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

0) 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



Edited 2 time(s). Last edit at 07/15/2016 12:01AM by j.abc6.