Hello, I have created cortical surfaces using Freesurfer
and then did : @SUMA_Make_Spec_FS -fspath fsaverage/surf -sid fsaverage -ld 10 -GIFTI
as well as for all the subjects I have.
Now I would like to know the mesh indices (standard mesh generated with ld=10 in SUMA) from the Desikan-Killiarny Atlas. I saw that @SUMA_Make_Spec_FS automatically generated dset files for the other atlas (Destrieux Atlas (?h.aparc.a2009s.annot)) but not for Desikan-Killiany Atlas (?h.aparc.annot). Then when I tried to modify @SUMA_Make_Spec_FS to also read ?h.aparc.annot, I encountered the problem with FSread_annot.
If I type:
FSread_annot -input lh.aparc.a2009s.annot -dset ../SUMA/lh.aparc.a2009s.annot.niml.dset
The output is below and it worked.
++ Notice FSread_annot (SUMA_FSread_annot.c:298 @14:53:59):
Guessed FS annot version of 2009
++ Notice FSread_annot (SUMA_FSread_annot.c:310 @14:53:59):
Guessed left hemisphere
++ Notice FSread_annot (SUMA_FSread_annot.c:332 @14:53:59):
Using /usr/local/freesurfer/FreeSurferColorLUT.txt
++ Notice FSread_annot (SUMA_FSread_annot.c:343 @14:53:59):
Setting -FScmaprange to [13100 13199]
But if I type:
FSread_annot -input lh.aparc.annot -dset ../SUMA/lh.aparc.annot.niml.dset
++ Notice FSread_annot (SUMA_FSread_annot.c:303 @14:55:16):
Assuming FS annot version of -1
++ Notice FSread_annot (SUMA_FSread_annot.c:310 @14:55:16):
Guessed left hemisphere
oo Warning SUMA_readFSannot (SUMA_Surface_IO.c:2397):
bad nbins (-2) or len (36).
Color table will not be created,
and annotation values will be used instead
of indices into a colormap.
You can use -FScmap option to specify
a colormap in an external file.
Fatal Signal 11 (SIGSEGV) received
SUMA_readFSannot
FSread_annot
Bottom of Debug Stack
** AFNI version = AFNI_2011_12_21_1014 Compile date = Jul 7 2015
** [[Precompiled binary linux_xorg7_64: Jul 7 2015]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Memory usage: chunks=46 bytes=3299162
** Crash log is appended to file /home/yiwen/.afni.crashlog
It seems to me that the Desikan-Killiany Atlas (?h.aparc.annot) is not recognized. I would appreciate very much if anyone could help me out.
Thank you very much in advance,
Yiwen
