Hi Minjie,

You'll want to give tksurfer the name of one of the "regular" surfaces (e.g., inflated, pial, etc.) as the third positional argument and then view your FA file as an overlay ( -overlay rh.fa.vol2surf2.w ). The former gives the surface geometry information (where the vertices are and which are connected in the mesh) while the latter gives an arbitrary scalar value associated with each vertex (in your case, FA).

Best, Michael

On Wed, Dec 21, 2011 at 11:39 AM, Minjie Wu minjiewu@gmail.com wrote:

Dear Surfer,

I was trying to project a DTI FA image onto the T1 WM surface (for now), and eventually into the fsaverage as in a recent paper: Phillips OR, Nuechterlein KH, Asarnow RF, Clark KA, Cabeen R, Yang Y, et al. Mapping corticocortical structural integrity in schizophrenia and effects of genetic liability. Biological psychiatry. 2011;70(7):680-9.

1. align the lowb.nii.gz from DTI data to T1.mgz image using

bbregister to create the register.dat file. bbregister --s 20808 --mov lowb.nii.gz --reg lowb2orig.dat --dti --init-fsl

2. project FA into surface space

mri_vol2surf --mov dtifit_FA.nii.gz --reg lowb2orig.dat --hemi rh --o rh.fa.vol2surf2.w --projfrac 0 --interp nearest --surf white --out_type paint

Here is the error message when I tried to check the surface in subject T1 space

[Minjie-Wus-Mac-Pro:subjects/20808/dmri] minjiewu% tksurfer 20808 rh fa.vol2surf2.w subject is 20808 hemi is rh surface is fa.vol2surf2.w surfer: current subjects dir: /Volumes/Lion/projects/surface/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Volumes/Lion/projects/surface/subjects/20808/dmri checking for nofix files in 'fa.vol2surf2.w' Reading image info (/Volumes/Lion/projects/surface/subjects/20808) Reading /Volumes/Lion/projects/surface/subjects/20808/mri/orig.mgz surfer: Reading header info from /Volumes/Lion/projects/surface/subjects/20808/mri/orig.mgz nquads=14348288, nvertices=1 ERROR: MRISread: file '/Volumes/Lion/projects/surface/subjects/20808/surf/rh.fa.vol2surf2.w' has many more faces than vertices! Probably trying to use a scalar data file as a surfa

Thank you very much for your help.

Minjie _______________________________________________ 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.