Hi Rotem

that's always a problem with FA estimation (the partial volume stuff I mean). It's hard to diagnose this without seeing some images. Can you send some of the registration?

cheers Bruce

On Tue, 26 Feb 2013, Rotem Saar wrote:

Hi Bruce,   Thanks for your answer and sorry about the delay in mine. Registration seems fine, but I came up with some questions regarding it -

1. When testing the registration, using the "compare" button, I can see both the diffusion and what is suppose to be the anatomical slices - but why

do the anatomical data it smoothed and doesn't look like a clear anatomical image ? can this be related ? maybe i did something wrong ?   2) Another thing I thought about was that the corpuse-callosum values are very high, but values for the ventricles are really low - so that even really small shifts in the registration can bring to a situation that values in the ventricles are higher than expected. Do u suggest manual intervention in registration that will mainly follow the mid-sagittal slice ? I don't mean ignoring the others, but mainly test the fit according the mid-sagittal slice.   If u have any other ideas for why this is happening - I would appreciate it if u share them with me in order to think of a solution.   Thanks !   Rotem

2013/2/18 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Rotem

  that does sound high. Have you checked the registation between your diffusion data and the anatomicals?

  cheers
  Bruce


  On Mon, 18 Feb 2013, 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_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

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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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