Hello, I’m trying to run the HCP pipeline using qunex_suite-0.97.1.sif on my institution’s HPC (running centOS 8) and am running into an issue with the setup_hcp step:
Running setup_hcp
================
===> Setting up HCP folder structure for 1133
---> Creating base folder /work/long/qunex//sessions/1133/hcp/1133/unprocessed
... skipping 4 [unknown sequence label, please check]
... skipping 3 [unknown sequence label, please check]
---> creating subfolder T2w
---> linking 2.nii.gz to 1133_T2w_SPC1.nii.gz
---> creating subfolder T1w
---> linking 1.nii.gz to 1133_T1w_MPR1.nii.gz
Here’s the command I’m running:
container=/path/to/qunex_suite-0.97.1.sif
qunex_container setup_hcp \
--container="$container" \
--bind=$qunexdir/ \
--sourcefolder="$qunexdir/sessions/1133"
and here are the contents of the bids dir:
$ ls -l $qunexdir/sessions/1133/bids/sourcedata/sub-1133/*
-rw-r--r--. 1 ark19 root 514 Jun 15 12:16 /work/long/qunex/sessions/1133/bids/sourcedata/sub-1133/bids2nii.log
/work/long/qunex/sessions/1133/bids/sourcedata/sub-1133/anat:
total 21766
-rwxr-xr-x. 1 ark19 root 2465 Jun 15 12:16 sub-1133_acq-FLAIR_T2w.json
-rwxr-xr-x. 1 ark19 root 5906637 Jun 15 12:16 sub-1133_acq-FLAIR_T2w.nii.gz
-rwxr-xr-x. 1 ark19 root 2409 Jun 15 12:16 sub-1133_T1w.json
-rwxr-xr-x. 1 ark19 root 12311478 Jun 15 12:16 sub-1133_T1w.nii.gz
/work/long/qunex/sessions/1133/bids/sourcedata/sub-1133/fmap:
total 3614
-rwxr-xr-x. 1 ark19 root 3158 Jun 15 12:16 sub-1133_magnitude.json
-rwxr-xr-x. 1 ark19 root 1865576 Jun 15 12:16 sub-1133_magnitude.nii.gz
-rwxr-xr-x. 1 ark19 root 3227 Jun 15 12:16 sub-1133_phasediff.json
-rwxr-xr-x. 1 ark19 root 1132556 Jun 15 12:16 sub-1133_phasediff.nii.gz
and the hcp_mapping.txt file:
# -- This is the mapping file for a QuNex study
# -- Structural sequences
T1w => T1w
T2w acq-FLAIR => T2w
magnitude => FM-Magnitude
phasediff => FM-Phase
Previously, i had 2 magnitude images which were named “magnitude1” and “magnitude2” with corresponding lines in the mapping file in this step worked just fine, but then i ran into problems in the preFreesurfer step and realized that i needed to combine the two into a single 4D image (as I had done previously running the pipeline using the HCP bids container). i just made small tweaks to the file names / files to accommodate, so not sure why it stopped working then.
I also tried manually setting up the sessions/…/hcp/…/unprocessed dir following the structure from the previous successful runs with the 2 magnitude images, but then ran into this error when running a test of the preFreesurfer step, so i must have missed something:
------------------------------------------------------------
Session id: 1133
[started on Thursday, 15. June 2023 12:29:29]
Test running HCP PreFreeSurfer Pipeline [HCPStyleData] ...
---> T1w image file present.
---> T2w image file present.
---> Magnitude Field Map 1 file present.
---> Phase Field Map 1 file present.
ERROR: Unknown error occured:
...................................
Traceback (most recent call last):
File "/opt/qunex/python/qx_utilities/hcp/process_hcp.py", line 764, in hcp_pre_freesurfer
fmmag = hcp['fieldmap'][int(fmnum)]['magnitude']
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'
what do i need to be checking to make sure i get the sequence label correct?
Thanks!