Thank you Anastasia, I'll try this. Best wishes, Barbara
On 12/08/2016 23:19, Anastasia Yendiki wrote: > Hi Barbara - This can be done with mri_vol2surf. The projection that's > described in that passage can be done with --projdist-max -6 6 1, and the > surface smoothing with --surf-fwhm 6. There are other options in > mri_vol2surf, I'd recommend playing with the settings to see what works > better for your data. > > Best, > > a.y > > > On Fri, 5 Aug 2016, Barbara Kreilkamp wrote: > >> Dear Freesurfers and TRACULA experts, >> >> Thank you for your help so far. I am trying to map the endpoints of the >> tract probability distributions onto the cortical surface (as mentioned >> in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos). >> >> I've somehow gathered that I need to do this (example one endpoint): >> >> flirt -ref /mri/orig/T1.nii.gz -in >> dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init >> /dmri/xfms/diff2anat.bbr.mat >> >> I then loaded the images in Freeview and they look reasonable together >> with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv >> dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz >> >> What I don't get is how to do this: >> >> "we projected the tract endpoints onto the gray/white matter surface by >> sampling along the surface normal vector, anywhere within 6 mm (3 >> DWI-space voxels) of the gray/white junction and then smoothing along >> the surface with a 2D Gaussian kernel of 6mm full width at half max." >> (Solsnes et al. 2016) >> >> Any help would be greatly appreciated. >> >> Best wishes, >> Barbara >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
