Hi Sherryse
mostly I'll leave this for Doug. Have you tried using bbregister directly? It might be embedded within reg-feat2anat, I'm not sure Bruce On Fri, 30 May 2014, Sherryse Corrow wrote:
Thanks Bruce. The problem is that the registration itself is not working properly.
Recap: The goal is to view the functional data on the inflated brain. We ran recon-all, checked that registration, then attempted to register the functional data to the free surfer anatomical. My understanding is that running reg-feat2anat should create a folder (featdir/reg/freesurfer) with register.dat and anat2exf.register.dat files in (among others). The folder is created and some of the files are created, but those two are not.
Although, I should note that there is a file created within this folder called anat2exf.register.dat.init. But I am not sure what the ³init² is for or what it means.
The terminal output from running reg-feat2anat is attached. I can see now that there are errors in the output (I am slowly figuring how how to use FreeSurfer!).
Any suggestions you have are greatly appreciated! Thanks!
Sherryse
Date: Tue, 27 May 2014 12:21:30 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Registration of Functional Data to the Inflated Brain
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