Sorry for the mistake: I wanted to correlate the DTI metrics inside this single voxel with the concentration of the metabolites (the output of LCMODEL) inside the voxel.
From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Alshikho, Mohamad J. Sent: Monday, February 2, 2015 1:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Calculate the DTI metrics inside a single voxel Dear Doug and Bruce, I have a single voxel spectroscopic data (SVS) and a (DTI) data for the same subjects. I wanted to correlate the DTI metrics inside this single voxel with the DTI metrics inside the voxel. In order to do that I used the following steps: 1. I used mri_convert to convert the T1 slice prescription dicom image to nii format mri_convert 562000-000004-000001.dcm t1_MRS_svs.nii 2. I genetrate the SVS voxel using the following command line: mri_volsynth --vol svs.nii --pdf const --dim 40 40 40 1 --res 0.5 0.5 0.5 1 -cdircos <Column vector> --rdircos <Row Vector> --sdircos <VOI normal> --c_ras <VOI position> 3. I viewed the SVS voxel as an overlay on the T1 image to be sure that SVS is in the correct position tkmedit -f t1_MRS_svs.nii -ov svs.nii -fthresh 0.9 4. I co-registered the T1 slice prescription image with the corresponding T1.mgz using the following command line: bbregister --t1 --mov t1_MRS_svs.nii --init-fsl --reg t1.reg.dat --s subject 5. I registered the single voxel and the FreeSurfer anatomical space (svs.reg.dat): tkregister2 --mov svs.nii --int t1_MRS_svs.nii t1.reg.dat --reg svs.reg.dat --noedit --subject <subj> 6. I mapped the single voxel into the anatomical space: mri_vol2vol --mov svs.nii --reg svs.reg.dat --fstarg --interp nearest --o svs.anat.nii 7. I mapped the FA map into the anatomical space: mri_vol2vol --mov fa.nii --reg svs.reg.dat --fstarg --interp nearest --o fa.anat.nii 8. I computed the dti metrics inside the SVS mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/aparc+aseg.mgz --ctab-default --i fa.anat.nii --mask /autofs/space/marvin_001/users/MRI/WMA/svs/wmvcalc/${subj}/svs.anat.nii --sum svs_fa.summary.dat Kindly, Is this plan correct? and do you suggest me any other steps? I am sorry for this long email but as always I am looking forward to learn from you. Many thanks, Mohamad
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