[Freesurfer] Doubts regarding maximum thickness

[Pedro Paulo Oliveira Jr]

We are conducting a study and so far have analyzed 40 subjects using
FreeSurfer.

 

We have some doubts regarding cortical thickness:

 

1)  Why the maximum value of cortical thickness in lh.thickness or
rh.thickness is 5.0 mm? We have case in which clearly the thickness is
greater than that in some areas.

2)  In the thickness scale for one individual there are colors for
negative values. We don't see a topological or mathematical sense in
negative thickness, is there any info on that?

3)  We found out that in many cases even in healthy subjects the Insular
cortex area presents 5.0 mm thickness in a great area. We think the
algorithm may face difficulties in this area since its much convoluted. Is
that assumption true?

 

Thanks in advance for the help.

 

Pedro Paulo Oliveira Jr

InRad - HCFMUSP

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RE: [Freesurfer] Switch hemispheres

[Pedro Paulo Oliveira Jr]

I think you can:

rename the lh.* files to xx.* 

rename the rh.* files to lh.*

rename the xx.* files to rh.*

 

 

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Inês Souta
Sent: quinta-feira, 6 de setembro de 2007 12:22
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Switch hemispheres

 

Hi,

After processing the hole image I realized that the orientation of the
original .mgz file was wrong and I've ended up with switched hemispheres.
The right hemisphere is where the left should be, and vice-versa. Otherwise
the orientation is right. Since I've already made manual edits, is the
anyway of switching hemispheres without having to re-process the hole image
again? 

Thanks,

Ines

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RE: [Freesurfer] thickness and curvature

[Pedro Paulo Oliveira Jr]

While we don't have access to de source code it would be interesting that
most of the "tunning" keys are documented.

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Don Hagler
Sent: segunda-feira, 17 de setembro de 2007 04:01
To: [EMAIL PROTECTED]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness and curvature

I looked at the code and found another option for mris_thickness: -N for 
neighborhood size.
For mris_make_surfaces, the default is 20, but for mris_thickness, the 
default is 2.  So setting it to 20 gave the correct result.

>From: "Don Hagler" <[EMAIL PROTECTED]>
>To: [EMAIL PROTECTED]
>CC: freesurfer@nmr.mgh.harvard.edu
>Subject: Re: [Freesurfer] thickness and curvature
>Date: Sun, 16 Sep 2007 23:23:50 -0700
>
>Hi Bruce,
>
>Thanks for the info.
>
>mris_curvature gave me identical results as mris_make_surfaces with 10 
>smoothing steps.
>
>mris_thickness gave slightly different values compared to 
>mris_make_surfaces.  Many vertices were identical, but many were not and 
>some were off by as much as 0.2 mm.
>
>Is there any reason to think that mris_make_surfaces and mris_thickness 
>would have differences in how the thickness measurements are done?  I'm 
>doing this with version 3.0.2 at present.
>
>Don
>
>
>>From: Bruce Fischl <[EMAIL PROTECTED]>
>>To: Don Hagler <[EMAIL PROTECTED]>
>>CC: freesurfer@nmr.mgh.harvard.edu
>>Subject: Re: [Freesurfer] thickness and curvature
>>Date: Sun, 16 Sep 2007 20:44:11 -0400 (EDT)
>>
>>Hi Don,
>>
>>I just added some help to these utilities:
>>
>>./mris_curvature
>>usage: ./mris_curvature [options] 
>>
>>This program will compute the second fundamental form of a cortical 
>>surface.
>>It will create two new files ..H and ..K 
>>with the
>>mean and Gaussian curvature respectively.
>>valid options are:
>>
>> -w   save curvature files (will only generate screen 
>>output without this option)
>> -max save  1st (max) principal curvature in 
>>?h..max file
>> -min save  2nd (min) principal curvature in 
>>?h..min file
>> -a perform  iterative averages of curvature 
>>measure before saving
>>
>>
>>  ./mris_thickness
>>usage: ./mris_thickness [options]   
>>
>>This program measures the thickness of the cortical surface and
>>writes the resulting scalar field into a 'curvature' file >file>.
>>
>>valid options are:
>>
>>-maxuse  to threshold thickness (default=5mm)
>>
>>
>>is there anything else you need? This will be in the next release.
>>
>>Bruce
>>On Sun, 16 Sep 2007, Don Hagler wrote:
>>
>>>I see that mris_make_surfaces is normally used to generate thickness and 
>>>curvature.  I would like to generate the ?h.thickness and ?h.curv files 
>>>without running mris_make_surfaces (I already have white and pial 
>>>surfaces).
>>>
>>>Can mris_thickness and mris_curvature (or other programs) give the same 
>>>results?  Those two programs are not heavily documented, so any help on 
>>>which options to use (to give the same results as mris_make_surfaces) 
>>>would be appreciated.
>>>
>>>_
>>>Kick back and relax with hot games and cool activities at the Messenger 
>>>Café. http://www.cafemessenger.com?ocid=TXT_TAGHM_SeptHMtagline1
>>>___
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>>>Freesurfer@nmr.mgh.harvard.edu
>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>
>_
>A place for moms to take a break! 
>http://www.reallivemoms.com?ocid=TXT_TAGHM&loc=us
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RE: [Freesurfer] pictures from the freesurfer digest

