR(0.0076): PEDirection(i): DwellTime(8.1e-06)

12  :                :localizer_3D_2 (9X5X5) [2/3] i00004: TR(0.0076): PEDirection(i): DwellTime(8.1e-06)

13  :                :localizer_3D_2 (9X5X5) [3/3] i00007: TR(0.0076): PEDirection(j-): DwellTime(8.1e-06)

21  :SE-FM-AP        :SpinEchoFieldMap_AP: TR(8.152): PEDirection(j-): EchoSpacing(0.000570006): DwellTime(2.5e-06): se(1)

31  :SE-FM-PA        :SpinEchoFieldMap_PA: TR(8.152): PEDirection(j): EchoSpacing(0.000570006): DwellTime(2.5e-06): se(1)

41  :boldref1:rest   :rsfMRI_AP_SBRef: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(rsfMRI_SBRef): se(1)

51  :bold1:rest      :rsfMRI_AP: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(rsfMRI): se(1)

61  :                :t2_tirm_FLAIR: TR(8): PEDirection(i): DwellTime(6e-06)

71  :boldref2:neutral_natref1:tfMRI_neutral_nature_video_AP_SBRef: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_neutral_nature_video_AP_SBRef): se(1)

81  :bold2:neutral_nat1:tfMRI_neutral_nature_video_AP: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_neutral_nature_video_AP): se(1)

91  :boldref3:neutral_painref1:tfMRI_neutral_painting_video_AP_SBRef: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_neutral_painting_video_AP_SBRef): se(1)

101 :bold3:neutral_pain1:tfMRI_neutral_painting_video_AP: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_neutral_painting_video_AP): se(1)

111 :T1w             :T1w_MPRAGE_RL: TR(2.4): DwellTime(9.8e-06): se(1)

121 :T1w             :T1w_MPRAGE_RL: TR(2.4): DwellTime(9.8e-06): se(1)

131 :boldref4:social_diaref1:tfMRI_social_dialogue_video_AP_SBRef: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_social_dialogue_video_AP_SBRef): se(1)

141 :bold4:social_dia1:tfMRI_social_dialogue_video_AP: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_social_dialogue_video_AP): se(1)

151 :boldref5:social_dynref1:tfMRI_social_dynamic_video_AP_SBRef: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_social_dynamic_video_AP_SBRef): se(1)

161 :bold5:social_dyn1:tfMRI_social_dynamic_video_AP: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_social_dynamic_video_AP): se(1)

171 :T2w             :T2w_SPC_RL: TR(3.2): PEDirection(i): DwellTime(2.6e-06): se(1)

181 :T2w             :T2w_SPC_RL: TR(3.2): PEDirection(i): DwellTime(2.6e-06): se(1)

191 :boldref6:emot_nbackref1:tfMRI_EmotionalNBack_AP_SBRef: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_EmotionalNBack_SBRef): se(1)

201 :bold6:emot_nback1:tfMRI_EmotionalNBack_AP: TR(0.75): PEDirection(j-): EchoSpacing(0.000575072): DwellTime(2.5e-06): filename(tfMRI_EmotionalNBack): se(1)

211 :DWI:dir6_PA_SBRef:dMRI_MB4_6dirs_d15D45_PA_SBRef: TR(3.5): PEDirection(j): EchoSpacing(0.000770008): DwellTime(2.6e-06): se(1)

221 :DWI:dir6_PA     :dMRI_MB4_6dirs_d15D45_PA: TR(3.5): PEDirection(j): EchoSpacing(0.000770008): DwellTime(2.6e-06): se(1)

231 :DWI:dir185_AP_SBRef:dMRI_MB4_185dirs_d15D45_AP_SBRef: TR(3.5): PEDirection(j-): EchoSpacing(0.000770008): DwellTime(2.6e-06): se(1)

241 :DWI:dir185_AP   :dMRI_MB4_185dirs_d15D45_AP: TR(3.5): PEDirection(j-): EchoSpacing(0.000770008): DwellTime(2.6e-06): se(1)

Thank you in advance!

Gili

demsarjure · May 12, 2026, 7:21am

Hi,

I see you are using 0.99.2d which is super old. This seems like a bug where hcp_icafix is not recognizing the hcp_filename=userdefined option and is trying to find files that use the automated naming convention (bolds 1, 2, 3, etc.).

