Dear FreeSurfers,
suppose I should estimate the mean cortical thickness on a number N of ROIs
(for instance, the left inferior temporal, the left middletemporal, and the
left superior temporal). How would you suggest me to proceed?
- Just performing a simple average of the 3 cortical thickness
Hi,
I apologise if this is only on my end but I can't seem to download any of the
updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful
last week so I wonder if something's changed?
Thanks
Kx
--
Kirstie Whitaker, PhD
Research Associate
Department of Psychiatry
Hi all!
Sorry for my late answer but I went on holiday and I didn't have access to
my mail.
The background is normal in original dicoms and it is not an avarage of
more than one run.
The problem I reported was solved in all cases converting dicoms to nifti
with dcm2nii and using the oriented
Hello,
I was wondering if FS has an output mask (labelled volume) for each tissue
types (gm+wm+venctricular_csf) that I can then turn into each subject's
native space. I understand I can use aseg.mgz or even aparc+aseg.mgz and
then run mri_label2vol. But then how do I get correspondent labelling
Hi Kirstie - This was a glitch related to yesterday's storage cluster
maintence. It's been fixed now, so please try again.
a.y
On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
Hi,
I apologise if this is only on my end but I can't seem to download any of the
updates from
Yep! Working now - thank you very much :)
Kx
On 20 August 2014 12:23, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
Hi Kirstie - This was a glitch related to yesterday's storage cluster
maintence. It's been fixed now, so please try again.
a.y
On Wed, 20 Aug 2014, Kirstie
Dear Don,
Thanks alot for the attachment. I have installed it as recommended and
tried the following and I started to get the error message below
imaging@imaging-ThinkCentre-20:~$ freeview
bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter:
Permission denied
When using sudo
Hi Anastasia and the freesurfer list,
I've been working on getting the latest version of tracula to run and I thought
I would post here the errors that I've worked around. It's all been based on
looking through the mailing list archives but I thought it would be useful to
add them here all in
Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You
are a model user :)
On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
Hi Anastasia and the freesurfer list,
I've been working on getting the latest version of tracula to run and I
thought I would post here the errors
Dear Freesurfer gurus,
I am trying to create an FSDG file for my data set and I have a question
regarding discrete variables.
So say this is my data: Two discrete variables (two with two levels, one with
eight), one continuous variable.
I'm interested in one discrete variable
Thanks for the reply Zeke.
I understand what you are saying about the VM. So my question is now, how do we
help our users to optimize FreeSurfer for their large scale data sets?
We have a couple of Red Hat Enterprise Linux 6 64bit machines with the newest
FreeSurfer installed
Hello all,
Traditionally I have only processed FS data using a single core per person, but
processing many people at once. Now we have caught up with the backlog of
scans, we have a continuos trickle of scans coming in 1 by 1. I was wondering
if anyone has tested how the speed-up of open-mp
Hi Hanna, use #2
doug
On 08/20/2014 10:36 AM, Isotalus, Hanna wrote:
Dear Freesurfer gurus,
I am trying to create an FSDG file for my data set and I have a
question regarding discrete variables.
So say this is my data: Two discrete variables (two with two levels,
one with eight), one
Try loading aseg.mgz as the aux volume so you can see the number at a
particular voxel. If the color is not correct, see what the number is
and what it corresponds to in the LUT
doug
On 08/19/2014 05:57 PM, C.P. Frost wrote:
Hi all,
I'm trying to use Freeview to display subcortical regions
hi andrew,
i haven't done many systematic comparisons but there are a few practical
considerations to take into account. in recon-all, i believe a few steps
are affected by the openmp option and that creates resource
underutilization. processors run idle when those steps are not being run.
in my
Hi Ali,
Sorry it didn’t work “out of the box.”
It was kind of a long shot.
That interpreter is for an i86 64bit system running linux.
If you are running a Mac or have a 32bit os or … it will be a problem.
If it’s the right one, it needs to be enabled for execution with the following
command:
Hi
I tried for three days download freesurfer even today but pressing the
download link in http://surfer.nmr.mgh.harvard.edu/fswiki/Download
These are fallen and message This web page is not available
I have understood that the site was in maintenance, however the links do
not even respond.
On 20 August 2014 14:27, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You
are a model user :)
Thank youalthough unfortunately not quite the best user - I still have
problems...
I think I lied in my earlier
It appears to work for me. Try this link to download directly:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg
Once downloaded, go here for installation notes:
http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall
This should work on OSX
I am running analysis where I am taking fMRI data using Freesurfer to
project it onto the cortical surface and load it into Brainstorm to use as
a constraint on the source reconstruction. I am able to do all the steps
just fine, the problem I am encountering is that Freesurfer creates a
surface
Hello,
The latest version of mri_tessellate can be downloaded using this the
following link:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate
It would be wise to backup your existing version befor overwriting it
with the version contained in the link above.
Thanks for the reply, Doug.
The main problem is that areas not included in my custom table appear
colored in freeview. These areas' numbers correctly correspond to their
indices on the default FreeSurferColorLUT, although they don't appear
labeled in the info panel, nor are they listed to the
Andrew,
I basically agree with everything Satra is saying. Just as an added
piece if info, Ive included a chart which did a systematic study of
recon-all processing times with different number of cpus in parallel.
These results are a bit old (and might be for low-res data) but the
general
Opps... I forgot the attachment. Here it is.
-Zeke
Original Message
Subject: Re: [Freesurfer] Open MP parallel processing scaling factor?
Date: Wed, 20 Aug 2014 15:24:14 -0400
From: Z K zkauf...@nmr.mgh.harvard.edu
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu,
Hi Surfers
I want to use bbregister to register my MRA scans to the structural
scans. The first attempts by using these parameters came out OK but not
perfect:
bbregister --s Subject_ID --mov MRA.nii --init-fsl --reg register.dat
--bold
However, there are obvious problems around frontal
Dear Mailing List,
I have just completed a QDEC (v5.1.0) analysis of the following design:
Measure:thickness
Smoothing (FWHM):10
Hemisphere:lh
2 Discrete (Fixed Factors):group (2 levels, AtRisk Control) and
gene (2 levels, CC TTorTC)
1 Nuisance Factos:age
On
Thanks Zeke
Bruce
On Aug 20, 2014, at 1:55 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:
Hello,
The latest version of mri_tessellate can be downloaded using this the
following link:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate
It would be wise to
Hi
I am reposting my message, hoping someone can give me some hint to get my
problem solved. Thanks in advance!!
On Mon, Aug 18, 2014 at 10:42 PM, Jidan Zhong jid...@gmail.com wrote:
Hi Freesurfer experts,
I was doing some manual editing on our subjects which are patients with
lesions. I
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