Thanks so much for your help, but I have one more problem. The original issue was transferring the images I had in afni back into an SPM compatible format (NIFTI or ANALYZE). The original images that I transformed to a BRIK file are in the format I.number (sorry, I do not know the name of this image format. This is raw data though, and there are about 100 of these files per subject). An example of the exact command I used is:
to3d -session 040624b -prefix 040624b -anat ../rawdata/040624b/I*
It was on this dataset that I drew the ROI. Is there any way to find out exactly how afni re-oriented these images, so that I can transfer them backwards and then transfer to SPM?
Thanks,
Ian
