Hi Freesurfer experts,
I have a set of RAS coordinates in the Freesurfer fsaverage space. What is the
easiest way to transform them to MNI152 space?
Thanks.
- Archana
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multiply them by this matrix
$FREESURFER_HOME/average/mni152.register.dat
On 09/25/2014 11:00 AM, Venkataraman, Archana wrote:
> Hi Freesurfer experts,
>
> I have a set of RAS coordinates in the Freesurfer fsaverage space. What is
> the easiest way to transform them to MNI152 space?
>
> Thanks.
>
Just to be clear, $FREESURFER_HOME/average/mni152.register.dat seems to contain
a 4x4 matrix (M). So, if my RAS coordinates are (x,y,z), I would do the
following:
M*[x y z 1]'
where the coordinates are stacked as a column vector? Or do I multiply on the
left?
Thanks.
- Archana
> -Orig
yes!
On 09/25/2014 12:04 PM, Venkataraman, Archana wrote:
> Just to be clear, $FREESURFER_HOME/average/mni152.register.dat seems to
> contain a 4x4 matrix (M). So, if my RAS coordinates are (x,y,z), I would do
> the following:
>
> M*[x y z 1]'
>
> where the coordinates are stacked as a column vec
I ran the MNI152 average through recon-all and it seemed to do ok. You
can get it from here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152.tar.gz
I don't know what kind of accuracy you are looking for, but for cortex,
you should work strictly in the surface and avoid volum
Hi Reza, I think that this should work.
doug
set subjectlist = (subject1 subject2 ...)
1. Create a template from a single subject
make_average_surface --subjects $subjectlist[1] \
--out iter00 --template-only --surf-reg sphere.reg
2. Register each subject to this template, including first
s
Dear Freesurfers,
If I am planning to do a longitudinal analysis, I understand that the LME
Model is probably the most appropriate choice. However, it says on the
website that it is for univariate and mass-univariate analyses. I would
need a longitudinal model that can handle *multivariate* stat
Thank you Doug for your comprehensive response. This looks clear, and I am
going to try it out. Just one question for now:
In step 1 (create a template from a single subject), I do not yet have
"sphere.reg". Should I write "--surf-reg sphere"?
make_average_surface --subjects $subjectlist[1] \
oops, sorry, that should have been sphere not sphere.reg
On 09/25/2014 01:35 PM, Reza Rajimehr wrote:
> Thank you Doug for your comprehensive response. This looks clear, and I am
> going to try it out. Just one question for now:
>
> In step 1 (create a template from a single subject), I do not yet
Dear Doug,
Thank you for your email.
On Wed, Sep 24, 2014 at 8:57 AM, Douglas N Greve
wrote:
>
>
>> 2) While most of the CBF to T1 registrations using the transformation for
>> the PD to the T1 image worked reasonably, there are a few where the
>> registration is a little off (almost exclusivel
Dear FreeSurfer List,
I like to introduce you to a new set of reference brain networks
(cognitive components) estimated from 10,449 experiments and 83
behavioral tasks from the BrainMap database, which can be downloaded
here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainmapOntology_Yeo2015.
The
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