Re: [Freesurfer] From NIfTI T1 to its volume cortical thickness map in MNI152 space.

Hi again,

Any suggestions at least conceptual to the path I should follow to obtain cortical thickness volumetric data in MNI space?

Thanks!

On Sun, Jun 8, 2014 at 6:54 PM, Fred Sampedro fredsampedro@gmail.com wrote:

Dear FreeSurfer experts,

I am interested in analyzing group differences in cortical thickness with an application-specific GLM model that is build to work on MNI152 volume data. For that, my plan is to obtain a "cortical thickness volume in MNI152 space" for each of my MRI scans. My input data are nifti T1 scans. Here is my pipeline proposal for each T1 scan:

INPUT: FOO_SUBJECT.nii

FREESURFER CALLS (in $SUBJECTS_DIR): 1) recon-all -i FOO_SUBJECT.nii -subjid foosub 2) recon-all -all -subjid foosub 3) mri_surf2vol --surfvalpath /foosub/surf/lh.thickness --o foosub_cth_vol_lh #(?) 4) mri_surf2vol --surfvalpath /foosub/surf/rh.thickness --o foosub_cth_vol_rh #(?) 5) #should I merge lh and rh (?) how (?) let it be foosub_cth_vol 6) fslregister --s foosub_cth_vol --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat #should I convert it to MNI152 space (?) and how (?) 6) mri_fwhm --i foosub_cth_vol --o smoothed_foosub_cth_vol # should I smooth it (?) and how (?)

OUTPUT to statistical analysis: smoothed_foosub_cth_vol (?)

As you can see, I am pretty new to freesurfer and I have a lot of technical and conceptual gaps in this pipeline.

Any advice on how to robustly accomplish this task would be much appreciated, as well as any advice regarding whether it would be a bad idea to try to carry out this kind of procedure in the first place. The context of the application is to apply the same ad-hoc statistical groupal analysis to PET, VBM GM, and cortical thickness data for all subjects.

Thanks a lot in advance, Fred Sampedro