Hi Sherryse

you only need to register the anatomicals to the funtionals once, then sample the functional data onto the surface using mri_vol2surf. This will create a surface overlay that can be visualized on any of the surfaces for that subject (e.g. lh.white, lh.pial, lh.inflated)

cheers Bruce On Tue, 27 May 2014, Sherryse Corrow wrote:

Hi FreeSurfer Team,

Please help out a FreeSurfer newbie!  We are having an issue with mapping our functional data onto the inflated brain.  When we finish the mapping, it seems that much of the data is showing up in white-matter space, and therefore, cannot be seen on the external surface of the brain. We later discovered that we were likely using the wrong registration matrix. However, it doesn’t seem like the one we are supposed to use is being produced during recon-all.  I am new to FreeSurfer and would greatly appreciate some assistance!

To provide you with more detail.

Problem: When we run the command line below, and then open the folder experiment.feat/reg/freesurfer, there is no anat2exf.register.dat file.  However, there is a file called: anat2exf.register.dat.init.

Command Line: Reg-feat2anat -feat OurFeatDirectory.feat -subject P143

Terminal Output: There is no terminal output.  No error of any kind.

Log File: Attached.

Thanks, Sherryse

P.S. We submitted this issue previously but were not getting a response, so we tried again in case our thread wasn’t working properly.

--  Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow@eyecarecentre.org