I suggest you try using the latest QuNex version.

Best, Jure

gilinaggar · May 19, 2026, 9:03am

Hey Jure,

when using the most recent version this worked. Thank you so much!

now i’ve been getting stuck when trying to run the hcp_msmall command. The script I used:

qunex_container hcp_msmall
–batchfile=“${STUDY_FOLDER}/processing/batch.txt”
–sessionsfolder=“${STUDY_FOLDER}/sessions”
–sessions=“${SESSIONS}”
–hcp_icafix_bolds=‘emot_nback1,rest,social_dyn1,social_dia1,neutral_nat1,neutral_pain1’
–hcp_msmall_bolds=‘rest’
–hcp_icafix_highpass=2000
–bind=“/home/docker/volumes/hcppipelines/gilinaggar:/home/docker/volumes/hcppipelines/gilinaggar”
–hcp_matlab_mode=“compiled”
–container=“${QUNEX_CONTAINER}”
–parsessions=3
–hcp_filename=userdefined

the output I got when trying to run the command:


qunex hcp_msmall --sessionsfolder="/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions" --hcp_icafix_bolds="emot_nback1,rest,social_dyn1,social_dia1,neutral_nat1,neutral_pain1" --hcp_msmall_bolds="rest" --hcp_icafix_highpass="2000" --hcp_matlab_mode="compiled" --parsessions="3" --hcp_filename="userdefined" --batchfile="/home/docker/volumes/hcppipelines/gilinaggar/couples_study/processing/batch.txt" --sessions="041"

---------------------------------------------------------
# Generated by QuNex 1.3.0 [QIO] on 2026-05-18_14.25.45.631561#
=================================================================
qunex hcp_msmall \
  --sessionsfolder="/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions" \
  --hcp_icafix_bolds="emot_nback1,rest,social_dyn1,social_dia1,neutral_nat1,neutral_pain1" \
  --hcp_msmall_bolds="rest" \
  --hcp_icafix_highpass="2000" \
  --hcp_matlab_mode="compiled" \
  --parsessions="3" \
  --hcp_filename="userdefined" \
  --sessions="/home/docker/volumes/hcppipelines/gilinaggar/couples_study/processing/batch.txt" \
  --sessionids="041"
=================================================================

Starting multiprocessing sessions in /home/docker/volumes/hcppipelines/gilinaggar/couples_study/processing/batch.txt with a pool of 3 concurrent processes


Adding processing of session 041 to the pool at Monday, 18. May 2026 14:25:45
Running external command: # Generated by QuNex 1.3.0 [QIO] on 2026-05-18_14.25.45.742923#
------------------------------------------------------------
Running external command via QuNex:

/opt/HCP/HCPpipelines/MSMAll/MSMAllPipeline.sh \
  --path="/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp" \
  --session="041" \
  --fmri-names-list="rsfMRI" \
  --multirun-fix-names="" \
  --multirun-fix-concat-name="" \
  --multirun-fix-names-to-use="" \
  --output-fmri-name="rfMRI_REST" \
  --high-pass="2000" \
  --fmri-proc-string="_Atlas_hp2000_clean" \
  --msm-all-templates="/opt/HCP/HCPpipelines/global/templates/MSMAll" \
  --output-registration-name="MSMAll_InitialReg" \
  --high-res-mesh="164" \
  --low-res-mesh="32" \
  --input-registration-name="MSMSulc" \
  --myelin-target-file="/opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii" \
  --matlab-run-mode="0"
------------------------------------------------------------
You can follow command's progress in:
/home/docker/volumes/hcppipelines/gilinaggar/couples_study/processing/logs/comlogs/tmp_hcp_msmall_rfMRI_REST_041_2026-05-18_14.25.45.742923.log
------------------------------------------------------------
Running external command: # Generated by QuNex 1.3.0 [QIO] on 2026-05-18_16.36.47.693330#
------------------------------------------------------------
Running external command via QuNex:

