Hello Dr. Fischl,

Thanks for the feedback. Can the flattened patches be "re-inflated" into surface files again after being flattened? 

I am also continuing to run into the issue with the label2vol function where I end up with a volume that is completely filled. The steps I have been following to reach this point are 

1: Run mri_annotation2label --subject subjectname --hemi lh --outdir out

2: mri_label2vol --label $labelgeneratedfromstep1 --temp rawavg.mgz --subject subjectname --hemi lh --o outputdirectory --fillthresh .3 --reg register.dat --proj frac 0 1 .1

Honestly I am not sure what the --proj field actually means and so I have been just using the 0 1 .1 that I found in examples of mri_label2vol. Could this be the problem? 

Thanks,

Zachary Humphrey

On Tue, Aug 8, 2017 at 3:51 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

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

cheers
Bruce

 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? 

Thanks,
Zachary Humphrey

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