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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liang
March 31, 2015 01:49PM
Hi AFNI folks

I would like to transform a surface niml dset (called tmp.1d.dset) in ico space to fsaverage space (i.e, mni305) and have a trouble in running it.

These steps was what I tried:

1) run @SUMA_Make_Spec_FS in the folder $FREESURFER_HOME/subjects/fsaverage6, and create a SUMA folder

2) enter SUM folder and copy the dset data (i.e.. tmp.1d.dset for a right hemisphere) to this folder. Typing this command

SurfToSurf -i_fs ../surf/rh.smoothwm -i_fs std.141.rh.smoothwm.asc -prefix rh.tmp.gii -closest_possible 2 -dset tmp.1d.dset

rename rh.tmp.gii.dset (not sure why this file was created) to rh.tmp (without any extension)

3) display the transformed atlas in freesurfer, but got the following errors:

$ tksurfer fsaverage6 rh tmp
subject is fsaverage6
hemi is rh
surface is tmp
surfer: current subjects dir: /Applications/freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Users/liangwang
checking for nofix files in 'tmp'
Reading image info (/Applications/freesurfer/subjects/fsaverage6)
Reading /Applications/freesurfer/subjects/fsaverage6/mri/orig.mgz
surfer: Reading header info from /Applications/freesurfer/subjects/fsaverage6/mri/orig.mgz
tksurfer.bin(30940) malloc: *** mmap(size=1090011136) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
MRISalloc(14342208, 76): could not allocate faces
Cannot allocate memory
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Subject Author Posted

transform niml dset to FS

liang March 31, 2015 01:49PM

Re: transform niml dset to FS

rick reynolds March 31, 2015 09:49PM

Re: transform niml dset to FS

liang April 01, 2015 07:21AM