Hi FreeSurfers,
As the subcortical segmentation fails fairly often on my high resolution
data I want to skip it by using the noaseg flag, but Im currently
encountering another issue.
1.)During the fix stage of autorecon2 I receive following error during
mris_euler_numbers (also if
Dear All!
First of all, I'm completely newbie to freesurfer. So far I only used
FSL (mainly), rarely SPM and NordicICE.
I need to do a VBM study to compare 2 groups each containing 50 subjects
for GM density (already done with FSL), volumetry (not yet done), and
cortical thickness and surface
--
Hello group
I am new to freesurfer. I have two problems. Please accept my apologies if
these queries are bit naïve!
Any help will be much appreciated. I am trying to autorecon1 a single image
obtained from Philips 3T as dicom output. I use MacOS X11 terminal.
1. I am not able to use
HI Nick!
I generated and ran the scribt, but it gives me following error message:
ERROR: dimension mismatch between X and contrast
/Users/steimke/Rosa_MRTs/qdec/Untitled/tmp.mri_glmfit-sim-77641/lh-Avg-thickness-Age-Cor.mtx
X has 2 cols, C has 12 cols
I have to admitt that I did not
Gergo
Take a look in the Tutorial section of the wiki. Probably you'll find out that
you can do the whole study using FreeSurfer.
Cheers
PPJ
Enviado do meu celular Nokia
-Msg original-
De: Orsi Gergely
Enviada: 30/07/2009 05:53:47
Para: freesurfer@nmr.mgh.harvard.edu
Assunto:
Hi Gergely,
it should be pretty straightforward. You need to run recon-all on all
your subjects, then go through the qdec tutorial and use it to apply the
simple two-class GLM.
cheers,
Bruce
On Thu, 30 Jul 2009, Orsi Gergely wrote:
Dear All!
First of all, I'm completely newbie to
Hi William
FreeSurfer doesn't have a command environment like that. The problem is
probably that FSL isn't in your path.
cheers,
Bruce
On Thu, 30 Jul 2009, William Sohn
wrote:
Hi freesurfer community
I installed freesurfer on my mac however after I installed it FSL stopped
working. When
Hi Lena,
you definitely want to avoid analyze format, as it will remove the
direction cosine information you need for example to tell left from right
(it's probably why you have a flip).
We don't have much experience with dicom. Have you tried using -it dicom in
mri_convert to be explicit
Hi Falk,
can you really not afford the 6 minutes or so of scan time to get a good
1mm dataset? We have analyzed a bunch of 7T data successfully, although it
probably isn't as automated as 1.5 and 3T. The error you are getting we
only see when you have run out of disk space. It sounds like
Hi:
How can I solve the following error ?
ubuntu:~ tksurfer rezende rh pial
surfer: current subjects dir: /home/image/bin/freesurfer/subjects
surfer: not in scripts dir == using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /home/image
surfer: Reading
Hi Gonzalo,
are you running over vnc or something similar?
Bruce
On Thu, 30 Jul 2009, Gonzalo
Rojas wrote:
Hi:
How can I solve the following error ?
ubuntu:~ tksurfer rezende rh pial
surfer: current subjects dir: /home/image/bin/freesurfer/subjects
surfer: not in scripts dir == using
setenv doublebufferflag 1
And then run tksurfer
Enviado do meu celular Nokia
-Msg original-
De: Gonzalo Rojas
Enviada: 30/07/2009 10:48:45
Para: freesurfer@nmr.mgh.harvard.edu
Assunto: [Freesurfer] tksurfer error in ubuntu...
Hi:
How can I solve the following error ?
ubuntu:~
Hi,
I am processing several multiple comparison jobs on launchpad:
'mri_glmfit-sim --glmdir
lh.physio2_chol_final.cvram.115.thickness.07092009.doss.30.glmdir --sim
mc-z 5000 1.3 mc-z.pos.1.3 --sim-sign pos --bg 6'
and I believe that the job is almost finished running the simulation (it
has
try taking a look at:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Orsi Gergely wrote:
Dear All!
First of all, I'm completely newbie to freesurfer. So far I only used
FSL (mainly), rarely SPM and NordicICE.
I need to do a VBM study to compare 2 groups each containing
1. What's your cmd line and what does it say when it fails? See
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for more useful info you
can send.
2. Without the mat file, the geometry on them could be horribly wrong. I
would suggest loading it into tkmedit to make sure that it is oriented
Hi Victoria,
Regarding mri_surfcluster,
You can still use mri_surfcluster with --in --csd --sum --cwsig flags.
more info,
mri_surfcluster --help
thanks
pratap
Hi,
I am processing several multiple comparison jobs on launchpad:
'mri_glmfit-sim --glmdir
If enough iterations have been run, then you can just use what it has
created. To do this, just re-run with the --no-sim option. If you need
more iterations, then you can rename the csd files that are there.
Currently, they will be numbered 001, 002, ..., 006. Just rename them to
something
Rosa,
Was this script generated after an analysis was successfully run? You
will need to run an analysis first (ie, selecting your factors, etc,
press Analyze, then select a contrast for display in the Display tab),
then you can use the mri_glmfit-sim script generator feature.
I can't think of
I've seen this happen if two analyses were run using the same output
directory. Some of the contrasts won't get deleted the 2nd time it is run.
doug
Nick Schmansky wrote:
Rosa,
Was this script generated after an analysis was successfully run? You
will need to run an analysis first (ie,
Rosa,
you can either delete the directory 'Untitled' before running the
analysis (although I thought qdec did this already), or you should just
set your Design Name to something other than the default
'Untitled' (which will save stuff in a directory of that name).
Nick
On Thu, 2009-07-30 at
We effectively have a Brodmann atlas in that the labels in fsaverage can
be used to get probabilities of being in an array of Brodmann areas (and
we just got another set of them that we just started working on).
On Thu, 30
Jul 2009, Nick Schmansky wrote:
Luis,
I'm forwarding this to the
Hi,
I am running Ubuntu 8.04 and freesurfer V4.3.0. It worked well once upon a time.
However, I get this error about the mghRead as follows.
*~$ recon-all -autorecon1 -s liwentao_1 -i /mnt/data2/data/trauma/**
liwentao_1.mgz*
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.3.0
Current
does mri_convert work on the sample data? that is:
cd $FREESURFER_HOME/subjects/bert/mri
mri_convert orig.mgz test.mgz
if it does, then there is something wrong with your file
'liwentao_1.mgz'.
Nick
On Fri, 2009-07-31 at 09:51 +0800, leemon albert wrote:
Hi,
I am running Ubuntu 8.04 and
What if you rename the file liwentao_1.mgz to liwentao_1.mgh.gz
mv liwentao_1.mgz liwentao_1.mgh.gz
and gunzip it
gunzip liwentao_1.mgh.gz
this should work. If this doesn't work, it means the file is corrupted.
If it works, use the resulting file liwentao_1.mgh as an input to
recon-all
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