[Pedro Paulo Oliveira Jr]

Digests don't deliver images and attachments.

You can enter:
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Login in the bottom of the page and change your settings from Digest to all
messages. 

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: terça-feira, 18 de setembro de 2007 18:39
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] pictures from the freesurfer digest

Hello all,

I am subscribed to the freesurfer list in digest format. If someone sends 
pictures to the list I am not able to see/open them from the digest or from 
the archives. Is there an option I need to change? Or do I need to switch 
off digest mode completely?

Thanks in advance,

Chris Bell
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Re: [Freesurfer] recon-all in background

[Pedro Paulo Oliveira Jr]

Notice that usually  when ssh disconect for any reason the process stop unless 
you use nohup in csh or disown -a in bash.

Pedro Paulo Oliveira Jr.

-- mens. original --
Assunto:Re: [Freesurfer] recon-all in background
De: Bruce Fischl <[EMAIL PROTECTED]>
Data:   23/09/2007 00:59

of course
On Sat, 22 Sep 2007, Xiangchuan Chen wrote:

> Hi all,
>
> Can I run recon-all in background? The command line looks like this:
>
>ssh node11 "recon-all -autorecon1 -subjid XXX" &
>
> Thanks in advance,
>
> Xiangchuan Chen
>
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>
>
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[Freesurfer] Some methodological questions

[Pedro Paulo Oliveira Jr]

I have some methodological doubts and I think somebody can give a hint.

 

1)  I have read the paper from Neuroimage 2006 comparing Scanner, Field
Strength, etc in thickness measurements.  Is it possible to assume that we
can mix in our study group images that come from different MRI Scanners?

2)  We have some very high resolution histological data of full brain
and correspondent MRI images also acquired post-mortem. Is it possible to
use histological data in FreeSurfer or just SPGR?

3)  Does slice thickness affect group studies. I mean we have some
subjects with slice thickness 0.6mm and other with 0.8mm.

 

Thanks in advance,

 

Pedro Paulo Oliveira Jr.

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RE: [Freesurfer] problems

[Pedro Paulo Oliveira Jr]

1) Yes. mri_convert x249.img 001.mgz
2) It's missing libstd++.so.5. I suggest you run find / -name "libstd*"
-print
If you find a libstd++.so.6 for instance create a libstd++.so.5 as a
symbolic link.
3) It's ok.

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
mgh.harvard.edu] On Behalf Of ???
Sent: quinta-feira, 4 de outubro de 2007 05:30
To: freesurfer
Subject: [Freesurfer] problems

Hi,

  I had downloaded the freesurfer to my  system (Linux Fedora Core 4)
and had completed all the installation procedures.

Question 1:

  I would like to convert analyze format to .mgz. What command line do I
use?

Can I type "mri_convert x249.img 001.mgz "?


Question 2:

  When I type "recon-all -s x249 -nuintensitycor", it doesn't run and
has a error" nu_correct." What would I do to resolve the problem?



