Hi Tim,
you could spatialize normalize the data before running mri_convert, the
only down side is that you have added an interpolation to the processing
that you didn't need to, and so sacrificed some resolution. You will
probably want to create a talairach.xfm file in the subject's
mri/transforms directory that is the identity so that the software knows
that the data is in talairach coordinates (you'll also have to add a line
to the mri/orig/COR-.info file speficying where the transform is with:
xform subjects_dir/subject name/mri/transforms/talairach.xfm
Note that this must be done before the rest of the processing so that the
other steps both know that the data has been talairached, and also
propagate that information down the pipeline.
cheers,
Bruce
Bruce Fischl email: [EMAIL PROTECTED]
Mass. General Hosp. NMR Center.tel:(617)-726-4897
Rm. 2328, Building 149, 13th Street fax:(617)-726-7422
Charlestown, MA 02129 USA
On Fri, 9 Aug 2002, Timothy Souza wrote:
Hi all,
I'm a fairly new user of Freesurfer, although I have been a user of AFNI
for some time. I have a question related to using MNI space in freesurfer.
Currently we have been normalizing our data to the MNI_avg_152 template,
using FLIRT in FSL. I understand that Freesurfer can be set up to use MNI
tools for this process, which is implemented during the cortical
reconstruction stream. Is there any reason why we wouldn't be able to use
MNI normalized data as our raw data before running mri_convert? Will
converting raw data to COR format remove this data from MNI space, and put
it into a new space? Or, is there a particular reason why MNI normalization
occurs midstream in the freesurfer process?
Thanks,
Tim Souza
--
Timothy Souza
Brown University
Department of Neuroscience
[EMAIL PROTECTED]
ph: 401-863-1258
fax: 401-863-1074
