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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MCI
April 12, 2013 04:35PM
Hi,

I want to define a 2D square region on a SUMA flatmap and obtain the indices / values of the corresponding AFNI voxels that map to that region.

A couple of years ago, I was using Surf2VolCoord to get this mapping between AFNI volume coordinates and flatmap surface coordinates in two steps:


Surf2VolCoord -i_fs /data/surf/$1/SUMA/lh.smoothwm.asc -grid_parent Processed/pb02.SUBJ.rall.scale_aligned_cropped_detrend+orig -sv "$1"_SurfVol_stripped_Alnd_Exp+orig > Processed/lhsurfNodeMapping.txt

Surf2VolCoord -i_fs /data/surf/$1/SUMA/lh.full.flat.patch.3d.asc -grid_parent Processed/pb02.SUBJ.rall.scale_aligned_cropped_detrend+orig > Processed/lhflatModel.txt

cut -d' ' -f5,6 Processed/lhflatModel.txt > Processed/lhflatVerts.txt
cut -d' ' -f15,16,17 Processed/lhsurfNodeMapping.txt > Processed/lhvoxelPositions.txt
paste Processed/lhvoxelPositions.txt Processed/lhflatVerts.txt > lhVoxel2Flat.txt


However, these commands written verbatim no longer work; when running either of the Surf2VolCoords commands I get the following error:


-- Error Surf2VolCoord_demo (SUMA_Surf2VolCoord_demo.c:447):
Have -1 dims for xyz, and 3 for surf.


Do you have any suggestions on what could have changed about Surf2VolCoords in the meantime or perhaps another way to get the mapping?

Thanks,
MCI
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Subject Author Posted

Surf2VolCoord update problem?

MCI April 12, 2013 04:35PM

Re: Surf2VolCoord update problem?

ziad April 12, 2013 06:40PM

Re: Surf2VolCoord update problem?

MCI April 13, 2013 03:43PM