Hi Mohamed, that looks great, very clear. We'll have to engage your
services to write some of our wiki pages :)
doug
On 2/2/15 1:05 PM, Alshikho, Mohamad J. wrote:
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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