': No such file or directory
I don’t know why that happens.
*From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Pedro Paulo de
Magalhães Oliveira Junior
*Sent:* 17 June 2009 15:14
*To:* Ahmed, F, Me
*Cc:* freesurfer
I'm not sure Scuba is in active development.
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0 www.Netfilter.com.br
2009/6/10 akram ak...@nmr.mgh.harvard.edu
Hello,
I remember
I think FreeSurfer has more reliability. In houndreds of manually
segmented hippocampi we found FreeSurfer measures to be pretty stable.
the manually segmented hippocampi usually has 15% - 20% less volume.
However we still don't know which method is more accurate. There's a
study right now in USP
Hi.
I/O is not quite the bounding issue.
I would invest in CPU and them in memory.
cheers
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0 www.Netfilter.com.br
2009/5/28 Luke
Software used for clinical purposes need a FDA approval in US.
FreeSurfer main target is research. If you use it for clinical purposes you
are on your own risk.
cheers.
PPJ
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
Software used for clinical purposes need a FDA approval in US.
FreeSurfer main target is research. If you use it for clinical purposes
you are on your own risk.
cheers.
PPJ
You should use:
ozgun.oza...@gmail.com
7235
*CZag.N9G9Ekc
Only three lines in license file
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br
2009/5/14
Take a look at:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br
2009/4/30 Elina Pitri
#!/bin/bash
cd #your directory where qdec data are stored.
set numsubject = 17 #your value
for i in `seq 1 $numsubject`
do
mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.mgh
mris_convert -c $i.mgh ../../fsaverage/surf/lh.inflated lh.$i.asc
done
Did you use
2009/4/23 marina.lo...@crccorp.es
Hi Pedro Paulo,
I tried to use your script (qdec-coord) to extract individual thickness
data from my plot in qdec, but I have a couple of questions:
- I found the output from the instruction in a file called* lh.l.asc *in my
working directory
Probably you updated the kernel (or the OS did by himself) and the
restricted drivers (ATI/NVidia) are not enabled by default.
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0
...@med.cornell.edu
Thanks for the quick responses. Is there an easy way to enable these
drivers? (We unfortunately don't have an IT linux expert here).
At 03:38 PM 4/23/2009, Pedro Paulo de Magalhães Oliveira Junior wrote:
Probably you updated the kernel (or the OS did by himself) and the
restricted
You can use slicer 3
---
Pedro Paulo de M. Oliveira Junior
2009/4/18 asaf achiron achirona...@gmail.com
hi group,
Is there a way to reconstruct in 3d the hippocampus or thalamus
segmentation in Freesurfer?
this is for verification
Dana,
I have done some recon-all in NPH patients and didn't have any problems with
NPH with large ventricles.
Best Regards
PPJ
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0
Can you try converting directly Dicom to mgz?
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br
2009/4/2 Kelly Silva kcasi...@yahoo.com.br
We started with
FPS
8021 frames in 5.1 seconds = 1587.792 FPS
thanks,
Elisa
2009/4/1 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
Try running glxgears
Can you post the output of *dmesg *command
2009/4/1 Elisa Dell'Oglio dellog...@bwh.harvard.edu
Thanks you. I actually tried
If you are using tcsh
setenv doublebufferflag 1
in bash
export doublebufferflag=1
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br
On Wed, Apr 1, 2009
the error message:
surfer: ### redraw failed: no gl window open
Is there anything else that you would suggest to try?
Thank you in advance,
Elisa
2009/4/1 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
If you are using tcsh
setenv doublebufferflag 1
in bash
export
time and patience.
Elisa
2009/4/1 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br
It seems that you are using running this Centos inside a VMWare.
TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in
current vmware
This paper may help you:http://www.jneurosci.org/cgi/reprint/25/34/7840.pdf
http://www.jneurosci.org/cgi/reprint/25/34/7840.pdfAnd also this threads:
http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2005-December/002092.html
If you are using tcsh
setenv doublebufferflag 1
in bash
export doublebufferflag=1
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br
On 1 de abril de 2009
Can you post the output of dmesg command?
Are you using vmware? TkSurfer works fine in Virtualbox (2.1.4) but I'm not
sure it'll do in current vmware. If you are using it I suggest you to
migrate your virtual machine to VirtualBox: http://www.virtualbox.org/
Have you tried setting the autoredraw
I think you have a problem in the voxel size.
*The physical sizes are (280.00 mm, 280.00 mm, **492.00 mm**), which cannot
fit in 256^3 mm^3 volume.*
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
---
I think you mean FreeSurfer?
