Hi Ziad,

I was able to get alignment to work after a lot of experimenting, but the volume that the surface was created from in caret does not line up properly right after the surface is made. For some reason, the combination of

1) export the original T1 afni files to nifti
2) segment the nifti files in caret
3) use caret's file conversion program to change the nifti file back to afni format
4) use @SUMA_AlignToExperiment to align the surface to the original afni T1 volume

From there the rest of suma works great. If I try to view the surface overlaid on the volume there are different problems with each volume up to the last step.

Clicking anywhere on the surface when overlain on the afni volumes from 1) causes the cursor to go to the far posterior/inferior corner of the viewing window

The nifti file from 2) doesn't have scaling problems, just an offset problem that appears to be related to the location of the AC

@SUMA_AlignToExperiment has errors when run with 2) and aligns improperly when run with 3) in nifti format

I'm assuming there is a step I'm messing up when preparing the volume for segmentation in caret. I'm using the T1 volumes in orig space, performing ACPC alignment in caret, and generating surfaces from this. Is it better to perform ACPC alignment in afni before bringing the image into caret? I'm using caret 5.61 and the latest release of afni. I'm sure there is more straightforward way to do this process, I just haven't had any luck finding documentation on using caret 5.61 with suma as it appears freesurfer may be the preferred method for doing this kind of thing.

Thanks,
Matt