Import dicom raising No such file or directory error

Issues
1

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!

2

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.

3

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

4

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