You can find this in aseg.stats inside stats directory in each subject.
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
--- Novo Netfilter 3.0 www.netfilter.com.br
On
Yes.
Use the script in UserContributions section of the Wiki
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/ppaulo/qdec-coord
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
---
There is a researcher here who is getting this error in version 4.2.0, I
have uploaded the 001.mgz to the ftp:
TEMPLATE DEFORMATION
second estimation of the COG coord: x=150,y=117, z=145, r=8362
iterations
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4
Some links that may be helpful:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
http://surfer.nmr.mgh.harvard.edu/fswiki/MultipleComparisons
Hope it helps.
PPJ
Besides what Krish told you, you should disable effects in Ubuntu
preferences-appearance. Otherwise you'll have a window without border.
Also, you should turn on Auto redraw in TKSurfer.
Notice that setenv is for csh, if you are using bash you should do
export doublebufferflag=1
tksurfer
Hi,
Can you add this paper to the Wiki page?
Cortical thickness reduction of normal appearing cortex in patients
with polymicrogyria - Oliveira Jr, Pedro Paulo; Leite, Claudia;
Valente, Kette; Shergill, Sukhwinder; Amaro Jr, Edson; - Journal of
Neuroimaging - 2008 - In Press
Tks
PPJ
The FreeSurfer http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer
Development
Team is hosting a two-day course for beginner and experienced users of
FreeSurfer http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer. Day 1 will
be an introduction
Hi Anderson,
I don't remember if I showed you here in Sao Paulo our Freesurfer
processing.
I think you could have a cluster or for better power consumption a Blade
Server to run several recon-all at same time (don't forget to reserve at
least 1GB Ram per core)
To visualize your data you can use
on when GPU might become a
requirement, or how essential it might become?
That's because what is going to a brand new system may quickly become
obsolete for FreeSurfer if the GPU stuff comes along soon.
Thanks a lot!
Anderson
Pedro Paulo de Magalhães Oliveira Junior wrote:
Hi Anderson,
I
Hi,
I'm running 100 cases in a MacPro with 8 core and in all cases I'm receiving
this message in skull strip step:
GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073732725
RIGHT_CERCSF_MIN=1, CSF_intensity=2, CSF_MAX=218 , nb = -1073752790
LEFT_CER CSF_MIN=0,
Hi,
Freesurfer do present thickness in mm.
Also the p-Value is from the GLM model used in QDEC (mri_glmfit)
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
On Mon, Dec 22, 2008 at 09:50, b9403208
I think tcsh are recommended for historical reasons. However you can use bash.
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter SpeedComm Telecom
On Fri, Nov 28, 2008 at 12:02, Jared Price [EMAIL PROTECTED] wrote:
(or
scripts) on how to do this, it would be greatly appreciated.
thanks,
mishkin
On Thu, Oct 2, 2008 at 9:08 PM, Pedro Paulo de Magalhães Oliveira
Junior [EMAIL PROTECTED] wrote:
Sure.
y.mgh is the volume created by QDEC when you start a stat design.
You'll find it usually in $SUBJECTS_DIR
I think Douglas can answer better this but I think you can find some help
in:
http://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats
and in:
http://wideman-one.com/gw/brain/fs/surfacefileformats.htm
2008/10/6 Tommaso De Marco [EMAIL PROTECTED]
Dear Doug Greve,
I have tried to use mri_surf2vol
] Behalf Of Pedro Paulo
de
Magalhães Oliveira Junior
Sent: 03 October 2008 21:25
To: Joao Pereira
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Voxel resolution impact / skull stripping and
biascorrection replacement
João,
Here is my opinion:
I have worked
João,
Here is my opinion:
I have worked on resolutions distinct than 1mm3 isotropic and usually I have
no problem. What do you mean by false negatives in your cohort study?
I think you should avoid seeding data with skull striped by other program to
the pipeline.
Best Regards,
PPJ
2008/10/3
? That would be:
tksurfer $subject $hemi sphere.reg -overlay
$SUBJECTS_DIR/$subject/surf/$hemi.thickness
cheers,
Bruce
On Mon, 22 Sep 2008, Pedro Paulo de Magalhães Oliveira Junior wrote:
Sorry for the question but in order to generate the visualization of the
spherical mapping of, for instance
Hi,
I don't know if someone know the answer, however I found this question an
interesting one:
In Dale99 paper, Neuroimage, the authors stats that all recon process would
take 90 minutes. Is there a way, using recon-all script to follow the same
steps they used in that paper?
