Hi Doug,

Thanks for your answer.
I changed the last step as u suggested, but I think I need to clarify my question:
Indeed values of the CC looks OK, but don't u think other values, like the ventricles are too high ?

When I first run the script, I got all values and looked the the CC - it looked fine. Then, I wanted to validate with some other regions, just to show that I got the appropriate (low) FA values for regions I don't expect to see high values in - and things looked odd (too high).

I remember Bruce also writing me that the values seems a little high, but we didn't further discuss. I read the following this link: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual

"The CC has an average FA of about 0.75, gyral parcellations are about 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as expected because the CC is highly directional with no crossing fibers so we would expect the CC to have the highest FA. The gyral white matter is also directional but has fibers crossing in them, so one expects the FA to be lower than CC. The gray matter (putamen) is still lower. The ventricle has no fibers, so we expect it to have the lowest FA".

All my values are above 0.4....

Additionally, if in the last step I'm writing --seg /usr/local/freesurfer/subjects/Rotem_try/mri/wmparc.mgz

why do I get 182 regions ? in my wmparc.stats I have only 70...

I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help.

Attached is the table again,

Thanks
Rotem

The values look about right in the table. Your pipeline looks ok,
thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output
of mri_vol2vol (fa_FOLDER-NAME.nii).
doug

On 03/17/2013 02:16 AM, Rotem Saar wrote:
>
> 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_FOLDER-NAME.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 (see attached), 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 ?
> Can u guide me regarding what I can do to solve the problem ? in
> addition I attached a figure of the corpus-callosum, in which I'm
> interested - i't seems that the green area in not big enough, is
> this fixable ?
>
> Thanks !
>
> Rotem