External Email - Use Caution
Hi Tom,
you could try mris_convert with the -c option. E.g.:
mris_convert -c ~/data/study1/subject1/surf/rh.sulc.nii.gz ~/data/study1/subject1/surf/rh.white ~/blah.gii
The command requires an existing surface file that matches the per-vertex data as the 2nd argument (for reasons I don't know). You should be able to use the fsaverage surface files that come with FreeSurfer for your use case ($FREESURFER_HOME/subjects/fsaverage/lh.white and rh.white).
If one does not have a surface file, one could do the conversion in Python using nibabel or in R using freesurferformats (an example conversion script for R is at [1]).
Best,
Tim
[1] https://secure-web.cisco.com/1RtVk5D3a5pa2F0Y5i6qeQjYlGh7SZtHbvUZm25RHiWPDyw...
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
On 09/23/2021 9:25 PM Tom Vanasse thomas.j.vanasse@gmail.com wrote:
External Email - Use Caution
Hello,
I have a question regarding the conversion of functional fsaverage lh and rh files (created from the Yeo lab MNI to fsaverage projection software: https://secure-web.cisco.com/1nRJbdVDTJHwxxGMU9q1fmvcPt_Df0AIfr6uIaGGD96UkPw...) to a *gifti file*.
For example, 'rh.sub-13_ses-fmri1_task-awak_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold_cleaned.allSub_RF_ANTs_MNI152_orig_to_fsaverage.nii.gz'
This is necessary because my end goal is to then transform that gifti file, using wb_command, to the fs_LR HCP surface.
Any help would be greatly appreciated,
Tom _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Nw9WsEP0xGhkuCnuvFpxtwNeaEDvp83t2Lv87DuPCMMI7W...