You should save it out as nifti (see MRIwrite.m and MRIread.m). I would suggest using MRIread.m to read in your file in order to create the proper header information, then replace the pixel data with your analyzed data, then use MRIwrite.m to save it out. Then use bbregister to register this volume to the anatomical, then use mri_vol2surf to sample it to the surface (either native anatomical or to some other subject).
doug
Jason Connolly wrote:
Dear freesurfer experts:
I have been using matlab to analyze a retinotopic dataset.
However, the 3D volumes are not in standardized space (and I wish to display multiple maps from different subjects on one surface).
Although the initial segmentations were done in freesurfer, my question is:
Is it possible to take matlab arrays that contain 3D space anatomical coordinates and phase information (on a voxel by voxel basis) and display these on a standardized inflated freesurfer-generated surface?
If so, is the pipeline documented?
Many thanks,
Jason.
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