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

History of AFNI updates  

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December 22, 2004 01:22PM
Knowing little about FreeSurfer, I'll jump in recklessly nonetheless. AFNI's +x coordinate is Left and +y is Posterior, but FreeSurfer's is probably +x=Right and +y=Anterior. So x and y need to be negated to transform from one to the other, probably.


It would be easy to try this out for Option 2. I don't recall,
are there "# comment lines" at the top of rh.IT.1D, or is it
all just numbers? If it is just numbers, you can try:

awk '{printf "%f %f %f\n", -$2, -$3, $4}' rh.IT.1D > rh.IT.RAI.1D

This will just extract those 3 columns, negating the first
two (note again that awk uses 1-based indexing for the
columns). Then you can just use rh.IT.RAI.1D in your
3dSurf2Vol command, without using the option,
'-sxyz_orient_as_gpar', and without any column indices.

Hopefully one of these two options will work out for you.

- rick

Subject Author Posted

3dSurf2Vol - labels to AFNI

Jennine December 22, 2004 10:13AM

Re: 3dSurf2Vol - labels to AFNI

Robert Cox December 22, 2004 01:00PM

Re: 3dSurf2Vol - labels to AFNI

rick reynolds December 22, 2004 01:22PM

Re: 3dSurf2Vol - labels to AFNI

Jennine December 22, 2004 01:25PM

Re: 3dSurf2Vol - labels to AFNI

rick reynolds December 22, 2004 01:09PM

Re: 3dSurf2Vol - labels to AFNI

Jennine December 22, 2004 01:34PM