Dear all,
I am trying to figure out how to bring my fMRI data from FSL to the
freesurfer surface.
The way I understood it from the tutorial 3.0 Surface-based Group
Functional Analysis(
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat)
There are two possibilities of combining
Hello
Sorry for reposting again.
Would really appreciate a feedback on the following mail.
Thanks in advance for your time
Raka
- Forwarded Message
From: raka maitra rakamai...@yahoo.com
To: Douglas N Greve gr...@nmr.mgh.harvard.edu
Sent: Fri, January 15, 2010 9:34:02 PM
Subject: Re:
In the mri_glmfit.log file, there is a SearchSpace this will be in mm2
for surfaces and mm3 for vols. There will also be a mask.mgh file. You
can run mri_segstats on this to give you the number of elements that are
== 1.
doug
Stefan Brauns wrote:
Hi there,
I am running surface based
It would probably be more like this:
1. 00.5000
1. 0 -0.5000
01.0.5000
01. -0.5000
The 1st col codes subject 1. The 1st row is the 1st measure of subject 1
and the 2nd row is the 2nd measure of subject 1.
doug
raka
Hi, there,
In rebuild_gca_atlas.csh, I read something like:
# A talairach registration should be generated for this first subject as well,
# in order to align the final atlas to the Talairach space.
Is this talairach registration file the same as the talairach.xfm under each
subject's
yes. be sure to double-check it with tkregister2.
On Tue, 2010-01-19 at 12:24 -0600, Guang Zeng wrote:
Hi, there,
In rebuild_gca_atlas.csh, I read something like:
# A talairach registration should be generated for this first subject
as well,
# in order to align the final atlas to the
usually around 140k/hemi. If you make a label and save it as a label file
it will have 1 line/vertex
On Tue, 19 Jan 2010, Stefan Brauns wrote:
Hi there,
I am running surface based analysis of cortical thickness using FreeSurfer.
Sometimes I constrain the analysis to certain regions of the
If you do:
$mris_calc overlay stats
the first line reported back will be the number of vertices. So, if you
want to know how many vertices on the left hemisphere:
$mris_calc lh.thickness stats
and look at the
Size[ XXX ]
where XX will be number of vertices.
Stefan Brauns
Hi, there,
Are there any place in FreeSurfer Wiki or journal paper explain why FreeSurfer
need to atlases; Subcortical and Surface?
Thanks!
Guang
_
Hotmail: Trusted email with
if one wants to get at the brain only (similar to bet), is brainmask.mgz the
best file to use? on some of our data, we are noticing a lot of eyeball.
i presume one can use aseg as an alternative. is this more recommended than
brainmask.mgz? also, is the total brain volume computation based on
aparc+aseg.mgz is probably better. See
surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume for the answer to your
question.
Satrajit Ghosh wrote:
if one wants to get at the brain only (similar to bet), is
brainmask.mgz the best file to use? on some of our data, we are
noticing a lot of eyeball.
Dear experts,
I like to find Tarairach and MNI coordinate from volume index (data has
been already processed with recon-all) off line using Matlab.
Which transform should I use to find it ?
Thank you.
Hiroyuki
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Hello -
I have two questions:
1) I noticed on wm.mgz volumes that were segmented properly, that even when the
ventricles were
automatically filled in, on some slices they are somewhat patchy (partially
filled in with white, with some black/blank voxels).
Do these patchy wm fill-ins require
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