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 <fis...@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 >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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