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 <fis...@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 >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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