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.
