proc_func does not proceed

[KobaCemal]

Dear developers,

I am trying to run micapipe on my datasets. I manage to get through -proc_structural, -proc_surf, -post_structural, and -GD. However, I face an error for both of my datasets at -proc_func step. The error is below:

My code is here:

for sub in 001  
do
sudo docker run -ti --rm \
    -v ${bids}:/bids \
    -v ${out}:/out \
    -v ${fs_lic}:/opt/licence.txt \
    micalab/micapipe:v0.2.3 \
        -bids /bids -out /out -fs_licence /opt/licence.txt -threads 10 \
        -sub $sub \
         -proc_func -mainScanStr rest_bold
done

The datasets are in BIDS format. At least they pass the validator. And they both have the RepetitionTime info in their json files. I think the structural part would not work if there was a problem with the format.

My guess is that the problem comes from the line 85 of the proc_func (can be seen at the top of the screenshot). I would work on it but I cannot figure out how to edit a file in a docker image.

This is the folder structure of one if the datasets: ├── sub-001 │   ├── anat │   │   ├── sub-001_T1w.json │   │   └── sub-001_T1w.nii.gz │   └── func │   ├── sub-001_task-rest_bold.json │   └── sub-001_task-rest_bold.nii.gz ├── sub-002 │   ├── anat │   │   ├── sub-002_T1w.json │   │   └── sub-002_T1w.nii.gz │   └── func │   ├── sub-002_task-rest_bold.json │   └── sub-002_task-rest_bold.nii.gz ├── sub-003 │   ├── anat │   │   ├── sub-003_T1w.json │   │   └── sub-003_T1w.nii.gz │   └── func │   ├── sub-003_task-rest_bold.json │   └── sub-003_task-rest_bold.nii.gz

Since it maybe related, I will also add this recent unusual error when I try to run post_structural as well:

---

[ ERROR ]..... Subject sccb01 doesn't have a mri/ribbon.mgz: re-run -proc_surf /out/fastsurfer/sub-sccb01/mri/ribbon.mgz

---

Basically, it cannot generate the ribbon for some subjects and I need to rerun the proc_structural. Speaking of which, if you can tell how to run micapipe_cleanup on docker, that would be great because I could not follow it on the documentation.

Thank you for your help.

Best, Cemal

[KobaCemal]

Hello,

I solved the problem. The issue was wrong specification of -mainScanStr string. I fixed it and now it works. Thanks!