Question 3:

  It doesn't find talairach.xfm. What would I do to get the file?

thanks~~


FreeSurfer problem report

-

FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1

RedHat release: Fedora Core release 4 (Stentz)

Kernel info: Linux 2.6.11-1.1369_FC4 i686

-


 1) subject name
 x249
 2) the entire command-line executed

[EMAIL PROTECTED] ~]# ksh
 # tcsh
[EMAIL PROTECTED] ~]# setenv FREESURFER_HOME /usr/local/freesurfer
[EMAIL PROTECTED] ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh

[EMAIL PROTECTED] ~]# cd $SUBJECTS_DIR
[EMAIL PROTECTED] subjects]# cd x249/mri/orig
[EMAIL PROTECTED] orig]# mri_convert x249.img 001.mgz

[EMAIL PROTECTED] mri]# recon-all -s x249 -nuintensitycor

 3) the error message generated

 ERROR: nu_correct


 4) optionally include the subject's /script/recon-all.log


Thu Oct  4 13:38:14 CST 2007
/usr/local/freesurfer/subjects/x249
/usr/local/freesurfer/bin/recon-all
-s x249 -nuintensitycor
subjid x249
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.0.1
Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686
i686 i386 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize10240 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 32 kbytes
maxproc  16383

program versions used
$Id: recon-all,v 1.133.2.5 2007/09/17 16:38:00 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.7 2007/01/06 00:01:14 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion:
$Name: stable4 $  TimeStamp: 2007/10/04-05:38:14-GMT  BuildTimeStamp:
Sep 18 2007 04:54:49  CVS: $Id: mri_convert.c,v 1.146 2007/07/26
19:26:26 greve Exp $  User: root  Machine: cgu.edu.tw  Platform: Linux
 PlatformVersion: 2.6.11-1.1369_FC4  CompilerName: GCC
CompilerVersion: 30400
FLIRT version 5.4.2
$Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $
mri_convert --version
stable4
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info
ProgramVersion: $Name: stable4 $  TimeStamp: 2007/10/04-05:38:14-GMT
BuildTimeStamp: Sep 18 2007 04:54:49  CVS: $Id: tkregister2.c,v
1.86.2.1 2007/08/15 15:39:42 nicks Exp $  User: root  Machine:
cgu.edu.tw  Platform: Linux  PlatformVersion: 2.6.11-1.1369_FC4
CompilerName: GCC  CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED]
(i686-pc-linux-gnu) on 2005-11-15 at 21:02:27
ProgramName: mri_normalize  ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $  TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49  CVS: $Id: mri_normalize.c,v 1.52
2007/01/02 21:34:40 nicks Exp $  User: root  Machine: cgu.edu.tw
Platform: Linux  PlatformVersion: 2.6.11-1.1369_FC4  CompilerName: GCC
 CompilerVersion: 30400
ProgramName: mri_watershed  ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $  TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49  CVS: $Id: mri_watershed.cpp,v
1.67 2007/06/29 13:40:47 fischl Exp $  User: root  Machine: cgu.edu.tw
 Platform: Linux  PlatformVersion: 2.6.11-1.1369_FC4  CompilerName:
GCC  CompilerVersion: 30400
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion:
$Name: stable4 $  TimeStamp: 2007/10/04-05:38:15-GMT  BuildTimeStamp:
Sep 18 2007 04:54:49  CVS: $Id: mri_segment.c,v 1.33 2007/02/14
19:59:27 fischl Exp $  User: root  Machine: cgu.edu.tw  Platform:
Linux  PlatformVersion: 2.6.11-1.1369_FC4  CompilerName: GCC
CompilerVersion: 30400
ProgramName: mri_label2label  ProgramArguments: -all-info
ProgramVersion: $Name: stable4 $  TimeStamp: 2007/10/04-05:38:15-GMT
BuildTimeStamp: Sep 18 2007 04:54:49  CVS: $I

RE: [Freesurfer] TkmEdit message

[Pedro Paulo Oliveira Jr]

Have you installed the X11Update2006 package from Apple?  I think that
fixes this problem.  A copy of it is here:
 

  
http://surfer.nmr.mgh.harvard.edu/pub/dist/X11Update2006.dmg

 

Which OS are you using?

