Dear Afni connoisseurs,
I hope this finds you healthy and operational.
Say I have three datasets: A.nii.gz, B.nii.gz, and C.nii.gz where
B.nii.gz is an anat in orig space
A.nii.gz is an MNI-space version of B.nii.gz created with 3dAllineate and 3drefit -view +tlrc -space MNI . AFNI recognizes it as such, so far so good.
C.nii.gz is a functional dset in orig space
The problem is that when viewing volume B in AFNI, whereami is disabled despite my efforts to set -wpar and -apar options. Can you advise as to what should be done to the three datasets so that AFNI recognizes the parentage properly and enables whereami when viewing data in orig space?
Sorry for the custom route there, but the xform to MNI space had to be derived by catenating multiple transformations so I could not go the @auto_tlrc route, say.
We are operational and in business. Regarding the questions, this is a fairly arcane topic that is confusing to everyone. I am not sure it is possible to have the warp on demand from orig to tlrc work with NIFTI, which is essentially what is needed. So a few recommendations:
- Use AFNI format. Besides the warp parent and anat parent, you would also need the WARP_DATA attribute in your MNI dataset. That doesn’t go into the NIFTI dataset now. With AFNI format, then the paired naming +orig, +tlrc would be parsed from the directory.
- Transform the atlas you want to the native (+orig equivalent) space. This seems the most straightforward in most ways. Copy the atlas and labeltables from the desired atlas. The script @animal_warper has code for transformations including nonlinear warps. If you want whereami GUI capabilities too, a SessionAtlases.niml file would include the definition for the native space atlas.
- Removal of warp-on-demand from the GUI. The WOD feature is tricky for everyone, so we (Bob) are looking into removing it. With nonlinear warping now prevalent, you probably don’t want a pipeline reliant on it.
Will do. Thank you, Daniel!