Dear Doug,

I have uploaded the files to the "filedrop" (file name: Rotem_try.tar.gz) and activated the link (I hope I did it OK).

I will appreciate your help as I'm stuck - can't see the problem...:)

Thanks for all your help !!

Rotem

------------------------------

Message: 9
Date: Thu, 11 Apr 2013 12:51:38 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] DTI: problems with (high) FA values
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5166EA1A.8000701@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

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 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
> >
> >
> >
> >
> > _______________________________________________
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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