/opt/HCP/HCPpipelines/DeDriftAndResample/DeDriftAndResamplePipeline.sh \
  --path="/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp" \
  --subject="041" \
  --fix-names="tfMRI_EmotionalNBack@rsfMRI@tfMRI_social_dynamic_video_AP@tfMRI_social_dialogue_video_AP@tfMRI_neutral_nature_video_AP@tfMRI_neutral_painting_video_AP" \
  --high-res-mesh="164" \
  --low-res-meshes="32" \
  --registration-name="MSMAll_InitialReg_2_d40_WRN" \
  --maps="sulc@curvature@corrThickness@thickness" \
  --smoothing-fwhm="2" \
  --high-pass="2000" \
  --motion-regression="TRUE" \
  --dedrift-reg-files="/opt/HCP/HCPpipelines/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@/opt/HCP/HCPpipelines/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii" \
  --concat-reg-name="MSMAll" \
  --myelin-maps="MyelinMap@SmoothedMyelinMap" \
  --myelin-target-file="/opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii" \
  --matlab-run-mode="0"
------------------------------------------------------------
You can follow command's progress in:
/home/docker/volumes/hcppipelines/gilinaggar/couples_study/processing/logs/comlogs/tmp_hcp_dedrift_and_resample_MSMAll_InitialReg_2_d40_WRN_041_2026-05-18_16.36.47.693330.log
------------------------------------------------------------

------------------------------------------------------------
Session id: 041 
[started on Monday, 18. May 2026 14:25:45]
Running HCP MSMAll pipeline [HCPStyleData] ...

Comparing bolds with those specifed via parameters
     ... all bolds specified via hcp_icafix_bolds are present

Single-run HCP ICAFix on 6 bolds

------------------------------------------------------------
---> Processing MSMAll rfMRI_REST
     ... bold image tfMRI_EmotionalNBack present
     ... bold image rsfMRI present
     ... bold image tfMRI_social_dynamic_video_AP present
     ... bold image tfMRI_social_dialogue_video_AP present
     ... bold image tfMRI_neutral_nature_video_AP present
     ... bold image tfMRI_neutral_painting_video_AP present

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

/opt/HCP/HCPpipelines/MSMAll/MSMAllPipeline.sh
    --path="/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp"
    --session="041"
    --fmri-names-list="rsfMRI"
    --multirun-fix-names=""
    --multirun-fix-concat-name=""
    --multirun-fix-names-to-use=""
    --output-fmri-name="rfMRI_REST"
    --high-pass="2000"
    --fmri-proc-string="_Atlas_hp2000_clean"
    --msm-all-templates="/opt/HCP/HCPpipelines/global/templates/MSMAll"
    --output-registration-name="MSMAll_InitialReg"
    --high-res-mesh="164"
    --low-res-mesh="32"
    --input-registration-name="MSMSulc"
    --myelin-target-file="/opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii"
    --matlab-run-mode="0"
------------------------------------------------------------


Running HCP MSMAll
---> logfile: /home/docker/volumes/hcppipelines/gilinaggar/couples_study/processing/logs/comlogs/done_hcp_msmall_rfMRI_REST_041_2026-05-18_14.25.45.742923.log


 --- Failed during processing of group DeDriftAndResample with error:


------------------------------------------------------------
---> Processing DeDriftAndResample
     ... bold image tfMRI_EmotionalNBack present
     ... bold image rsfMRI present
     ... bold image tfMRI_social_dynamic_video_AP present
     ... bold image tfMRI_social_dialogue_video_AP present
     ... bold image tfMRI_neutral_nature_video_AP present
     ... bold image tfMRI_neutral_painting_video_AP present

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

/opt/HCP/HCPpipelines/DeDriftAndResample/DeDriftAndResamplePipeline.sh
    --path="/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp"
    --subject="041"
    --fix-names="tfMRI_EmotionalNBack@rsfMRI@tfMRI_social_dynamic_video_AP@tfMRI_social_dialogue_video_AP@tfMRI_neutral_nature_video_AP@tfMRI_neutral_painting_video_AP"
    --high-res-mesh="164"
    --low-res-meshes="32"
    --registration-name="MSMAll_InitialReg_2_d40_WRN"
    --maps="sulc@curvature@corrThickness@thickness"
    --smoothing-fwhm="2"
    --high-pass="2000"
    --motion-regression="TRUE"
    --dedrift-reg-files="/opt/HCP/HCPpipelines/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@/opt/HCP/HCPpipelines/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii"
    --concat-reg-name="MSMAll"
    --myelin-maps="MyelinMap@SmoothedMyelinMap"
    --myelin-target-file="/opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii"
    --matlab-run-mode="0"
------------------------------------------------------------


