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
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Heidi Gröhn, PhD
CMRR
University of Minnesota
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