Two resting state scans: before and after TMS

[dkp]

We have two runs of rsfmri in a single session:

tree inputs/sub-219/ses-itbs/func
inputs/sub-219/ses-itbs/func
├── sub-219_ses-itbs_task-rest_run-01_bold.json
├── sub-219_ses-itbs_task-rest_run-01_bold.nii.gz
├── sub-219_ses-itbs_task-rest_run-01_events.tsv
├── sub-219_ses-itbs_task-rest_run-02_bold.json
├── sub-219_ses-itbs_task-rest_run-02_bold.nii.gz
└── sub-219_ses-itbs_task-rest_run-02_events.tsv

I'd like to process them separately, so I specified and ran two separate docker commands:

docker run -ti --rm \
    -v ${PWD}/inputs:/bids_dataset:ro \
    -v ${PWD}/outputs:/output_directory \
    -v ${PWD}/working:/tmp \
    -v ${PWD}/inputs/code/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt \
    micalab/micapipe:latest \
    -bids /bids_dataset \
    -out /output_directory \
    -sub 219 -ses itbs \
    -proc_rsfmri \
    -mainScanStr task-rest_run-01_bold -mainScanRun 1

and

docker run -ti --rm \
    -v ${PWD}/inputs:/bids_dataset:ro \
    -v ${PWD}/outputs:/output_directory \
    -v ${PWD}/working:/tmp \
    -v ${PWD}/inputs/code/freesurfer_license_file.txt:/opt/freesurfer-6.0.0/license.txt \
    micalab/micapipe:latest \
    -bids /bids_dataset \
    -out /output_directory \
    -sub 219 -ses itbs \
    -proc_rsfmri \
    -mainScanStr task-rest_run-02_bold -mainScanRun 2

Only the first run claims to have completed. How can I get separate output for each run?

[dkp]

Follow up: I ran run-01 first and then renamed the func directory, then I ran run2. I guess this works.

[rcruces]

Hi, you found a great solution to this. As we also encountered a similar issue we implemented a different solution to process multiple functional acquisitions in the same derivatives output directory. The code is part of the 0.1.3 release, we are currently building the container and the readTheDocs will be updated with this new functionality. The new modality is called -proc_func and it allows to process multiple functional acquisitions (not at the same time) as well al multi echo acquisitions. I'll tell you when the container is ready

[rcruces]

The following versions including our newest version v0.2.0 can handle this issues, please take a look and try it!

https://github.com/MICA-MNI/micapipe/releases/tag/v0.2.0