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(a)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(a)eyecarecentre.org
>
>