AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Yiwen
July 16, 2015 09:23AM
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
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Subject Author Posted

Problem porting Desikan-Killiany Atlas (?h.aparc.annot) to standard mesh in SUMA

Yiwen July 16, 2015 09:23AM

Re: Problem porting Desikan-Killiany Atlas (?h.aparc.annot) to standard mesh in SUMA

mstrotta August 08, 2018 09:51PM