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!

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