Qsiprep not applying sdc: hcp style pipeline

[gspitz]

Summary of what happened:

Dear Neurostars,
I am trying to run qsiprep, applying an hcp style pipeline with equal number of AP and PA volumes. However, it appears that sdc is not being applied correctly, or at all.
The Summary section indicates: "Susceptibility distortion correction: None"

Any suggestions? Please let me know if any further information would be helpful.

Best,

Command used (and if a helper script was used, a link to the helper script or the command generated):

qsiprep-0.21.4.sif \
/bids /output participant \
-w /output \
--participant-label 001 \
--omp-nthreads 1 \
--n_cpus 8 \
--skip-bids-validation \
--output-resolution 1.5 \
--distortion-group-merge average \
--fs-license-file /important_files/license.txt

Version:

0.21.4

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity/Apptainer

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

Please see the images below:

[Steven]

Hello @gspitz,

For future posts like this, please use the Software Support category, which organizes your post and prompts you for important information. You can see I did this for you this time (but there is some info you did not provide). What happens if you change the file names to be BIDS valid, by changing _AP_/_PA_ to be _dir-AP_/_dir-PA_? Can you also return the full command, including the singularity run preamble? When you rerun, try putting the working directory outside the BIDS folder, and please do not skip BIDS validation and return the BIDS validation report.

Best,
Steven

[gspitz]

Thank you @Steven.
Changing to BIDS valid names did the trick!