--
I have included a script to export these values to a spreadsheet
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/ppaulo/excelICV-aseg
2008/9/4 Bruce Fischl [EMAIL PROTECTED]
p.s. we probably do something similar to the loose-fitting mask as we
only use non-brain locations
I think you are right
I bet you can choose to control FDR locally (clustering?)
2008/8/28 jorge luis [EMAIL PROTECTED]
Dear Glen, there is something you have to take into account when using FDR
separately at various regions of a parcelled brain. It do not control de
Global FDR if the null
Manja,
I think FDR can be different for each hemisphere since they are taken apart
during processing.
Best Regards,
Pedro Paulo Jr
2008/8/27 Manja Lehmann [EMAIL PROTECTED]
Hi,
We've noticed that FDR correction produces different p-values for the left
and right hemispheres. We found that
李日 ,
Index is the number of the vertex.
Volume is 335490.0mm3
Norm mean, stddev refers to the pixel intensity values in these areas.
2008/8/18 李日 [EMAIL PROTECTED]
Hello:
I have run the recon-all command and it finished without errors. The
FreeSurfer has generated a stats file
Irene,
Have you checked if these patients who don`t have aseg.stats in their stats
directory have the recon-all finished correctly.
Best Regards
Pedro Paulo Jr
2008/8/14 irene [EMAIL PROTECTED]
Hi all,
I need data which are in the aseg.stats file (which is in the stats file).
Some
Hi 李日,
1) Is the cortical thickness of the area where you passed the mouse over.
2) Is the index of the vertex in the cortical model.
3) Red line select the threshold limit for red color in the map, green line
select the interface between red/yellow coloring.
Regards,
Pedro Paulo Jr.
the thickness
values into the volume but I am not sure what to type in the command line or
what steps should I follow to do this. Sorry I am very new to freesurfer.
Thanks alot
Ali
--
*From:* Pedro Paulo de Magalhães Oliveira Junior
*Sent:* Wed 13/08/2008 14:23
I think the manual is spread among the wiki pages.
However I think to start up the best way is using the tutorials:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials
Pedro Paulo Jr
2008/8/13 Eliezer Kanal [EMAIL PROTECTED]
Hello folks -
I recently downloaded freesurfer and am slowly
Hi Ali,
Beyond the advice of Bruce, in your University there are some people who
has experience in FreeSurfer. In the Brain Body Centre you can talk to
Marije Jansen, I think she can indicate some local expert in FreeSurfer.
Best Regards,
Pedro Paulo Jr
2008/7/27 Bruce Fischl [EMAIL
Hi,
Some time ago I have asked a question similar to this and the answer was a
page with a template:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation
I would like to ask two questions:
1) Is this template a copy paste one?
2) Is there any concern regarding plagiarism using
Nick,
When you cite this cordinates in a paper, what is the name you use?
Best Regards,
PPJ
2008/7/8 Nick Schmansky [EMAIL PROTECTED]:
Feng-Xian,
The coordinates are surface coordinates. qdec does not display the Tal
coords, but I think this will be added in a future release.
You can
I would try:
chmod -R 777 /usr/tmp
2008/7/6 Woo-Suk, Tae [EMAIL PROTECTED]:
Dear FreeSurfer experts!
I had a error message when I ran a subjects on cluter super-computer.
It seemed that the error was caused by permission on /usr directory.
How can I correct this problem?
Woo-Suk, Tae
Some versions of LibTiff have the zlib compression support disabled.
Do you have an older version of LibTiff in your Mac?
2008/7/1 Jan Kalkus [EMAIL PROTECTED]:
Hi everyone,
I'm trying to make a monkey template using mris_make_template. So
far, every time I run the
The problem is if the libtiff was compiled with zlib or not.
I think it would be nice to rebuild your libtiff from ports:
http://tiff.darwinports.com/
2008/7/1 Jan Kalkus [EMAIL PROTECTED]:
I have libtiff 3.8.2.
On Jul 1, 2008, at 12:06 PM, Pedro Paulo de Magalhães Oliveira Junior
wrote
Hi Nicolas,
This week in Brisbane you can find some of the developers of FreeSurfer to
discuss this issue.
My thoughts are: manually traced hippocampi is a still open problem. In 1.5T
in a good quality SPGR or even in 3T it's a difficult task and many times
very operator dependant.
In
Hi,
1) It uses fsaverage cordinate system unless you have your own averege
subject set.
2) It used log p value scale. I don`t think it make sense in QDEC to use mm.
Best Regards
Pedro Paulo Jr
2008/6/24 Feng-Xian Yan [EMAIL PROTECTED]:
Hi,
After I ran the qdec and analyzed my
There are two options:
1) You don't have libGLU installed.
