Outputs of Multi-Scale Brain Parcellator¶
Note
Multi-Scale Brain Parcellator outputs are currently being updated to conform to the BIDS Common Derivatives specification (see BIDS Common Derivatives Extension).
Multi-Scale Brain Parcellator Derivatives¶
Processed, or derivative, data are written to <bids_dataset/derivatives>/cmp/sub-<subject_label>/
. In this folder, a configuration file generated and used for processing each participant is saved as sub-<subject_label>_anatomical_config.ini
. It summarizes pipeline workflow options and parameters used for processing.
Anatomical derivatives in the original T1w
space are placed in each subject’s anat
subfolder including:
anat/sub-<subject_label>_desc-head_T1w.nii.gz
anat/sub-<subject_label>_desc-brain_T1w.nii.gz
anat/sub-<subject_label>_desc-brain_mask.nii.gz
anat/sub-<subject_label>_label-WM_dseg.nii.gz
anat/sub-<subject_label>_label-GM_dseg.nii.gz
anat/sub-<subject_label>_label-CSF_dseg.nii.gz
The five different brain parcellation are saved as:
anat/sub-<subject_label>_label-L2018_desc-<scale_label>_atlas.nii.gz
where <scale_label>
: scale1
, scale2
, scale3
, scale4
, scale5
corresponds to the parcellation scale.
Additionally, the description of parcel labels and the updated FreeSurfer color lookup table are saved as:
anat/sub-<subject_label>_label-L2018_desc-<scale_label>_atlas.graphml
anat/sub-<subject_label>_label-L2018_desc-<scale_label>_atlas_FreeSurferColorLUT.txt
Finally, parcel volumetry results for each scale are saved in a TSV file as:
anat/sub-<subject_label>_label-L2018_desc-<scale_label>_stats.tsv
FreeSurfer Derivatives¶
A FreeSurfer subjects directory is created in <bids_dataset/derivatives>/freesurfer
.
freesurfer/
fsaverage/
mri/
surf/
...
sub-<subject_label>/
mri/
surf/
...
...
The fsaverage
subject distributed with the running version of
FreeSurfer is copied into this directory.