I’m moving a conversation here from the slack forum. The bolded part below is the most current question.
POST 1
I’m working through the abide1_processing_steps.md file. In preparation, I zipped the BIDS compatible ABIDE1 data and copied it to the $my_study_folder/sessions/inbox/BIDS location. I’m hitting a bit of a snag at following part
# --- prepare data
/gpfs/project/fas/n3/software/qunexdev/bin/qunex_container setup_hcp \
--sessionsfolder="$my_study_folder/sessions" \
--sessions="$batch_file" \
--container="$qunex_container" \
--scheduler="SLURM,time=0-01:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=day"
When I run the command, I get the following message, indicating that no jobs are being run.
--> QuNex will run the command over 0 sessions. It will utilize:
Scheduled jobs: 0
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.
When I look at the batch.txt file that $batch_file points to, it appears to just be commented descriptions.
POST 2
After going through the error logs, I think the problem is the specification of “sessions” with the create_session_info
command.
/gpfs/project/fas/n3/software/qunexdev/bin/qunex_container create_session_info \
--sessionsfolder="$my_study_folder/sessions" \
--sessions="
HCPA001
" \
--container="$qunex_container" \
--overwrite=no \
--scheduler="SLURM,time=0-01:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=day"
The "HCPA001"
is what’s created in the tutorial video during the import of the DICOMs.
It was then suggested I take a look at the following wiki page: https://bitbucket.org/oriadev/qunex/wiki/UsageDocs/OnboardingBIDSData
POST 3
That page focuses on the import_bids
command. Usage is described, but I don’t have a clear idea what the result should be. The abide1_processing_steps.md file includes the following step
/gpfs/project/fas/n3/software/qunexdev/bin/qunex_container import_bids \
--sessionsfolder="$my_study_folder/sessions" \
--container="$qunex_container" \
--check=any \
--scheduler="SLURM,time=0-01:00:00,ntasks=1,cpus-per-task=1,mem-per-cpu=8000,partition=day"
It runs without issue. However, afterwards, the “/info/bids/” folder is empty. I’m not quite sure what “mapping” takes place, but I’m guessing data from the zip should be unpacked into that location, no?