Hi Freesurfer (FS) users,

I am a new user in the world of FS and I am trying to normalize rsfMRI EPI series to CVS MNI space. I would like to do it without resampling the EPI images to 1*1*1mm3 resolution.

I've registered EPI series to FS T1 space by using following command (after bbregister), with --no-resample flag, after which the resolution of the EPI images did not change. 

mri_vol2vol --mov EPI.nii.gz --targ ...subject/mri/wmparc.mgz --interp trilinear --o EPI_in_FS_T1_space.mgz --reg EPI_in_FS_T1_space.dat --no-resample --no-save-reg

After that I used the following command to apply normalization to CVS MNI, but I cannot find any similar option to maintain the low resolution. Output is always on 1*1*1mm3 resolution.

applyMorph --template ../cvs_avg35_inMNI152/mri/norm.mgz --transform ..subject/cvs_mni/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.tm3d \vol EPI_in_FS_T1_space.mgz EPI_in_MNI.mgz trilinear

In summary, how would I maintain the resolution of the EPI images after normalization? By the way, I am using Freesurfer 5.3.

Your help is very much appreciated, Thanks,

Heidi

%%%%%%%%%%%%%%%%

Heidi Gröhn, PhD

CMRR

University of Minnesota

%%%%%%%%%%%%%%%%