Can whereami be run on ORIG space?

AFNI Message Board
1

Hello!

I am wondering if afni’s whereami command can be run on a dataset that is still in its ORIG space and hasn’t been aligned with a Talairach, MNI, or other template. It seems to be disabled on the GUI for ORIG space datasets (although you can still run the command line utility for the dataset, perhaps the returned atlas information isn’t necessary meaningful or correct).

My first question is can I use whereami to obtain a label from a standard atlas (like Talairach daemon) if my dataset is in ORIG space?

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?

On a side note, I am considering getting all of my datasets in TT space using @auto_tlrc as a preprocessing step, then feeding these datasets into freesurfer so that I can use both the TT daemon and the freesurfer segmentations/parcellations with whereami. :slight_smile:

Thanks,
Mike

2

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>