In order to upload the freesurfer output to brainlife:
bl data upload --output /network/lustre/iss01/home/saeed.zahran/mne_data/MNE-sample-data/subjects/sample --project 625d36f9cc8ab2b339ea4687 --datatype neuro/freesurfer --subject FRS --session 1
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The functions in mne that deal with forward model takes the inputs as:
subject=subject, subjects_dir=subjects_dir,
subjects_dir is the subjects directory and subject is subject name
so the subjects_dir should be the parent directory where freesurfer output is staged and subject should be set to "output".
brainlife stores all freesurfer directory under "output
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on brainlife parent of output is usually the object id
so, when brainlife givess a config like this
| Code Block |
|---|
{
"parcellation": "aparc",
"freesurfer": "../62bcba44fd504b9f17ad2be0/61164b436135cd2478c53c88/output",
} |
we can take path specified by freesurfer and use the basename(output) as the subject name, and dirname(../62bcba44fd504b9f17ad2be0/61164b436135cd2478c53c88) as the subject_dir
This can be solved using the below code:
subject=os.path.basename(config["freesurfer"])
subjects_dir=os.path.dirname(config["freesurfer"])
Links to the App:
https://github.com/zahransa/app-forward
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