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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