Running HCP DeDriftAndResample

ERROR: Running HCP DeDriftAndResample failed with error Unknown error
... 
command executed:
/opt/HCP/HCPpipelines/DeDriftAndResample/DeDriftAndResamplePipeline.sh \
  --path="/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp" \
  --subject="041" \
  --fix-names="tfMRI_EmotionalNBack@rsfMRI@tfMRI_social_dynamic_video_AP@tfMRI_social_dialogue_video_AP@tfMRI_neutral_nature_video_AP@tfMRI_neutral_painting_video_AP" \
  --high-res-mesh="164" \
  --low-res-meshes="32" \
  --registration-name="MSMAll_InitialReg_2_d40_WRN" \
  --maps="sulc@curvature@corrThickness@thickness" \
  --smoothing-fwhm="2" \
  --high-pass="2000" \
  --motion-regression="TRUE" \
  --dedrift-reg-files="/opt/HCP/HCPpipelines/global/templates/MSMAll/DeDriftingGroup.L.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii@/opt/HCP/HCPpipelines/global/templates/MSMAll/DeDriftingGroup.R.sphere.DeDriftMSMAll.164k_fs_LR.surf.gii" \
  --concat-reg-name="MSMAll" \
  --myelin-maps="MyelinMap@SmoothedMyelinMap" \
  --myelin-target-file="/opt/HCP/HCPpipelines/global/templates/MSMAll/Q1-Q6_RelatedParcellation210.MyelinMap_BC_MSMAll_2_d41_WRN_DeDrift.32k_fs_LR.dscalar.nii" \
  --matlab-run-mode="0"

---> logfile: /home/docker/volumes/hcppipelines/gilinaggar/couples_study/processing/logs/comlogs/error_hcp_dedrift_and_resample_MSMAll_InitialReg_2_d40_WRN_041_2026-05-18_16.36.47.693330.log

HCP MSMAll completed on Monday, 18. May 2026 17:11:06
------------------------------------------------------------


---> Final report for command hcp_msmall
... 041 ---> HCP MSMAll: bolds tfMRI_neutral_painting_video_AP done; MSMAll_InitialReg_2_d40_WRN failed
---> Not all tasks completed fully!

Would love your input about what I’m doing wrong if that would be possible.

Thank you so much in advance!

demsarjure · May 22, 2026, 7:02am

Hi,

There are more detailed logs called comlogs inside the QuNex study. Can you upload those for hcp_msmall and hcp_dedrift_and_resample? You can find them in <studyfolder>/logs or <studyfolder>/processing/logs depending on the version that the QuNex study was created with. I would like to take a look at those with errors, such as

/home/docker/volumes/hcppipelines/gilinaggar/couples_study/processing/logs/comlogs/error_hcp_dedrift_and_resample_MSMAll_InitialReg_2_d40_WRN_041_2026-05-18_16.36.47.693330.log

I also see you are still not using the latest QuNex version, right now that is 1.4.3 with 1.5.0 coming out in June or July 2026. When updating the container, also update the qunex_container script, simply pull a new one as described in the QuNex quick start (QuNex quick start using a container — QuNex documentation).

Best, Jure

gilinaggar · May 24, 2026, 1:08pm

Hey Jure, thank you for the reply! I pulled version 1.4.3 and will use it going forward.

Attached is the file of the log.

Thanks again,

Gili

error_hcp_dedrift_and_resample_MSMAll_InitialReg_2_d40_WRN_041_2026-05-24_10.51.42.323149.log (37.0 KB)

demsarjure · May 25, 2026, 7:03am

Hi,

Please try rerunning hcp_msmall with 1.4.3 and set --overwrite=”yes”. If I remember correctly there were some bugs in hcp_dedrift_and_resample that we recently fixed.

Best, Jure

gilinaggar · May 25, 2026, 12:54pm

Hey Jure,

I tried adding the overwrite but unfortunately it still didn’t work… Attaching the log, sorry in advance for all the trouble

Do you have an idea for what else might be causing that?

