Hi

Attached is some pictures that might help ? Is this what you meant ?
Looking at this again - something is weird but I can't say what...
I can ZIP the data of one subject and send it to you but I don't feel comfortable asking you to personally examine it...
Hopefully the upcoming course will shed some light on these problems...

thanks

Rotem

2013/2/26 Bruce Fischl <fischl@nmr.mgh.harvard.edu>

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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