Try running reg-feat2anat on your fmri data. This will register the
functional data to the subject's structure (which is not useful for this
case). But it will also compute the matrix which registers the
anatomical and mni152. This will be in
featdir/reg/freesurfer/anat2std.register.dat
Fir
Hi,
I did not receive a response to this yet. Does it mean it is not possible?
Thanks!!
Vina Goghari wrote:
Hi Doug,
Yes the FSL group analysis is in MN152 and then I want map that back
to each individual's brain that were analyzed and parcellated using
FreeSurfer, so I can extract thickness
Hi Doug,
Yes the FSL group analysis is in MN152 and then I want map that back to
each individual's brain that were analyzed and parcellated using
FreeSurfer, so I can extract thickness values from my fMRI regions of
interest if that is possible.
Thanks!
Vina
Douglas N Greve wrote:
So you're
So you're group analysis is in MNI152, and you want to map that to
fsaverage or back to each individual?
doug
Vina Goghari wrote:
Hello all,
I have group contrast fMRI activations analzyed by FSL Flame 1 that I
want to extract individual thickness data for each subject from data
processed by
Hello all,
I have group contrast fMRI activations analzyed by FSL Flame 1 that I
want to extract individual thickness data for each subject from data
processed by FreeSurfer? Is that possible and if so, how?
Thanks!
Vina
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F
I just updated this page to include instructions on how to do this
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat
Nick Schmansky wrote:
Gui,
Have you had a look at the tutorial page that describes the
FSL/Freesurfer integration?
https://surfer.nmr.mgh.harvard.edu/fswiki/F
Gui,
Have you had a look at the tutorial page that describes the
FSL/Freesurfer integration?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
see slide #4, and session 2b.
I can't offer any other help than this, as I do not have experience
performing this integration, but your approach is s
Hi-I am trying to work out a work flow of integrating fsl and freesurfer.
the basic goal is to do surface-based group analysis.
what I have now is the run1.feat, run2.feat and mean.gfeat for each subject
done by FSL Feat and the processing anatomy using recon-all in freesurfer.
so the question now
006 12:28:43 -0500
> To: "Clifford A. Smith, PhD" <[EMAIL PROTECTED]>
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] FSL/Freesurfer
>
> Clifford,
>
> After sourcing SetUpFreeSurfer.csh, but before starting FSL, type this:
>
> unsetenv TCLLI
Clifford,
After sourcing SetUpFreeSurfer.csh, but before starting FSL, type this:
unsetenv TCLLIBPATH
This should take care of the problem you are seeing. You may want to
include that line in your SetUpFreeSurfer.csh file.
Nick
On Tue, 2006-03-21 at 10:36 -0600, Clifford A. Smith, PhD wrote
Hi - I suspect that the simplest solution is to source the FreeSurfer
setup _before_ the FSl setup.
Cheers, Steve.
On 21 Mar 2006, at 16:36, Clifford A. Smith, PhD wrote:
I believe that I have read a post on this in the past, but I was
unable to run a search. I have FSL configured to start
Title: FSL/Freesurfer
I believe that I have read a post on this in the past, but I was unable to run a search. I have FSL configured to startup in X11 without a problem. Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem. But FSL will not work after I have ran the source S
-
Announcing: FSL & FreeSurfer Course
19-23 June 2006 - Siena, Italy
Organised by FMRIB Centre, University of Oxford,
Martinos Center for Biomedical Imaging, MGH &
Quantitative Neuroimaging Laboratory, Siena
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