ASLPrep fails to generate some freesurfer outputs

Software Support
1

Summary of what happened:

Hi!!

Just find out that in aslprep it is stated that if freesurfer is ran you will get the following outputs:

sub-<label>/[ses-<label>/]
   perf/
      <source_entities>_space-T1w_desc-aparcaseg_dseg.nii.gz
      <source_entities>_space-T1w_desc-aseg_dseg.nii.gz
      <source_entities>_hemi-[LR]_space-<label>_asl.func.gii

In my case I couldn’t find none of this three, though they are generated if I ran smriprep (v.0.16.1) and I found them in the anat folder. Besides they are listed as aslprep outputs (Outputs of ASLPrep — aslprep version documentation)

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

aslprep \
    neurodesktop-storage/Agueda/BIDS \
    neurodesktop-storage/Agueda/BIDS/derivatives/aslprep \
    participant \
    --participant-label sub-388 \
    --force-bbr \
    --basil \
    --ignore t2w \
    --fs-subjects-dir /Users/agueda/neurodesktop-storage/Agueda/BIDS/derivatives/freesurfer/sourcedat/freesurfer_pre/sourcedata \
    --bids-filter-file neurodesktop-storage/Agueda/BIDS/BIDS_filter_file.json \
    --fs-license-file neurodesktop-storage/Agueda/BIDS/license.txt \
    -vv \
    -w neurodesktop-storage/Agueda/BIDS

Version:

0.7.2

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

Docker

2

Hi @lucia_sanchez_aranda,

In the future please use the software support post category, which provides a template for you to organize your post. You can see I added it in for you. Please edit your post to add the requested information so it is easier to help you.

Best,
Steven

3

Do you have the log? I am curious if the FreeSurfer outputs were recognized given some of your earlier problems with neurodesk.

4

I have switch to run into docker and not in neurodesk, as it still does not work. Other freesurfer outputs are successfully generated and in the html report it shows that there was a pre existing directory with freesurfer outputs, so I do not think this could be a problem. No error reported in the end of the process

5

By any chance are the space-T1w_desc-*_dseg.nii.gz in the anat folder?

I’ll try to take a look at what’s happening in the next couple of days. Sorry for the delay.