-------- Forwarded Message --------

Subject:	TRACULA tract endpoints on cortical surface
Date:	Fri, 5 Aug 2016 12:03:02 +0200
From:	Barbara Kreilkamp <bakk.hbg@googlemail.com>
To:	Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

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