 

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Anil Roy
Sent: quinta-feira, 4 de outubro de 2007 22:17
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TkmEdit message

 

Hi,

When I run tkmedit, I receive the following message. It doesn't seem to
affect the functionality. Could you explain why this message shows up.

Xlib:  extension "XFree86-DRI" missing on display ": 0.0".

Thanks,

Anil.

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RE: [Freesurfer] help on installation under VMWARE + suse 10.2

[Pedro Paulo Oliveira Jr]

I'm not sure VMWare is full OpenGL compliant, other options are Qemu or Xen,
this last one has a better performance. Maybe you should try to use an
exclusive Linux machine.

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Xue,Gui
Sent: quinta-feira, 4 de outubro de 2007 16:22
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] help on installation under VMWARE + suse 10.2

hi-I am trying to install freesurfer my computer with the following 
settings:

Operating system: Win XP
Open Suse10.2 running under vmware workstation 6.0.
Display card: NVIDIA Quadro FX 3400/4400.

The problem I have is that the tksurfer doesn't work well, like what's 
described on the wiki, only small part of the surfer was shown. I 
updated the display card driver, but it didn't fix the problem. I wonder 
if anyone has successfully configure the system to make it work.

Thanks a lot!
gui
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RE: [Freesurfer] Displaying cortical thickness

[Pedro Paulo Oliveira Jr]

Martin,

I'm working on this too. I think you may want to do a group analysis so the
pointer is:
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferGroupAnalysis

The recon-all process should pass step 1, 2 and 3 and not just 3. So you
should run: recon-all -all -s subjid

Also you can use the files: lh.aparc.a2005s.stats and rh.aparc.a2005s.stats
to check cortical thickness. Notice that some areas are thin in controls
also. So it would be better to create a normative base of normal subjects.
Notice also that you can use SPSS or other software with this data.

If you need further help please contact.

Best Regards

Pedro Paulo Oliveira Jr

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Martin Kavec
Sent: segunda-feira, 8 de outubro de 2007 08:38
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Displaying cortical thickness

Hi,

I would really appreciate a help (steps or a link to description) on how to 
display cortical thinning on an inflated surface. I ran a subject through 
recon-all -autorecon3 and now I would basically want to see, where (s)he has

abnormal thickness of the cortex.

Thanks a lot in advance,

Martin
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RE: [Freesurfer] problems

[Pedro Paulo Oliveira Jr]

You can execute:

cd /usr/lib
ln -s libstd++.so.6 libstd++.so.5


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Feng-Xian Yan
Sent: segunda-feira, 8 de outubro de 2007 10:27
To: Pedro Paulo Oliveira Jr
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problems

Hi, Pedro Paulo Oliveira:
   Thank you for your answers. But, I'm a rookie of Linux.
I don't know what do you mean and how to do that for the answer 2?
Can you tell me detail and get me some command lines?
Thank you again.