Solution: Go to
http://rpm.pbone.net/index.php3/stat/3/srodzaj/1/search/libGLU.so.1()(64bit)
and install LibGLU
2) You have another version:
to find out run: find / -name libGLU.so* -print
Best Regards,
Pedro Paulo JR
2008/6/24 Damian
You mena for FDR estimation?
2008/6/23 Catherine Hartley [EMAIL PROTECTED]:
Hi,
I understand that there are tools under development implementing Gaussian
Random Field correction for multiple comparisons. If there is a usable
version available (and a brief description of how to use it),
You mean for FDR estimation?
2008/6/23 Pedro Paulo de Magalhães Oliveira Junior [EMAIL PROTECTED]:
You mena for FDR estimation?
2008/6/23 Catherine Hartley [EMAIL PROTECTED]:
Hi,
I understand that there are tools under development implementing Gaussian
Random Field correction
Actually is Pedro Paulo, but no problem.
I'm not sure if Fortran Libraries were static linked in 4.0.5
So just in case try installing this.
Best Regards,
Pedro Paulo Jr,
2008/6/20 Jose Miguel Selman [EMAIL PROTECTED]:
Hi Narly:
You will probably need this also. I did the same move recently
Hi Pedro,
If you are using NVidia I suggest you to check if you are using latest
Ubuntu native Nvidia driver.
Best Regards,
Pedro Paulo Oliveira Jr.
2008/6/18 Pedro Brito Cruz [EMAIL PROTECTED]:
Dear all,
i'm a newbie using FreeSurfer and recently installed the CentOS 4 x86_64
version on
Hi,
I think some of us are in Melbourne these days in the HBM.
If somebody is interested in exchanging experiences in FreeSurfer usage we
can meet somewhere in this event.
Actually I was looking for Doug :)
Regards,
Pedro Paulo Oliveira Jr
___
PROTECTED]:
he's there somewhere :)
On Sun, 15 Jun 2008, Pedro Paulo de Magalhães Oliveira Junior wrote:
Hi,
I think some of us are in Melbourne these days in the HBM.
If somebody is interested in exchanging experiences in FreeSurfer usage we
can meet somewhere in this event.
Actually I
Hi,
Installing Slicer3 yesterday I have noticed that it seems to have a QDEC
module.
Is there any documentation on this?
Thanks
Pedro Paulo Jr
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
I had the same problem with 4.0.4
The solution is:
Install G77 (Fortran). Link:
http://prdownloads.sourceforge.net/hpc/g77-intel-bin.tar.gz?download
Regards,
PPJ
2008/5/20 Nick Schmansky [EMAIL PROTECTED]:
Jose,
Which distribution did you install? You can find out by typing:
cat
Martin,
I have an still unpublished work comparing VBM and FS in Alzheimer. I
can say to you that FS provides result much more accurate in this
area.
Best Regards,
Pedro Paulo Jr
2008/5/14, Bruce Fischl [EMAIL PROTECTED]:
Hi Martin,
1. FS uses geometry to do inter-subject registration,
Do you have pointers for this paper?
2008/5/15 Bruce Fischl [EMAIL PROTECTED]:
p.s. Natalie Voets at Oxford also has a study on this and might have some
comments...
On Thu, 15 May 2008 [EMAIL PROTECTED] wrote:
Hi Martin,
Not to belabor this topic but one of the major advantages in using
Teddy,
If you want I have some scripts (very alpha version) to convert the
files in stats directory to SPSS format.
Best regards,
PPJ
2008/5/5 Doug Greve [EMAIL PROTECTED]:
This would just be a spreadsheet, so you can use somethign like R or SPSS.
doug
Nick Schmansky wrote:
Teddy,
As
I think this page can give you an insight:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions_2fScripts_2fppaulo_2fqdec_2dcoord
2008/5/1 Mishkin Derakhshan [EMAIL PROTECTED]:
Hi,
I know that at some point in the pipeline, the surfaces are registered
to a common sphere, and thus I'm
You have to install XGL lib.
Which distro do you have?
2008/4/27 Lars M. Rimol [EMAIL PROTECTED]:
Hi,
I downloaded the freesurfer-Linux-rh9-stable-pub-v4.0.3-full, and I followed
the instructions on your website
Hi,
In the section Please Cite our Software from the Wiki
(http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/cite.php) we
can find some guidelines to cite FreeSurfer.
In writing material and methods section of the papers we publish I
usually try to describe the FreeSurfer reconstruction
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