Issue when processing hcp_fMRIVolume

Description:

I’m having troubles when trying to process hcp_fmri_volume, similar to this previous post but in the opposite direction: https://forum.qunex.yale.edu/t/resolved-hcp-fmri-volume-fails-to-detect-automated-naming-scheme-for-bold-image-processing/678. In my case the folders are named BOLD_1, BOLD_2, etc., while qunex looks for BOLD_1_AP, BOLD_2_PA, etc.

A second issue is that using empty quotes for the TOPUP configuration file does not set it to the default, as mentioned in the documentation: https://qunex.readthedocs.io/en/latest/api/gmri/hcp_fmri_volume.html:

–hcp_bold_topupconfig (str, default detailed below):
A full path to the topup configuration file to use. Set to ‘’ if the default is to be used or of TOPUP > distortion correction is not used.

Below is an example runlog file including the errors mentioned above. I also attached the batch file used. Thank you.

Estephan

# Generated by QuNex 0.94.14 on 2022-10-28_16.39.07.866726
#


============================= LOG ================================


# Generated by QuNex 0.94.14 on 2022-10-28_16.39.07.732824
#
=================================================================
gmri hcp_fmri_volume \
  --sessionsfolder="/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions" \
  --parsessions="52" \
  --parelements="4" \
  --hcp_filename="automated" \
  --sessions="/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/batch_K99Aim2.txt" \
  --sessionids="20001,20002,20004,20005,20006,20008,20010,20011,20012,20013,20015,20016,20018,20019,20021,20022,10001,10002,10004,10005,10006,10007,10009,10011,10013,10014,10015,10018,10019,10021,10022,11004,11006,10012,10016,10023,10024,10030,10031,10033,10034,10035,10036,10037,10038,10039,10041,10042,11009,11015" \
=================================================================

Starting multiprocessing sessions in /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/batch_K99Aim2.txt with a pool of 52 concurrent processes


------------------------------------------------------------
Session id: 10016 
[started on Friday, 28. October 2022 16:39:07]
Running HCP fMRI Volume pipeline [HCPStyleData] ... 
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Gradient distortion coefficients file present.
---> Looking for spin echo fieldmap set images [PA/AP].
     ... identified folder SpinEchoFieldMap1
     ... phase positive PA spin echo fieldmap image present
     ... phase negative AP spin echo fieldmap image present
     ... identified folder SpinEchoFieldMap2
     ... phase positive PA spin echo fieldmap image present
     ... phase negative AP spin echo fieldmap image present
---> ERROR: Could not find TOPUP configuration file: ''.

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
     ... phase encoding direction: AP
     ... unwarp direction: j-
     ... using image specific EchoSpacing: 0.000580009 s
     ... using spin echo fieldmap set 1
         -> SE Positive image : 10016_BOLD_PA_SB_SE.nii.gz
         -> SE Negative image : 10016_BOLD_AP_SB_SE.nii.gz
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10016/hcp/10016/unprocessed/BOLD_1_AP/10016_BOLD_1_AP.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 2
     ... phase encoding direction: PA
     ... unwarp direction: j
     ... using image specific EchoSpacing: 0.000580009 s
     ... using spin echo fieldmap set 1
         -> SE Positive image : 10016_BOLD_PA_SB_SE.nii.gz
         -> SE Negative image : 10016_BOLD_AP_SB_SE.nii.gz
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10016/hcp/10016/unprocessed/BOLD_2_PA/10016_BOLD_2_PA.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 3
     ... phase encoding direction: AP
     ... unwarp direction: j-
     ... using image specific EchoSpacing: 0.000580009 s
     ... using spin echo fieldmap set 2
         -> SE Positive image : 10016_BOLD_PA_SB_SE.nii.gz
         -> SE Negative image : 10016_BOLD_AP_SB_SE.nii.gz
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10016/hcp/10016/unprocessed/BOLD_3_AP/10016_BOLD_3_AP.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 4
     ... phase encoding direction: PA
     ... unwarp direction: j
     ... using image specific EchoSpacing: 0.000580009 s
     ... using spin echo fieldmap set 2
         -> SE Positive image : 10016_BOLD_PA_SB_SE.nii.gz
         -> SE Negative image : 10016_BOLD_AP_SB_SE.nii.gz
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/10016/hcp/10016/unprocessed/BOLD_4_PA/10016_BOLD_4_PA.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