2007/10/4, Pedro Paulo Oliveira Jr <[EMAIL PROTECTED]>:
> 1) Yes. mri_convert x249.img 001.mgz
> 2) It's missing libstd++.so.5. I suggest you run find / -name "libstd*"
> -print
> If you find a libstd++.so.6 for instance create a libstd++.so.5 as a
> symbolic link.
> 3) It's ok.
>
> -Original Message-
> From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
> mgh.harvard.edu] On Behalf Of ???
> Sent: quinta-feira, 4 de outubro de 2007 05:30
> To: freesurfer
> Subject: [Freesurfer] problems
>
> Hi,
>
>  I had downloaded the freesurfer to my  system (Linux Fedora Core 4)
> and had completed all the installation procedures.
>
> Question 1:
>
>  I would like to convert analyze format to .mgz. What command line do I
> use?
>
> Can I type "mri_convert x249.img 001.mgz "?
>
>
> Question 2:
>
>  When I type "recon-all -s x249 -nuintensitycor", it doesn't run and
> has a error" nu_correct." What would I do to resolve the problem?
>
>
>
> Question 3:
>
>  It doesn't find talairach.xfm. What would I do to get the file?
>
> thanks~~
>
>
> FreeSurfer problem report
>
> -
>
> FREESURFER_HOME: /usr/local/freesurfer
>
> Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1
>
> RedHat release: Fedora Core release 4 (Stentz)
>
> Kernel info: Linux 2.6.11-1.1369_FC4 i686
>
> -
>
>
>  1) subject name
> x249
>  2) the entire command-line executed
>
>[EMAIL PROTECTED] ~]# ksh
> # tcsh
>[EMAIL PROTECTED] ~]# setenv FREESURFER_HOME /usr/local/freesurfer
>[EMAIL PROTECTED] ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh
>
>[EMAIL PROTECTED] ~]# cd $SUBJECTS_DIR
>[EMAIL PROTECTED] subjects]# cd x249/mri/orig
>[EMAIL PROTECTED] orig]# mri_convert x249.img 001.mgz
>
>[EMAIL PROTECTED] mri]# recon-all -s x249 -nuintensitycor
>
>  3) the error message generated
>
> ERROR: nu_correct
>
>
>  4) optionally include the subject's /script/recon-all.log
>
>
> Thu Oct  4 13:38:14 CST 2007
> /usr/local/freesurfer/subjects/x249
> /usr/local/freesurfer/bin/recon-all
> -s x249 -nuintensitycor
> subjid x249
> setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
> FREESURFER_HOME /usr/local/freesurfer
> Actual FREESURFER_HOME /usr/local/freesurfer
> build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.0.1
> Linux cgu.edu.tw 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686
> i686 i386 GNU/Linux
> cputime  unlimited
> filesize unlimited
> datasize unlimited
> stacksize10240 kbytes
> coredumpsize 0 kbytes
> memoryuseunlimited
> vmemoryuse   unlimited
> descriptors  1024
> memorylocked 32 kbytes
> maxproc  16383
> 
> program versions used
> $Id: recon-all,v 1.133.2.5 2007/09/17 16:38:00 nicks Exp $
> $Id: mri_motion_correct.fsl,v 1.7 2007/01/06 00:01:14 nicks Exp $
> mri_convert -all-info
> ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion:
> $Name: stable4 $  TimeStamp: 2007/10/04-05:38:14-GMT  BuildTimeStamp:
> Sep 18 2007 04:54:49  CVS: $Id: mri_convert.c,v 1.146 2007/07/26
> 19:26:26 greve Exp $  User: root  Machine: cgu.edu.tw  Platform: Linux
>  PlatformVersion: 2.6.11-1.1369_FC4  CompilerName: GCC
> CompilerVersion: 30400
> FLIRT version 5.4.2
> $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $
> mri_convert --version
> stable4
> ProgramName: tkregister2_cmdl  ProgramArguments: --all-info
> ProgramVersion: $Name: stable4 $  TimeStamp: 2007/10/04-05:38:14-GMT
> BuildTimeStamp: Sep 18 2007 04:54:49  CVS: $Id: tkregister2.c,v
> 1.86.2.1 2007/08/15 15:39:42 nicks Exp $  User: root  Machine:
> cgu.edu.tw  Platform: Linux  PlatformVersion: 2.6.11-1.1369_FC4
> CompilerName: GCC  CompilerVersion: 30400
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by [EMAIL PROTECTED]
> (i686-pc-linux-gnu

RE: [Freesurfer] hyperthreading

[Pedro Paulo Oliveira Jr]

Brian,

With 2 quad core you have 8 processors. So you can run 8 tasks
simultaneously (only memory is shared.) Notice that each recon-all will need
1GB memory. So for 8 cores you need 8GB Ram at least.

>From the FAQ
"Q: How can I reduce the time of recon-all in a group of patients?
A: FreeSurfer run its process in a non-parallel environment, so you won't
have benefit from a dual core machine for a single case analysis. However if
you have many cases you can start two FreeSurfer recon-all process in the
same machine and theoretically you can reduce by half the time to analyze
your group of cases. A similar procedure can also be used in quad-core
environment. Note that to take benefit of a multi-core environment you need
to use a SMP kernel in your OS."

One Hyperthread core doesn't act as 2 processors.  "The advantages of
Hyper-Threading are listed as: improved support for multi-threaded code,
allowing multiple threads to run simultaneously, improved reaction and
response time." Since FreeSurfer is single threaded AFAIK  you usually won't
get much benefit from running two process in HT.


