Hi Jared,
mri_robust_register might be good for the task, the problem:
- only worked with structural intensity data so far
- I never tested it on 2D data. It should not be too difficult to get it
to run, though. Can you send me some of your images, and I will try to
add the functionality (if not t
Petr,
>From what directory is the command being run? If the directory
'temp/label/' doesnt exist in that dir, it will fail. You can also just
put the full pathname to the output file (arg of trglabel).
Nick
On Sat, 2009-08-15 at 01:07 +0200, p.s.bjer...@studmed.uio.no wrote:
> Hi,
>
> Have
Hi,
Have a question regarding the mri_label2label function. Trying to test it
for a subject (called "temp"). It seems to exit on writing the label file
in the subject folder. There should not be any problems with the write
permissions. Any idea? This is what I get (from command line):
---
just to add a factoid, from the ADNI data set, 793 subjects processed by
freesurfer:
Volume Mean: StdDev:
--- - ---
Left-Hippocampus 3184.335 604.930
Righ
Hi all,
I have some images (2-d (single slice)) from mouse brains which show
gene expression data from in-situ hybridization from several different
mice. I would like to align each of these images with one another.
Does anyone know of a really good tool for that sort of thing? Ideally
I am l
try recreating it (maybe you ran out of disk space?)
On Fri, 14 Aug 2009,
Rutvik Desai wrote:
> I get the same error when trying to load it in tksurfer.
>
> -
> reading colortable from annotation file...
> CTABreadFrom: could not allocate -2 bin table
> Cannot allocate memory
> Bus error
> --
is your segmentation protocol the same as the one we base our automated
segmentation on? For example, are fimbria and alveus considered part of
the hippocampus?
As far as left/right switches go, do you have any fiducial markers (e.g.
vitamin E tablets) in the images?
cheers
Bruce
On Sat, 15
I get the same error when trying to load it in tksurfer.
-
reading colortable from annotation file...
CTABreadFrom: could not allocate -2 bin table
Cannot allocate memory
Bus error
-
On Aug 14, 2009, at 4:31 PM, Bruce Fischl wrote:
> sounds like the annotation file is corrupted. Can you
sounds like the annotation file is corrupted. Can you load it in
tksurfer?
On Fri, 14 Aug 2009, Rutvik Desai wrote:
> We get the following error on one subject when running
> mris_anatomical_stats. The same command workson other subjects who were
> generated the same way. Using
> freesurfer-Darwi
Hi, there,
I have some problem for the hippocampus segmentation results.
1. My structural data are originally in par-rec file. I used r2agui to
convert them into .nii format, then use recon-all -i to convert the .nii
data into freesurfer .mgz format. Based on these operations, I run
recon-all -a
Hi, there,
I have some problem for the hippocampus segmentation results.
1. My structural data are originally in par-rec file. I used r2agui to
convert them into .nii format, then use recon-all -i to convert the .nii
data into freesurfer .mgz format. Based on these operations, I run
recon-all -
Hi all,
I am interested in obtain a total gray matter volume and a total white
matter volume specific to the frontal lobes. How can this be done in
freesurfer?
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https://mail.nmr.mgh.harvard.edu/
We get the following error on one subject when running
mris_anatomical_stats. The same command workson other subjects who were
generated the same way. Using
freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5,
also tried freesurfer-Linux-rh9-stable-pub-v3.0.5. No heavy processes were
running on the mach
They are (or should be) the same and can be compared directly.
doug
Garth Coombs wrote:
> Hi,
>
> I am going to be running some new analyses on an old data set from
> another lab group that was collected in 2005/2006. Their group
> unpacked and analyzed using the f.nii.gz format; however, our
Yes, when you are running the simulation you should pass it the fwhm
(new versions *force* you to pass it a fwhm when running the simulation,
even if it is 0). And, yes, if you do not give it the proper fwhm (or
pass 0), then it will make it more likely that clusters will be deemed
significant.
Hi,
I am going to be running some new analyses on an old data set from
another lab group that was collected in 2005/2006. Their group
unpacked and analyzed using the f.nii.gz format; however, our lab
unpacks and anayzes the f.nii format. Since I will be comparing the
group from their lab w
Thanks, Doug. Just so I'm clear: passing mri_glmfit the value in
fwhm.dat is the *proper* thing to do, and not giving the simulation that
information on the residual smoothness would cause the p-value estimates
to be biased towards letting clusters in, yes?
-
Jim Porter
Graduate Student
Sid,
I haven't used SurfStat but would be interested in knowing the steps you
took to conduct your analysis. If you like, you could setup a wiki
account and document it on our site, or just send me some notes or
scripts and I can create the page.
It would be useful for use to replicate what yo
Try these commands:
mri_surf2surf --s subject --hemi lh --sval-tal-xyz white --tval-xyz
--tval lh.white.tal
mris_convert lh.white.tal lh.white.tal.asc
doug
Feng-Xian Yan wrote:
>
> Hi,
>
> I have some problems want to understand.
>
>
>
> (1) I want to analysis the cortical thickness diff
yes, that should be fine
On Fri, 14 Aug 2009, Ahmed, F, Me
wrote:
> Hello,
>
> I just have a quick question, when reinstalling FS, is it ok to use the
> license that I initially received when first installing it? Or must I
> register for a new license?
>
> Thank you and Kind regards,
> Fatima
If I could, I would!! But there is no one here on a regular basis that knows
Linux! Thank you for trying to help. I was just reading the instructions for
the installations, and I typed this command in:
tar tzf freesurfer-Linux---full.tar.gz
and that worked absolutely fine, it showed the content
I think you should grab some help from you local sys admin or some linux
user
2009/8/14 Ahmed, F, Me
> The same error occurred after typing that in
>
>
>
> *From:* Pedro Paulo de Magalhães Oliveira Junior [mailto:
> p...@netfilter.com.br]
> *Sent:* 14 August 2009 15:08
>
> *To:* Ahmed, F, Me
The same error occurred after typing that in
From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br]
Sent: 14 August 2009 15:08
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] installation problems
You can copy you tgz to /usr/local or in the directory
You can copy you tgz to /usr/local or in the directory where the tgz is
execute
tar -C /usr/local -xzvf f
reesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar.gz
2009/8/14 Ahmed, F, Me
> Ok, how do I get it in there?
>
>
>
> *From:* Pedro Paulo de Magalhães Oliveira Junior [mailto:
> p...@netfi
Ok, how do I get it in there?
From: Pedro Paulo de Magalhães Oliveira Junior [mailto:p...@netfilter.com.br]
Sent: 14 August 2009 15:01
To: Ahmed, F, Me
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] installation problems
My guess is: your tgz is not in /usr/local
--
My guess is: your tgz is not in /usr/local
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.Netfilter.com.br
--- New Netfilter Small Business
2009/8/14 Ahmed, F, Me
> He
You can use the same .license
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.0 www.Netfilter.com.br
--- New Netfilter Small Business
2009/8/14 Ahmed, F, Me
> Hello,
>
> I ju
Hello,
I am trying to reinstall FS, and I am having some difficulties. When I type in
the following command:
cd /usr/local
tar xzvf freesurfer-Linux---full.tar.gz
(replacing the -- with my Linux variant which is
freesurfer-Linux-centos4-stable-pub-v4.3.1)
I get the following error:
tar: free
Hello,
I just have a quick question, when reinstalling FS, is it ok to use the
license that I initially received when first installing it? Or must I register
for a new license?
Thank you and Kind regards,
Fatima
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