Sorry and many thanks,

Gili

error_hcp_dedrift_and_resample_MSMAll_InitialReg_2_d40_WRN_041_2026-05-25_10.58.35.979344.log (37.0 KB)

demsarjure · May 25, 2026, 2:03pm

This is weird, you are getting this error:

Sun May 24 11:01:54 UTC 2026:ReApplyFixPipeline.sh: While running '/opt/HCP/HCPpipelines/ICAFIX/ReApplyFixPipeline.sh --path=/home/docker/volumes/hcppipelines/gilinaggar/couples_study/sessions/041/hcp --subject=041 --fmri-name=tfMRI_EmotionalNBack --high-pass=2000 --reg-name=MSMAll --matlab-run-mode=0 --motion-regression=TRUE':
Sun May 24 11:01:54 UTC 2026:ReApplyFixPipeline.sh: ERROR: FSL_FIXDIR environment variable must be set
Sun May 24 11:01:54 UTC 2026:ReApplyFixPipeline.sh: ERROR: FSL_FIXDIR environment variable must be set
Sun May 24 11:01:54 UTC 2026:ReApplyFixPipeline.sh: ABORTING

So ERROR: FSL_FIXDIR environment variable must be set in ReApplyFixPipeline.sh. You can see that this error is not present in that script ( HCPpipelines/ICAFIX/ReApplyFixPipeline.sh at master · Washington-University/HCPpipelines · GitHub ) and the script has not been updated for over 2 years. Could it be that you are binding some kind of a weird version into the container or that your container environment is not exactly QuNex one? That error is not generated by the HCP Pipelines that are shipped with QuNex as this line of code is not in there.

Best, Jure

demsarjure · May 25, 2026, 2:05pm

As a test you can try using qunex/qunex_suite:1.5.0_dev_3_fs8 from Docker hub. This is an untested dev container that will be released by the end of June or July.

demsarjure · May 25, 2026, 2:21pm

Another thing you can try is to set the FSL_FIXDIR manually, add the following to the qunex_container call:

...
--bash_post="export FSL_FIXDIR=/opt/fsl/fsl/bin"
...

Let me know if any of the above works.

Best, Jure

demsarjure · May 26, 2026, 8:12pm

I think the issue is that for some reason your code is using hcp_fix instead of hcp_multirun_fix. Are you using the old, legacy single fix instead of multi fix? This is not advised, “single” hcp_fix is in there only for backwards compatibility, new processing should not use it. Can you paste your hcp_icafix command here so I can check.

Best, Jure

gilinaggar · May 27, 2026, 7:35am

Hey Jure,

thanks for all the inputs!

My hcp_icafix command:

qunex_container hcp_icafix \
    --sessionsfolder="${STUDY_FOLDER}/sessions" \
    --batchfile="${STUDY_FOLDER}/processing/batch.txt" \
    --sessions="${SESSIONS}"\
    --hcp_icafix_bolds='emot_nback1,rest,social_dyn1,social_dia1,neutral_nat1,neutral_pain1'\
    --bind="/home/docker/volumes/hcppipelines/gilinaggar:/home/docker/volumes/hcppipelines/gilinaggar"\
    --container="${QUNEX_CONTAINER}" \
    --parsessions=3 \
    --hcp_filename=userdefined

demsarjure · May 27, 2026, 8:24am

Ah, here is the culprit. Sorry for missing this before. To run the multi fix that should be run and not the legacy version, you should use:

   --hcp_icafix_bolds='fMRI_CONCAT_ALL:emot_nback1,rest,social_dyn1,social_dia1,neutral_nat1,neutral_pain1'\

So you specify <group_name>:<list_of_bolds>. If you wish to run over all BOLDs (if the comma separated list are all your bolds), you can simply remove this parameter and it will set it correctly automatically. Let me know how it goes.

Best, Jure

demsarjure · May 31, 2026, 8:56am

Hi,

Did we manage to resolve this issue?

Best, Jure

gilinaggar · May 31, 2026, 9:35am

Hey Jure, sorry for not updating, I wanted to go through the rest to make sure everything worked.

The answer is yes! after re-running icafix successfully, MSMall also worked.

thank you so much for all the help!

Gili