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connectomicslab / connectomemapper3

Connectome Mapper 3 is a BIDS App that implements full anatomical, diffusion, resting/state functional MRI, and recently EEG processing pipelines, from raw T1 / DWI / BOLD , and preprocessed EEG data to multi-resolution brain parcellation with corresponding connection matrices.
https://connectome-mapper-3.readthedocs.io
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Custom Atlases #38

Closed aswinchari closed 4 years ago

aswinchari commented 4 years ago

Hello,

Does anyone have experience with custom atlases on ConnectomeMapper3? Keen to try and use the Brainnetome atlas and was wondering which files to use as the nifty and graphml files?

Aswin

aswinchari commented 4 years ago

Just to update - I tried using the attached files for a single subject and the anatomical pipeline ran but I cant find the parcellation anywhere, only Lausanne. I used the nii file as the custom nifty file and the json as the graphml file. Am I doing something wrong?

Brainnetome.zip

sebastientourbier commented 4 years ago

Custom atlases was a feature available in CMP2 but while adopting BIDS in CMP3, we have to review a lot the way CMP is working and this feature is not working anymore for the moment. Following again the BIDS/BIDSApps philosophy, this would consist of specifying a BIDS derivatives directory obtained for instance by smriprep / dmriprep or fmriprep. I will close this "support" issue. The "custom" feature is now managed at the following "new feature" issue: #41 .