Running 4 BOLD images in parallel
---> ERROR: No hcp info for session, skipping this BOLD!
---> ERROR: No hcp info for session, skipping this BOLD!
---> ERROR: No hcp info for session, skipping this BOLD!
---> ERROR: No hcp info for session, skipping this BOLD!

HCP fMRIVolume completed on Friday, 28. October 2022 16:39:07
------------------------------------------------------------


===> Final report for command hcp_fmri_volume
... 10016 ---> HCP fMRI Volume: bolds 1, 2, 3, 4 not ready
===> Not all tasks completed fully!

Call:

subjID_list="20001,20002,20004,20005,20006,20008,20010,20011,20012,20013,20015,20016,20018,20019,20021,20022,10001,10002,10004,10005,10006,10007,10009,10011,10013,10014,10015,10018,10019,10021,10022,11004,11006,10012,10016,10023,10024,10030,10031,10033,10034,10035,10036,10037,10038,10039,10041,10042,11009,11015"; \
msi_resources_time=12:00:00; msi_resources_nodes=1; msi_resources_ntaskspernode=24; msi_resources_mem=64000; msi_queue=agsmall; msi_resources_jobname=K99Aim2_fMRIVolume; \
qunex_container hcp_fmri_volume \
--batchfile=${study_sharedfolder}/processing/batch_K99Aim2.txt --sessionsfolder=${study_sharedfolder}/sessions --sessions=${subjID_list} --parsessions=52 --parelements=4 \
--hcp_filename=automated \
--scheduler=SLURM,array,time=${msi_resources_time},nodes=${msi_resources_nodes},cpus-per-task=${msi_resources_ntaskspernode},mem=${msi_resources_mem},partition=${msi_queue},jobname=${msi_resources_jobname} \
--bind=${study_sharedfolder}:${study_sharedfolder} --container=${HOME}/qunex/qunex_suite-0.94.14.sif

batch_K99Aim2.txt (347.1 KB)

Hi,

for hcp_bold_topupconfig the documentation is a bit misleading, the problem is that what you are providing in the batch file does not get parsed as an empty string (""), but as a string with two single quotes in it ("''"), try changing _hcp_bold_topupconfig : '' to _hcp_bold_topupconfig :, so without the '' at the end. I will fix the documentation, it should say that if you do not set the parameter it will use the default.

I believe that we just recently fixed a bug with _AP/_PA suffixes and that should be in the next release. I think the problem was that setup_hcp did not correctly add AP/PA suffixes that volume then looks for. I think a workaround is to create a copy of the batch file and remove PEDirection(xy) entries from BOLD images and then use that batch file. This should be fixed in 0.95.2 which should be coming out over the next couple of days.

Jure

Thanks for the feedback Jure. One of things I tried regarding TOPUP configuration file was to leave the parameter empty as you described, but it still caused trouble as the log below shows. I’ll try the new qunex version once it is out. Thank you.

