a bunch of whereami and atlasing questions, input = coordinates

AFNI Message Board
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Hi AFNI masters - I’d appreciate your sage advice!

Our lab is trying to use afni tools to find atlas information for input coordinates. We’ve run into a couple of (probably) straightforward snaffoos. Your input would be awesome. Note: in rank order of exponentially decreasing priority

  1. Freesurfer atlasing: We’ve run @SUMA_Make_Spec_FS to convert freesurfer aparc and aseg files into [???]_rank.nii/.niml.lt/.log files. Now we want to access those volume labels via whereami. Since ‘whereami -show_atlases’ listed the [???]_rank stuff as space of ORIG, I tried the command

'whereami -coord_file coords.1D.coord -space ORIG -atlas aseg_rank'

I receive this error:


** ERROR: Unknown space_name ORIG
whereami NULL string out.

Do you have any advice on how to access those [???]_rank atlases?

  1. Clarification on talairach locations: The talairach labels of talairach.org (http://talairach.org/labels.txt) have 6 location descriptors for each labeled voxel. How does the output of ‘whereami -coord_file my_coords.1D -atlas TLRC’ map from those descriptors, if they do indeed map from them? If they do not map from them, is there a way to access the 6 descriptors in a nice way from AFNI?

  2. Accessing whereami outputs programatically: Silly first question: I assume that whereami can write to a text file but for the life of me can’t figure out how. What is the command for this? Less silly second question: Do you know of any nice wrappers to convert whereami text file outputs into nice data structures within python/matlab/R for the case of input coordinates?? If there aren’t any, I may make an attempt at a (hacky) one for matlab.

  3. Clarification on SUMA aparc.a2009s.annot.niml.dset: We noticed that for both native and remeshed-std surfaces, the .annot.niml.dset appends ‘wm_?h’ to the freesurfer surface labels. We’re confused as to why surface/cortical vertices have ‘wm’ in their label. Are we misininterpreting the wm? Or is there a data conversion explanation behind the labeling?

Thanks!
John

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I can address one of your questions–the error:

** ERROR: Unknown space_name ORIG
whereami NULL string out.

Looks like this error comes from there not being any ORIG template space. I’ve been able to resolve this error by adding the following xml block to the subject’s SessionAtlases.niml file (note you could also add this to a more general location where afni looks for atlases, such as ~/abin/AFNI_atlas_spaces.niml:

<TEMPLATE_SPACE
space_name=“ORIG”
generic_space=“ORIG”
comment=“Native space of subject”

</TEMPLATE_SPACE>

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Great advice, Mike! I’ll look at adding that ORIG definition into the SessionAtlases.niml file automatically by the@SUMA_Make_Spec_FS script.