Hi Celine - That's an interesting question. There's nothing implemented in there right now that would allow you to skip part of the tract in the along-the-tract stats. One (not very elegant) way to try to do something like this is:
1. Set the lesion voxels in the dmri/dtifit_FA.nii.gz volume to zero. (You'll want to save the original volume under some other name for backup first.) If you want the same for the diffusivities, repeat for the also for the MD, L1, L2, L3 volumes. 2. Run the dmri_pathstats command line that you'll find in trac-all.log for that subject. This will regenerate all the pathstats.* files, but now the parts of the tract that go through the lesions will have zero values (or very low, if they're mixed in with some neighboring voxels). Let us know if this worked! If not I may be able to implement something. a.y On Tue, 11 Feb 2014, Celine Louapre wrote: > Hi Anastasia and freesurfer experts, > I am trying to get DTI values along the tracts as in the pathstatbyvoxel > file, but excluding inflammatory WM lesions. I have masks of the WM > lesions that I could apply on the DTI maps, but then how could I compute > the DTI metrics along the tract with the exclusion of the lesion? (I guess > the last step of trac-all -path could be applied to DTI maps that were > masked by the lesions?) > I would like to keep the advantage of having the DTI weighted metrics in > particular. > Thanks a lot for your help! > Celine > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