-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Brian C.
Schweinsburg, Ph.D.
Sent: domingo, 14 de outubro de 2007 21:09
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] hyperthreading

Mike,
I have the two 3 GHz processor quad core mac pro with 12 gb of RAM. I can
run 7 freesurfers simultaneously and they all finish in about 24-28 hours
with FS version 4.x If I only run 7, I have no problem doing word
processing, email, etc. during the recons.

Brian


On 10/14/07 2:36 PM, "Nick Schmansky" <[EMAIL PROTECTED]> wrote:

> Mike,
> 
> I can't say I have benchmarked this myself, but I am guessing there
> would be only a small performance advantage, as memory access would be
> the bottleneck.  I don't know if each HyperThreaded CPU has its own
> memory cache.
> 
> Nick
> 
> 
> On Sat, 2007-10-13 at 21:43 -0500, Michael Harms wrote:
>> Hello,
>> 
>> Question about eking out maximum machine performance:
>> Is there a performance advantage (or alternatively penalty) for running
>> twice as many FreeSurfer jobs (simultaneously) as physical CPUs on a
>> Linux machine with HyperThreading enabled CPUs?  That is, say you have
>> two physical cores with HyperThreading -- the Linux OS treats this as
>> four logical processors.  However, given that Freesurfer is very
>> 'execute' intensive is there any advantage to be gained by running 4
>> rather than 2 FS jobs simultaneously?  Or will the total time per brain
>> with 4 simultaneous jobs be (on average) just twice as long?
>> 
>> thanks,
>> Mike H.
>> 
>> 
> 
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RE: [Freesurfer] Version 4.1 questions

[Pedro Paulo Oliveira Jr]

It´s 4.0.1 or 4.1?

 

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Kt Labadie
Sent: sexta-feira, 19 de outubro de 2007 15:36
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Version 4.1 questions

 

I have 2 questions related to version 4.1.

 

1) The ReconAllDevTable on the Martinos Center Freesurfer Wiki is not
updated to reflect the new steps in version 4.1.Does anyone have a
breakdown of these new steps?  I was not sure of the flags for these new
steps, or where they fit in (are they part of 2-pial, 2-cp or 3?)  Is the
wiki going to be updated to reflect this new version?

 

2) When I load an image in tkmedit (after it has been run all the way
through step 3) I get an error message and it won't load the aseg.  The aseg
is there, I just have to load it manually.  Did the following flag change
with the new version?

 


brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation
mri/aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

 

 

Thanks.

 

KT LaBadie

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RE: [Freesurfer] intrasubject segmentation variance

[Pedro Paulo Oliveira Jr]

Thomas,

 

There are some comments on your question.

 

Freesurfer is not multithreaded so it won't benefit from multicore unless
you start one analysis on each core.

 

Your running times are high. My Opteron usually takes 23 hs to perform the
recon-all in 3.0.5 version of FreeSurfer. One issue that can make the
running time much higher is a poor SPGR/MPRAGE data. Maybe if you send one
slice. Other issue that can raise the time is wrong volume orientation..

 

Best Regards,

 

Pedro Paulo Oliveira Jr

 

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Thomas Doering
Sent: segunda-feira, 22 de outubro de 2007 09:05
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] intrasubject segmentation variance

 

Dear freesurfers,

i was running Freesurfer on the same subject on two independent Computers. 

The first Computer PC1has 2 physical Intel processors with 2 logical each -
(dual core) - 1.6GHz with 4Gb Ram and the second PC2 has 2 physical Intel
processors with 4 logical - (quad core) - 3 GHz with 8 Gb Ram.

After running on these two Computers - i start at the exactly same time - i
got a surprising result: My faster Computer PC2 took 41h to run the subject
and the slower Computer took 31h. 

I wonder if somebody have some comment on this, because i have no idea what
is wrong ( When i have the Linux System Monitor on, watching the CPU
History, it seems that the slower PC hat a more effective occupation/usage
than the faster - switching faster between one CPU and the other one...)

