That is a good value, so the regis not the problem. If you upload your dt_recon folder as well as your recon-all folder for that subject I'll take a look. doug
On 04/11/2013 10:02 AM, Rotem Saar wrote:
Hi Douge,
In your last reply to my email (that contained questions regarding some really high FA values - see recent emails below), u asked me to write u the first value in register.dat.mincost - I'm copying the line I have:
0.280554 140.210312 156.795241 11.152485
Does this takes us one step further towards understanding the problem and its solution ?
Thanks for your time, Rotem
On 04/07/2013 06:48 AM, Rotem Saar wrote:
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 ?
*_yes, the ventricles look 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...
The wmparc includes all the subcortical and cortical regions too, but only the WM regions are reported in the wmparc.stats file. *_To only report the WM regions, add to mri_segstats --ctab $FREESURFER_HOME/_**_WMParcStatsLUT.txt_*
I'm probably doing something wrong, but I can't really point to the problem, thus asking for your help.
_*I don't know either. If I had to guess, I'd say it is a registration problem. What is the first value in register.dat.mincost?*_ doug
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 toconsult -
> I run the following script for getting the FA values frommy 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 theproblem ? in
> addition I attached a figure of the corpus-callosum, in which I'm > interested - i't seems that the green area in not bigenough, is
> this fixable ? > > Thanks ! > > Rotem
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