first, you'll need to get two new things:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cvs152.mri2.mm.tar.gz ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
cd $FREESURFER_HOME/subjects/cvs_avg35_inMNI152 tar xvfz cvs152.mri2.mm.tar.gz
# Make a backup of mri_vol2vol, then cp mri_vol2vol$FREESURFER_HOME/bin
Now, run mri_vol2vol like this mri_vol2vol --gcam EPI.nii.gz reg.lta $SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 output.nii.gz
where reg.lta is the output of bbregister (don't use the EPI.nii.gz that has been changed with --no-resample)
This will create an output with 2mm voxel size. If you really want to do 3mm, then you can try creating your own mri.3mm subdir like the mri.2mm subdir you just added.
On 08/05/2016 08:02 AM, Heidi Grohn wrote:
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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