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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mstrotta
October 15, 2017 08:24PM
> My second question is: suppose I have run
> Freesurfer and @SUMA_make_spec_FS and thus have
> aseg.nii and aparc*+aseg*.nii datasets. Since I
> gave Freesurfer surfaces in ORIG space, I should
> be able to lookup the label for any xyz coordinate
> in the subject's native space. Can I use
> whereami to obtain a label from a subject-specific
> FS atlas?
>

Looks like the answer is yes. The caveat is that the whereami command doesn't always work on the first try with ORIG datasets. Specifically, ORIG doesn't always get registered as a template space during the @SUMA_make_spec_FS pipeline. I fixed this by adding the following template_space xml block to my SessionAtlases.niml or ~/abain/AFNI_atlas_spaces.niml file (note that by editing an abin/ file, this change will probably not outlive an afni update_binaries call).

<TEMPLATE_SPACE
space_name="ORIG"
generic_space="ORIG"
comment="Native space of subject"
></TEMPLATE_SPACE>



Edited 1 time(s). Last edit at 10/16/2017 10:52AM by mstrotta.
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Subject Author Posted

Can whereami be run on ORIG space?

mstrotta October 10, 2017 10:25AM

Re: Can whereami be run on ORIG space?

mstrotta October 15, 2017 08:24PM