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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Graham Wideman
December 11, 2003 04:35AM
Folks:

Regarding SUMA's import of FS data using @SUMA_Make_Spec_FS.

I'm 99% certain there's a documentation error in the main SUMA instructions page at:

afni.nimh.nih.gov/ssc/ziad/SUMA/SUMA_do1.htm

Section I.D.1.b.i "Creating the specs file for FreeSurfer" says:
[...] "we assume that the .COR images are in LSP order".

This is probably incorrect. FS .COR image data is stored in (R-L, S-I, P-A) order, which I think is RSP in AFNI lingo.

For a visualization:
wideman-one.com/gw/brain/fs/coords/fscoords.htm

The actual script says:

if ( $neuro_ori == 1 ) then

to3d -prefix $afni_prefix -xSLAB 127.5L-R -ySLAB 127.5S-I -zSLAB 127.5P-A $cor_files

else

to3d -prefix $afni_prefix -xSLAB 127.5R-L -ySLAB 127.5S-I -zSLAB 127.5P-A $cor_files

endif

... which appears to have it correct, and contradicts the description in the instructions page.

Graham

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Subject Author Posted

SUMA R-L issue with FreeSurfer

Graham Wideman December 11, 2003 04:35AM

Re: SUMA R-L issue with FreeSurfer

Ziad Saad December 11, 2003 09:51AM

Re: SUMA R-L issue with FreeSurfer

Graham Wideman December 11, 2003 05:51PM

Re: SUMA R-L issue with FreeSurfer

Ziad Saad December 12, 2003 09:13AM