Hi David,
Have you downloaded the updates of mri_cvs_register from
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes ? We found some bugs
in the orginial 5.1 release and put the fixed versions at the above.
Let me know if that still does not solve the problem.
--Lilla
On Tue, 21 Jun
Hello all,
I'm attempting to use mri_convert in order to match the slice size and
thickness of T2 and PD images to the Freesurfer T1 images, after converting
the norm.mgz and the T2/PD images to .nii.gz. For the T2 I'm using:
mri_convert ${SUBJECT}/T2/T2.nii.gz -rl ${SUBJECT}/mri/norm.nii.gz
I thought the default was p10, so I just used that to try again, however
I'm still getting that error with no extra info in the log. what is the
name of the queue, maybe that is my problem:
command:
pbsubmit -q p10 -l nodes=1:opteron -m chinsel -c 'recon-all -s RMAUT021
-all -i
Dear Freesurfer experts,
we are testing a grid computer infrastructure for running freesurfer
analysis and are evaluating consistency and reliability of freesurfer
results across platforms.
Before we start our tests across platforms we conducted some freesurfer
analysis on the same computer and
Dear All,
We are making Volume-based analyses and I have a few questions.
1. The SupraTentorial BrainVolume is indicated in the aseg.stats. I found an
explanation on http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats about
the SupraTentorial Vol., but checking the formula by summing up
if you file drop these volumes we'll take a look
Bruce
On Wed, 22 Jun 2011, G.
William Chapman IV wrote:
Hello all,
I'm attempting to use mri_convert in order to match the slice size and
thickness of T2 and PD images to the Freesurfer T1 images, after converting
the norm.mgz and the T2/PD
Hi,
So I think I found the solution -
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical)
reg-feat2anat
aseg2feat or aparc2feat
New question:
Is there anyway to combine aseg2feat and aparc2feat? i.e. get all subcortical
and cortical segmentations registered to
Got it :
aseg2feat --feat featdir --seg aparc+aseg
On 06/22/11, Sudhin A. Shah sut2...@med.cornell.edu wrote:
Hi,
So I think I found the solution -
(http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RegisterFeatOntoAnatomical)
reg-feat2anat
aseg2feat or aparc2feat
New
Hi Michael
thanks for the info, we'll look into this. We are aware of some of the
issues with running multiple times, but need to look into it further when
we find the time
Bruce
On Wed, 22 Jun 2011, Michael Scheel wrote:
Dear Freesurfer experts,
we are testing a grid computer
Dear experts of the Freesurfer,
I am just learning freesurfer software and I was running recon-all for a
subject in my directory. I can view the volumes and surfaces and I would
be very grateful if you can list the next steps to be followed.
Do I need to make a data correction(check my data)
Hi Chindhuri
remove the -l nodes=1:opteron from your command line. Also, you
probably want to send emails like this to h...@nmr.mgh.harvard.edu in the
future, as they are Martinos-specific.
cheers
Bruce
On Wed, 22 Jun 2011, Chindhuri
Selvadurai wrote:
I thought the default was p10, so I
Hello,
Sorry to bother you at this time. I got some questions about the freesurfer
course.
I checked the materials on the following webpage
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
It seems like we could get all the materials from that website since when I
click all
the links they
do you mean the FreeSurfer course? Or the FSL/FreeSurfer course? In either
case you get hands-on experience and personal help in going through data.
cheers
Bruce
On Wed, 22 Jun 2011, Mu Xue wrote:
Hello,
Sorry to bother you at this time. I got some questions about the freesurfer
course.
I
Dear all,
Is it possible to find the coordinates (ras and MNI) of every vertex points on
a surface in matlab?
Thank you.
Hiroyuki
Notice: This UI Health Care e-mail (including attachments) is covered by the
Electronic Communications Privacy Act, 18 U.S.C.
Hi Antonella
we usually view the ?h.white and ?h.pial surfaces over the norm.mgz and
the aseg.mgz and check them all for accuracy. If things are not where you
think they should be, then you need to take one of the interventions
documented on the wiki.
cheers
Bruce
On Wed, 22 Jun 2011,
Hi Lilla,
Yes, sadly the problem still persists. The strangest part is that the same
error occurred when I tried to process bert (mri_cvs_register --mov bert)
using the VirtualBox Ubuntu package for FS on Windows. My only guess (as
suggested by one of the other users) is that it's a problem
Hi all:
After all recon-all -all processing has been completed for all subjects
,I want to obtain volume of specific structure of each subject(e.g., the volume
of Caudate Nucleus). But i have no idea about it,Are there some tools or
commands that can help?
I hope you can give me some
Take a look in aseg.stats file
-- iOS 4.3
Em 22/06/2011, às 23:09, ZhiLiangLong lagosslong1...@163.com escreveu:
Hi all:
After all recon-all -all processing has been completed for all subjects
,I want to obtain volume of specific structure of each subject(e.g., the
volume of Caudate
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