Hello,
I’m wondering if anyone has had similar issues as I have had with exporting/importing files (below) and can help?

In my analysis I:
-export anat+tlrc.HEAD image from AFNI to MRIcro
-convert to .hdr/.img format
-use Amira software for drawing an ROI mask on anat+tlrc.hdr
-convert ROImask.am (Amira file) to DICOM
-import the ROImask.dc3 back into AFNI
-convert to HEAD/BRIK using to3d
-resample the ROImask+orig to EPI grid
-use 3dmaskave to extract PSC values from each ROI.

In the past I have done all of the above steps, but using an anat+orig.HEAD file to start with. Using these steps with the anat+orig file, I have had no issues with the ROI mask lining up correctly with the anatomical image.

However, now I am exporting a +tlrc anatomical image from AFNI to use for drawing ROIs in Amira and when I convert back to AFNI using to3d, the mask does not line up and the ROIs have been altered slightly. I suspect this has something to do with the mask being in +orig space and the anatomical in +tlrc. But I am unsure how to get around this? I tried using adwarp to warp the ROImask+orig dataset to my anat+tlrc but it did not recognize the ROImask file as a valid dataset. But even if it did, warping would not fix the ROI alterations that occurred.
Also, I would prefer to limit the amount of transformations to the mask (as was my reasoning for drawing it on a talairached anat image).

Does anyone have any suggestions for how I can resolve this issue?

Thanks,
Kristen