# Generated by QuNex 0.94.14 on 2022-10-29_11.57.42.491650
#


============================= LOG ================================


# Generated by QuNex 0.94.14 on 2022-10-29_11.57.42.154206
#
=================================================================
gmri hcp_fmri_volume \
  --sessionsfolder="/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions" \
  --parsessions="52" \
  --parelements="4" \
  --overwrite="yes" \
  --sessions="/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/batch_K99Aim2.txt" \
  --sessionids="20001,20002,20004,20005,20006,20008,20010,20011,20012,20013,20015,20016,20018,20019,20021,20022,10001,10002,10004,10005,10006,10007,10009,10011,10013,10014,10015,10018,10019,10021,10022,11004,11006,10012,10016,10023,10024,10030,10031,10033,10034,10035,10036,10037,10038,10039,10041,10042,11009,11015" \
=================================================================

Starting multiprocessing sessions in /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/batch_K99Aim2.txt with a pool of 52 concurrent processes


------------------------------------------------------------
Session id: 20011 
[started on Saturday, 29. October 2022 11:57:42]
Running HCP fMRI Volume pipeline [HCPStyleData] ... 
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Gradient distortion coefficients file present.
---> ERROR: TOPUP requested but hcp_bold_topupconfig parameter is not set! Please review parameter file!

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
     ... phase encoding direction: AP
     ... unwarp direction: j-
     ... using image specific EchoSpacing: 0.000580009 s
     ... ERROR: Unknown distortion correction method: TOPUP! Please check your settings!
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/20011/hcp/20011/unprocessed/BOLD_1_AP/20011_BOLD_1_AP.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 2
     ... phase encoding direction: PA
     ... unwarp direction: j
     ... using image specific EchoSpacing: 0.000580009 s
     ... ERROR: Unknown distortion correction method: TOPUP! Please check your settings!
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/20011/hcp/20011/unprocessed/BOLD_2_PA/20011_BOLD_2_PA.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 3
     ... phase encoding direction: AP
     ... unwarp direction: j-
     ... using image specific EchoSpacing: 0.000580009 s
     ... ERROR: Unknown distortion correction method: TOPUP! Please check your settings!
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/20011/hcp/20011/unprocessed/BOLD_3_AP/20011_BOLD_3_AP.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 4
     ... phase encoding direction: PA
     ... unwarp direction: j
     ... using image specific EchoSpacing: 0.000580009 s
     ... ERROR: Unknown distortion correction method: TOPUP! Please check your settings!
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/20011/hcp/20011/unprocessed/BOLD_4_PA/20011_BOLD_4_PA.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

Running 4 BOLD images in parallel
---> ERROR: No hcp info for session, skipping this BOLD!
---> ERROR: No hcp info for session, skipping this BOLD!
---> ERROR: No hcp info for session, skipping this BOLD!
---> ERROR: No hcp info for session, skipping this BOLD!

HCP fMRIVolume completed on Saturday, 29. October 2022 11:57:42
------------------------------------------------------------


===> Final report for command hcp_fmri_volume
... 20011 ---> HCP fMRI Volume: bolds 1, 2, 3, 4 not ready
===> Not all tasks completed fully!

batch_K99Aim2.txt (347.1 KB)

We sorted out the issues with our servers, new version that fixes this should be out tomorrow or on Monday.

Sorry for the delay.

Jure

Estephan,

new version is now online. Please let us know if your issues have been resolved.

Jure

Hi Jure, I just tried but I got the same errors. Maybe I’m missing something? I attached here an example log and the batch file. I also took a screenshot of one of the sessions “unprocessed” folder.

qunex_container_job1_2022-11-15_12.00.52.594521.txt (8.9 KB)

batch_K99Aim2.txt (347.1 KB)

I will check what is happening with hcp_bold_topupconfig once more. There is a workaround for this, you can simply set hcp_bold_topupconfig to b02b0.cnf. Which is what is the HCP’s default that should be set automatically if the parameter is not provided. I will try to see what is going on here tomorrow.

As for missing BOLD files, QuNex is still appending the AP suffixes, which should be resolved in the latest patch. Can you rerun setup_hcp and create_batch command so the content of the batch file will be updated and then rerun please. The problem is that I am unable to recreate the issue on our end. And like mentioned before, also set hcp_bold_topupconfig in batch file to b02b0.cnf.

Let me know how things go.

Yes, following your advice now it started to run. Thanks Jure.

