In this case you would have six regressors:
1. control-offset
2. hiv-offset
3. control-age
4. hiv-age
5. control-ed
6. hiv-ed
If you want to test group thickness "regressing out" the effect of age
and ed, then you would just set the contrast to:
1 -1 0 0 0 0 0
Note that this will test it at ag
(1) probably using mri_segstats with "--annot fsaverage lh aparc" and
specifying the --y input to mri_glmfit as the "--i invol" and specify
a "--avgwf" output to get all the subjects.
(2) Yes, you would expected it. I'm not sure what it means if you
don't see it. Maybe a bug somewhere.
(3)
yes, it is
On Thu, 11 Jun 2009, Nasim Maleki wrote:
Dear Freesurfer developers,
I'm wondering whether the wmparc.stats is computed with a partial volume
correction at the boundaries of the structures.
Thank you,
Nasim
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Freesurfer mailing lis
You can mri_convert the output specifying the output type as -odt
short. Sorry, don't have any easy way to change the slicing.
doug
On Wed, 10 Jun 2009, xfore...@ucla.edu wrote:
Dear Freesurfer experts,
I'm trying to convert the annotation file into (binary Analyze file),
I tried the com
Hi Fatima,
You probably would find it easier easier to just point recon-all directly
at the dicoms with -i. It saves the conversion step. If you do the
conversion and put the runs in the orig dir then you don't need -i anymore,
it will find them.
cheers,
Bruce
On Wed, 17 Jun 2009, Ahmed,
FYI
-- Forwarded message --
Date: Tue, 16 Jun 2009 22:55:11 -0700
From: Tom Liu
Reply-To: FSL - FMRIB's Software Library
To: f...@jiscmail.ac.uk
Subject: [FSL] Postdoctoral Positions for EEG/fMRI Research at UC San Diego
The Center for Functional MRI at the University of Califo
Hi all,
Is there a way to convert results that I have on fsaverage to average7?
I need to do that to be compatible with some average7 results that go
into the same paper. When I use mri_surf2surf, activation is displaced.
Any advice would be appreciated.
This is what I've done:
mri_surf2surf
Sorry. I mistyped the first command
(Wrong) recon-all -i DICOM_FILE_DIR -o 001.mgz
(Correct) mri_convert -i DICOM_FILE_DIR -o 001.mgz
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter
PPJ,
Thank you for your response, I tried your procedure and got the following
message:
[...@localhost CON_ADAMS_MONIQUE]$ cp 001.mgz
$SUBJECTS_DIR/CON_ADAMS_MONIQUE/mri/orig
cp: cannot stat `001.mgz': No such file or directory
I don't know why that happens.
From: freesurfer-boun...@nmr.mgh
Fatima,
Try this simple procedure to get started.
1) Convert your dicom files to 001.mgz
recon-all -i DICOM_FILE_DIR -o 001.mgz
2) Inside your subjects_dir create a subdirectory like this:
mkdir -p $SUBJECTS_DIR/test01/mri/orig
3) copy your 001.mgz into that dir
cp 001.mgz $SUBJECTS_DIR/test01/m
Hi Roberto
Yes the transforms is bad but the important thing is that is works well
with
the 32 version so ...
Romain
roberto toro wrote:
Hi Roman,
did you check with tkregister2 what the transforms look like?
(use tkregister2 --mgz --s mySubjectID --fstal)
cheers,
roberto
On Wed, Jun 17, 20
Hello, I am new to using Freesurfer and am trying to run the recon-all stages
in order to get thickness values for brain regions. I have correctly
converted all my dicom images into the correct mgz format as instructed by your
manual and have carried out motion correction (even though I only have
Hi Roman,
did you check with tkregister2 what the transforms look like?
(use tkregister2 --mgz --s mySubjectID --fstal)
cheers,
roberto
On Wed, Jun 17, 2009 at 8:37 AM, romain valabregue <
romain.valabre...@chups.jussieu.fr> wrote:
> Hello
>
> I tried this new relase on 20 subject and I get the
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