[RESOLVED] Hcp_fmri_volume fails to detect automated naming scheme for BOLD image processing

Issues
1

I’m probably missing something obvious here in the batch settings, but I’m running into an issue during hcp_fmri_volume where the correct bold naming scheme is not being detected. This is happening with the containerized qunex_suite-0.94.8.sif. The error is

" —> Preprocessing settings (unwarpdir, refimage, moveref, seimage) for BOLD 4
… ERROR: Unknown distortion correction method: ! Please check your settings!
… ERROR: bold image missing, searched for [‘/gpfs/gibbs/pi/n3/Studies/ExTx2/sessions/pb12385/hcp/pb12385/unprocessed/BOLD_4/pb12385_BOLD_4.nii.gz’]!"

The bolds are actually named with _AP/_PA, e.g.,

/gpfs/gibbs/pi/n3/Studies/ExTx2/sessions/pb12385/hcp/pb12385/unprocessed/BOLD_4_PA
/gpfs/gibbs/pi/n3/Studies/ExTx2/sessions/pb12385/hcp/pb12385/unprocessed/BOLD_4_AP

Here is the call/logs

qunex_container=/gpfs/gibbs/pi/n3/software/Singularity/qunex_suite-0.94.8.sif

qunex_container hcp_fmri_volume \
    --sessionsfolder="$my_study_folder/sessions" \
    --batchfile="/gpfs/gibbs/pi/n3/Studies/ExTx2/processing/batch.txt" \
    --container="$qunex_container" \
    --scheduler="SLURM,time=1-00:00:00,ntasks=1,cpus-per-task=2,mem-per-cpu=10000,partition=pi_anticevic_z,account=anticevic_z"

Here is an error log: /gpfs/gibbs/pi/n3/Studies/ExTx2/processing/logs/runlogs/Log-hcp_fmri_volume-2022-09-01_07.53.17.319395.log

This always worked smoothly in version 0.93.2, e.g., logfile /gpfs/gibbs/pi/n3/Studies/ExTx2/processing/logs/runlogs/Log-hcp_fmri_volume-2022-04-03_19.37.19.317096.log

Thanks in advance for any insight.

2

Hi Rachael,

The batch file /gpfs/gibbs/pi/n3/Studies/ExTx2/processing/batch.txt doesn’t appear to have the correct batch parameters header. We recently renamed sessions/specs/batch.txt as sessions/specs/parameter.txt, so that it’s less confusing.

You can either replace the content of /gpfs/gibbs/pi/n3/Studies/ExTx2/sessions/specs/parameters.txt with /gpfs/gibbs/pi/n3/Studies/ExTx2/sessions/specs/batch.txt and rerun create_batch, or explicitly set the --paramfile parameter as the current batch parameters file when running create_batch.

Lining

3

Hello Lining, thanks for your reply and suggestions. I did as you suggested, but I am still getting the same error, e.g., in this output log:

/gpfs/gibbs/pi/n3/Studies/ExTx2/processing/logs/batchlogs/qunex_container_2022-09-07_09.58.29.194868.txt

I ran:

qunex create_batch \
    --sessionsfolder="$my_study_folder/sessions" \
		--sessions="pb12372,pb12385,pb12418,pb12429,pb12640,pb12655,pb12660,pb12675" \
--paramfile="/gpfs/gibbs/pi/n3/Studies/ExTx2/sessions/specs/parameters.txt"

and then:

qunex_container hcp_fmri_volume \
    --sessionsfolder="$my_study_folder/sessions" \
    --batchfile="/gpfs/gibbs/pi/n3/Studies/ExTx2/processing/batch.txt" \
    --container="$qunex_container" \
    --scheduler="SLURM,time=1-00:00:00,ntasks=1,cpus-per-task=2,mem-per-cpu=10000,partition=pi_anticevic_z,account=anticevic_z"

Any suggestions? Do I need to rerun my entire dataset through setup_hcp and the freesurfer steps for this to work?

4

Sorry if I wasn’t clear! If you want to use the original batch parameter file you need to set the paramfile parameter to that file like this. You also need to set overwrite to yes.

qunex create_batch \
    --sessionsfolder="$my_study_folder/sessions" \
    --sessions="pb12372,pb12385,pb12418,pb12429,pb12640,pb12655,pb12660,pb12675" \
    --paramfile="/gpfs/gibbs/pi/n3/Studies/ExTx2/sessions/specs/batch.txt" \
    --overwrite="yes"
5

Ahh, that did the trick. I see what you meant now–thank you for clarifying!