Hi Nick, I was recently trying to redo something you had helped me out with back in April (see below), but I now get this error: ERROR: Option --seg unknown
The wiki page still says this option exists, but I'm guessing is outdated https://surfer.nmr.mgh.harvard.edu/fswiki/mri_annotation2label#Detailsfor.27seg.27outputfilelabelnumbers Was this option deprecated at some point? Could you send me a version where this works, or is there another way, I can get what I'm after: >> to somehow get the contents of >> ?h.aparc.annot into ascii form. I know mris_annotation2label will kind >> of do this, but it creates one file for every label. What I'm loooking >> for is a single file with n rows corresponding to the n vertices in >> ?h.pial, and then next to each one, a number representing what label >> it belongs to (or what value to look up in the LUT). thanks, mishkin On Wed, Apr 8, 2009 at 4:19 PM, Nick Schmansky <ni...@nmr.mgh.harvard.edu> wrote: > Mishkin, > > This will create what you want: > > cd subj/label > mri_annotation2label --subject subj \ > --hemi lh \ > --annotation aparc \ > --seg lh.aparc.mgh > > replacing subj and lh with appropriate. > > then type: > > mris_convert -c ./lh.aparc.mgh \ > ../surf/lh.white \ > lh.aparc.asc > > and the output file (lh.aparc.asc) will have lines like this: > > 71586 -39.60123 -13.37572 -34.24242 1007.00000 > > which are: > > vno X Y Z labelno > > where labelno is found in $FREESURFER_HOME/FreeSurferColorLUT.txt, for > instance 1007 is ctx-lh-fusiform > > Nick > > > > On Tue, 2009-04-07 at 17:00 -0400, Mishkin Derakhshan wrote: >> Thanks. After reading up on the wiki it seems that a more general >> solution I'm loking for would be to somehow get the contents of >> ?h.aparc.annot into ascii form. I know mris_annotation2label will kind >> of do this, but it creates one file for every label. What I'm loooking >> for is a single file with n rows corresponding to the n vertices in >> ?h.pial, and then next to each one, a number representing what label >> it belongs to (or what value to look up in the LUT). >> can this be done somehow, or at the very least can I get the contents >> of ?h.*.annot into ascii format so I can manipulate things. >> >> thanks, >> mishkin >> >> >> On Tue, Apr 7, 2009 at 1:05 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> > Hi Mishkin, >> > >> > yes, the ?h.cortex.label should be created for every subject that labels >> > the >> > cortical regions of the surface. >> > >> > cheers, >> > Bruce >> > On Tue, 7 Apr 2009, Mishkin Derakhshan wrote: >> > >> >> Hello list, >> >> I would like to create a mask on fsaverage/surf/?h.pial that masks out >> >> the areas where the surface does not follow the cortex, but is just >> >> cutting across the mid line or across the brain stem. I know >> >> Freesurfer does this to maintain the surface toplogy, and I think it >> >> only does this in these two areas. >> >> Does a simple txt file with n vertices and a 0 or 1 value at each >> >> vertex exist somewhere? Has anyone on the list bothered to label this >> >> area manually and would be willing to share? >> >> thanks, >> >> mishkin >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> >> > >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