Another wrinkle. In my dataset, there are two participants that are missing fieldmaps so I need to run them in “LegacyStyleData” mode. When I do that, then I get the error that it cannot find the BOLD files again - this time because qunex is looking for the files named without the “_AP” or “_PA”.

How do you suggest I run these two participants in “LegacyStyleData” mode?

Command:

subjID_list="20017,11012"; \
msi_resources_time=12:00:00; msi_resources_nodes=1; msi_resources_ntaskspernode=24; msi_resources_mem=64000; msi_queue=agsmall; msi_resources_jobname=K99Aim2_fMRIVolume; \
qunex_container hcp_fmri_volume \
--batchfile=${study_sharedfolder}/processing/batch_K99Aim2.txt --sessionsfolder=${study_sharedfolder}/sessions --sessions=${subjID_list} --parsessions=52 --parelements=4 --overwrite=yes \
--hcp_processing_mode=LegacyStyleData --hcp_bold_biascorrection=LEGACY --hcp_bold_dcmethod=NONE \
--scheduler=SLURM,array,time=${msi_resources_time},nodes=${msi_resources_nodes},cpus-per-task=${msi_resources_ntaskspernode},mem=${msi_resources_mem},partition=${msi_queue},jobname=${msi_resources_jobname} \
--bind=${study_sharedfolder}:${study_sharedfolder} --container=${HOME}/qunex/qunex_suite-0.95.2.sif

log file output:

--> 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 ANTSDIR 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 FSL_GPU_SCRIPTS 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
e[32m e[0m
e[32mGenerated by QuNex e[0m
e[32m------------------------------------------------------------------------ e[0m
e[32mVersion: 0.95.2 e[0m
e[32mUser: moana004 e[0m
e[32mSystem: acn37 e[0m
e[32mOS: RedHat Linux #1 SMP Wed Aug 10 16:21:17 UTC 2022 e[0m
e[32m------------------------------------------------------------------------ e[0m
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e[32m        ██████\                  ║      ██\   ██\                        e[0m
e[32m       ██  __██\                 ║      ███\  ██ |                       e[0m
e[32m       ██ /  ██ |██\   ██\       ║      ████\ ██ | ██████\ ██\   ██\     e[0m
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e[32m        \___███\  \______/       ║      \__|  \__| \_______\__/  \__|    e[0m
e[32m            \___|                ║                                       e[0m
e[32m e[0m
e[32m e[0m
e[32m                       DEVELOPED & MAINTAINED BY: e[0m
e[32m e[0m
e[32m                    Anticevic Lab, Yale University e[0m
e[32m               Mind & Brain Lab, University of Ljubljana e[0m
e[32m                     Murray Lab, Yale University e[0m
e[32m e[0m
e[32m                      COPYRIGHT & LICENSE NOTICE: e[0m
e[32m e[0m
e[32mUse of this software is subject to the terms and conditions defined in e[0m
e[32m'LICENSES' which is a part of the QuNex Suite source code package: e[0m
e[32mhttps://gitlab.qunex.yale.edu/qunex/qunex/-/tree/master/LICENSES e[0m
e[32m e[0m
e[36m ---> Setting up Octave  e[0m


e[32m ........................ Running QuNex v0.95.2 ........................ e[0m


e[36m--- Full QuNex call for command: hcp_fmri_volume e[0m

e[36mgmri hcp_fmri_volume --sessionsfolder="/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions" --parsessions="52" --parelements="4" --overwrite="yes" --hcp_processing_mode="LegacyStyleData" --hcp_bold_biascorrection="LEGACY" --hcp_bold_dcmethod="NONE" --batchfile="/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/batch_K99Aim2.txt" --sessions="20017,11012" e[0m

e[36m--------------------------------------------------------- e[0m


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 0.95.2 on 2022-11-15_13.30.07.931597
#
=================================================================
gmri hcp_fmri_volume \
  --sessionsfolder="/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions" \
  --parsessions="52" \
  --parelements="4" \
  --overwrite="yes" \
  --hcp_processing_mode="LegacyStyleData" \
  --hcp_bold_biascorrection="LEGACY" \
  --hcp_bold_dcmethod="NONE" \
  --sessions="/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/batch_K99Aim2.txt" \
  --sessionids="20017,11012" \
=================================================================

