fMRI pipeline doesn't work - csf_mask

LTS5 / cmp_nipype

This repository is meant to host a beta version for the future release of the ConnectomeMapper.

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fMRI pipeline doesn't work - csf_mask #44

Open ncullen93 opened 8 years ago

ncullen93 commented 8 years ago

I still get an error saying "No such file ../Freesurfer/mri/csf_mask.nii.gz" when trying to run the fMRI pipeline. I have the latest commit... Is there a fix to this?

ncullen93 commented 8 years ago

Note this is only when Lausanne parcellation is specified. With NativeFreesurfer, the pipeline proceeds further.

davidrs06 commented 8 years ago

Hello ! Thanks for reporting it, we were not saving the CSF mask when the Lausanne parcellation was computed. The latest version of cmp_nipype should handle it properly now. Could you give it a try with your data and tell us if it works ?