Dear Shane,
to be honest I don't understand all what you are trying to do. The output of mris_convert should be not a nifti-file and generally Freeview should read gifti files as well. Anyway, if you have difficulties with converting gifti files to Freesurfer format you could also try CAT_SurfConvert which is located in cat12/CAT.XXX, where XXX stands for your system (glnx86/maci64/w32).
Furthermore, you could also try the surfcalc function in CAT12 to create an average across subjects and visualize that with CAT12.
Best,
Christian
On Sat, 7 Aug 2021 17:04:44 +0000, Shane Schofield <[log in to unmask]> wrote:
>Hi Christian,
>I have some DTI volumes in the subject surface space (using CAT12 GUI). I would like to generate group averaged maps (using tools such as mri_concat in Freesurfer etc) and view them in Freeview or Surfice. Could I get your thoughts on my pipeline?
>First, I resampled them to Freesurfer space, separately for each hemisphere to get the following:
>s12.rh.intensity_DTI_FA_NN.resampled.subject-ses-1_T1w.gii
>
>s12 = smoothingrh = right hemishpereintensity_DTI_FA = FA mapNN = Nearest Neighbour interpolation using ANTS
>When I tried using mris_convert, I got the error message:
>mris_convert s12.rh.intensity_DTI_FA_NN.resampled.subject-ses-1_T1w.gii s12.rh.intensity_DTI_FA_NN.resampled.subject-ses-1_T1w.reor.niimrisReadGIFTIfile: malformed data array [2] in file s12.rh.intensity_DTI_FA_NN.resampled.subject-ses-1_T1w.reor.gii: num_vertices=1 num_cols=163842 expected nvertices=163842, num_cols=1error: mris_convert: could not read surface file s12.rh.intensity_DTI_FA_NN.resampled.subject-ses-1_T1w.reor.gii
>Secondly, will I be able to use fsaverage surface as a template to view these resampled maps?
>Thank you for your help as always!
>Shane
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