Hi Zach

I think if you cut and flatten the cortical part of the surfaces, convert tha .annot files to separate label files, you can then use label2flat on each label to generate a flattened patch that is just taht label. I haven't used it in years (decades?), but I think it should work

On Tue, 8 Aug 2017, Zach Humphrey wrote:

Hello All, 
I have been attempting to convert Label files generated using
mri_annotation2label into surface files for use in external programs. In
order to do this I first need to convert the label files into freesurfer
binary. I have attempted to use the mri_label2vol function to generate an
mgz file which could then be converted into freesurfer binary but this has
resulted in mgz files which depict a solid cube rather than any brain
structure. Any ideas as to why this could be? 

I would also prefer to avoid ever converting the label files to a volume as
converting the volume file to a surface file results in a lower quality than
if the file has been maintained as a surface file throughout. Is there any
way to use the Desikan Atlas to "divide" say the lh.pial surface file and
generate a number of .pial files each consisting of one of the regions
described by the Desikan Atlas? 

Zachary Humphrey

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