Hi Freesurfers,

I have several processed resting time series files (processed through AFNI) and I'd like to convert them to MNI space. I have done this successfully for T1Volumes and some ROI masks using mri_convert and tried to use the same code for the resting series. However, I've run into a few issues - namely that the transformation cuts off part of the top of the cortex.

My code:

mri_convert -it nii -ot mgz CleanData_RestState.nii.gz CleanData_RestState.mgz

mri_convert CleanData_RestState.mgz --apply_transform transforms/talairach.xfm \
-oc 0 0 0 CleanData_RestState_talairach.mgz 

mri_convert CleanData_RestState_talairach.mgz \ cleanData_RestState_talairach.nii.gz


The final time series file, overlayed on the transformed T1Volume, is below.

Inline image 1

Any suggestions? How big a problem is this?


Thanks!
--
Paul Beach
DO/PhD candidate - Year VI
Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
 - MSU Cognitive and Geriatric Neurology Team (CoGeNT)