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App-forward
- ZAHRAN Saeed (Unlicensed)
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
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
on brainlife parent of output is usually the object id
so, when brainlife givess a config like this
{
"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"])
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