Starting multiprocessing sessions in /home/moanae/shared/project_K99_ChrTMDHCP_qunex01/processing/batch_K99Aim2.txt with a pool of 52 concurrent processes

---- Running local

Adding processing of session 20017 to the pool at Tuesday, 15. November 2022 13:30:07
=======================================================================================================================================
=======================================================================================================================================
=======================================================================================================================================
=======================================================================================================================================

------------------------------------------------------------
Session id: 20017 
[started on Tuesday, 15. November 2022 13:30:08]
Running HCP fMRI Volume pipeline [LegacyStyleData] ... 
---> PreFS results present.
---> FS results present.
---> PostFS results present.
---> Gradient distortion coefficients file present.

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 1
     ... No distortion correction used 
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/20017/hcp/20017/unprocessed/BOLD_1/20017_BOLD_1.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 2
     ... No distortion correction used 
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/20017/hcp/20017/unprocessed/BOLD_2/20017_BOLD_2.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 3
     ... No distortion correction used 
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/20017/hcp/20017/unprocessed/BOLD_3/20017_BOLD_3.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

---> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 4
     ... No distortion correction used 
     ... ERROR: bold image missing, searched for ['/home/moanae/shared/project_K99_ChrTMDHCP_qunex01/sessions/20017/hcp/20017/unprocessed/BOLD_4/20017_BOLD_4.nii.gz']!
     ... ERROR: bold reference image missing!
     ... using the HCPpipelines default BOLD mask

Running 4 BOLD images in parallel
---> ERROR: images or data parameters missing, skipping this BOLD!
---> ERROR: images or data parameters missing, skipping this BOLD!
---> ERROR: images or data parameters missing, skipping this BOLD!
---> ERROR: images or data parameters missing, skipping this BOLD!

HCP fMRIVolume completed on Tuesday, 15. November 2022 13:30:08
------------------------------------------------------------


===> Final report for command hcp_fmri_volume
... 20017 ---> HCP fMRI Volume: bolds 1, 2, 3, 4 not ready
===> Not all tasks completed fully!

Estephan,

we are looking into your issue and will provide guidance about how to best handle it over the next couple of days.

Jure

Estephan,

Could you please share the latest batch file that you used when you got the above error report?

Thanks!

All the best,

Grega

Sorry for the delay. I attached the batch file used when this error occurred.

Thank you.

batch_K99Aim2.txt (347.1 KB)

@Estephan, thank you for the batch file! We have identified the issue. AP/PA information is not appended to the BOLD images file name when searching for BOLD files in the context of no dcmethod specified, which is the case in you “Legacy” data. We’ll resolve the issue in the next release. In the meantime, there are two quick fixes that will enable you to process this data. The first possible fix is to remove the PEDirection() information for the BOLD files that will not be distortion corrected in the batch file and rerun steps from setup_hcp on. The second possible fix is to remove _AP/_PA part of the BOLD file names for those BOLD files that will not be distortion corrected. In this case, you can just rerun hcp_fmri_volume comand.

I am sorry for the inconvenience. We try to flexibly support many different scenarios and some combinations of data and options may sometimes fall through the cracks of our acceptance testing. In this case it is the combination of the presence of phase encoding information but no distortion correction method used. Than you for your patience in resolving this issue.

No problems, thanks for the clarification. Will the next release include the upcoming new version of the HCP pipelines (v4.7.0)? Because I might as well wait for it then. Cheers.

Yes, we are waiting for HCP folks to release 4.7, we plan to fold it together with our latest updates (the fix for the bug you found here and some improvements to the GLM engine).

Jure