[Freesurfer] Covert processed RS time series to MNI152

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.

[image: Inline image 1]

Any suggestions? How big a problem is this?

Thanks!