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
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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