Hi all,
I run into somthing that seems odd to me and wanted to consult - I run the following script for getting the FA values from my DTI scans:
1) dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec 2) tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii -fthresh 0.2 -fmax 1 4) mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s FOLDER-NAME --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat 5) tkregister2 --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_marsal.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg 6) mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii --sum /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME
I got a table with all the FA values, for each segment, but I suspect a problem: I think that the values are too high (I set the threshold to 0.2-1), am I right ? I'm attaching the table I got, and to be specific, I'm very much interested in the Corpus-Colosseum values, which are high (not surprising) but when I wanted to validate with some other structures, like the "left putamen" I saw 0.53 which is to my opinion too high ? I would really appreciate if you can have a look at the table I attached here. Can u guide me regarding what I can do to solve the problem ? Is that any way to confirm that after the mask, I am left only with white matter ?
Thanks !
Rotem