Hi Doug,
Thanks for your reply. I know how to run mri_glmfit-sim. What I'd like to
do is to apply a more liberal threshold to my data to examine the clusters
that fall outside of the MC-corrected threshold. To do this I applied the
mri_surfcluster command with a vertex-wise threshold of p .005,
Hi Doug,
just a very naive question about coordinate change: why do we need the
fourth component? I mean, shouldn't be the transformation matrix 3x3
instead of 4x4 for a coordinate change in 3D space?
thanks!
Gari
On Wed, Sep 11, 2013 at 12:52 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
Hi Gari,
The transformation actually consists of a 3 x 3 matrix and a 3 x 1
translation vector. The use of a 4 x 4 matrix allows the
representation of an affine transformation as a matrix multiplication
(http://en.wikipedia.org/wiki/Affine_transformation#Representation).
--Thomas
On Wed, Sep
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Hi.
I try to get information about the progress of my subjects out of the
log files, writing a script that reports about the progress and sends
progress messages.
For that I try to get the individual stages as progress indicator from
the
Hi all,
I know I can use mri_label2label and then mris_anatomical_stats -l to obtain
the label-based cortical thickness for each individual subject.
I also know that there is a tool called mri_annotation2label.
But is there a way to convert annotation to each individual subject, so that I
can
Dear FS team,
I'm using the web portal Neugrid (https://neugrid4you.eu/it) for the
analysis of my T1w MRI data with FreeSurfer. In particular, I'm using
the *reconall
-all*.
My question is about possible problems arising from different FS versions.
The version provided by Neugrid is the
Hi Doug,
It's pretty awesome. So accordingly,
MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) *
1
MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1
MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1
The
Suzanne,
p0.005 is the same whether its voxels or vertices.
The liberal nature of 20 voxels is vague to begin with as there is two
things contributing to how liberal 20 voxels are: (1) voxel size - 20 1mm
isotropic voxels is quite different from 20 3mm isotropic voxels; (2) The
number of voxels
To comment further on this.
It appears that - at least in our data - the talairach registration fails
frequently (i.e. in more than 60% of the cases) as a result of the larger
field inhomogeneities at high field. A good work-around is to use FLIRT for
doing the registration. So just use FLIRT to
Dear Douglas,
attached you´ll find the two y.fsgd file from the analysis run in GLM_FIT.
the results are completely different (the z-score converted age produces a
believable result, while the result correcting with raw age scores seems
completely wrong.
best regards
Olof
y.fsgd_raw_age
Hi,
I am finding a warning at recon-all when creating the folders:
INFO: could not find /Path/subject.mat file for direction cosine info.
INFO: use Analyze 7.5 hdr-hist.orient value: 1, coronal unflipped.
INFO: if not valid, please provide the information in /Path/subject.mat file
What are the
I have a somewhat strange question and hopefully someone can help me out.
I have a few hundred subjects that have all been run through recon-all, and
have gone through some QA. In some of the cases control points have been
added or brain masks have been modified etc, and recon-all has been
no, you'll need to figure out which series to give an a file from, but it
will figure out the other files in the same series.
Also, please cc the list so that others can answer
Bruce
On Wed, 11
Sep 2013, Pedro Rosa wrote:
Hi,
Thanks for your help.
Is freesurfer able to select T1-w dicoms
Dear all,
Is there a way to visualize vertex wise t-values (t-statistics), instead of
p-values, on a vertex map when you are doing group analyses? I successfully
generated the p-maps using mri_glfmfit, but I am wondering if vertex-wise maps
that represent t-values can be also generated and
Hello FreeSurfer experts,
I am doing volumetrics study. During the scan we get 2-3 mprage per scan for
a subject.
While running the FreeSurfer, if I want to use the three mprages for that
subject as an input file, may I just keep the three mgz files (001.mgz,
002.mgz and 003.mgz) in the orig
-- Forwarded message --
From: swathy p.s swathy.kare...@gmail.com
Date: Wed, Sep 11, 2013 at 1:47 AM
Subject: talairach transforms
To: freesurfer@nmr.mgh.harvard.edu
after motiioncor was runned sucessfully,getting error with talairach.comand
was as given bellow
[root@ml
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