2013/3/5 Rotem Saar <saar.ro...@gmail.com> > 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 <fis...@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 <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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