Another small question: 

In the final segmentation table, i noticed that there are some small
diferences between the results of PC1 and PC2: for ex.:

PC1:ctx - rh-caudalmiddle frontal = 5029 5029

PC2:ctx - -"- 5360 5360

, so a diference of ~6%. I guess these are variations due to the algorithm..

Are there some established limits for that diferences?

Thanks for help,

 

Thomas 

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[Freesurfer] Cerebellum Segmentation

[Pedro Paulo Oliveira Jr]

Yesterday I gave a course on FreeSurfer basics + usage for our Radiology
department in São Paulo University.

 

Two questions that I was not able to answer was:

1)  When will the source code of FreeSurfer be released?

2)  Is there some plan to include the cerebellum in the automatic
parcellation/segmentation? I think last question about this in this list was
in 2005.

Thanks

 

Pedro Paulo Jr.

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RE: [Freesurfer] freesurfer help

[Pedro Paulo Oliveira Jr]

Centos 5 uses libstdc++.so.6 

 

You need to create a symbolic link using ln -s

 

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Seth
Elkin-Frankston
Sent: segunda-feira, 29 de outubro de 2007 16:00
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] freesurfer help

 

Hello,

 

I'm running v.4.0.1 on CentOS 5. When attempting to run autorecon1 I receive
the error below. Any help is appreciated.

 

Thanks

Seth Elkin-Frankston

 

 

 



Iteration 1 Mon Oct 29 09:47:59 EDT 2007

nu_correct -clobber ./tmp.mri_nu_correct.mni.8422/nu0.mnc

./tmp.mri_nu_correct.mni.8422/nu1.mnc

[EMAIL PROTECTED]:/usr/local/freesurfer/subjects/Bo

bFS/mri/] [2007-10-29 09:47:59] running:

  /usr/local/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen

0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify

-b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir

/usr/tmp/nu_correct_8477/ ./tmp.mri_nu_correct.mni.8422/nu0.mnc

./tmp.mri_nu_correct.mni.8422/nu1.imp

 

/usr/local/freesurfer//mni/bin/volume_stats: error while loading shared

libraries: libstdc++.so.5: cannot open shared object file: No such file or

directory

nu_estimate_np_and_em: crashed while running volume_stats (termination

status=32512)

nu_correct: crashed while running nu_estimate_np_and_em (termination

status=32512)

ERROR: nu_correct

Linux lr8to10-dhcp-131-112.bumc.bu.edu 2.6.18-8.1.15.el5 #1 SMP Mon Oct 22

08:32:04 EDT 2007 i686 i686 i386 GNU/Linux

 

recon-all exited with ERRORS at Mon Oct 29 09:47:59 EDT 2007

 



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[Freesurfer] Freesurfer FAQ

[Pedro Paulo Oliveira Jr]

Hi,

 

I started the Wiki Page on FreeSurfer FAQ:
http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions_2fFAQ

 

Any corrections and suggestions are welcome! I think we can avoid some
questions to the list if we increase the FAQ.

 

Regards

 

Pedro Paulo Oliveira Jr.

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RE: [Freesurfer] equipment

[Pedro Paulo Oliveira Jr]

Hi,

Reading your e-mail address I noticed that you live in Taiwan, so I can
deduce that it's relatively cheap to you to buy IT products.

With this in mind my suggestion for high performance is:

Use a Quad-Core processor Intel Q6600 
Install at Least 4GB of Memory

If you prefer AMD you can use:
AMD Opteron Quad-Core Barcelona Model 2350 or Model 2347

Other alternative much more expensive is:
http://www.apple.com/macpro/  with 8 cores.

The number of cores is roughly the number of studies you can process
simultaneously. Notice that each process will take 20-24 hs.

Keep in mind that you need to use the fastest memory in order to achieve
maximum benefit from multi-core architecture.

Best Regards

Pedro Paulo Jr

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Feng-Xian Yan
Sent: sexta-feira, 9 de novembro de 2007 06:16
To: freesurfer
Subject: [Freesurfer] equipment

Hi,
   I want to use freesurfer to quantity cortical thickness, and I want
to use the software under Linux fedora core 4. What equipment for
computer do you recommend?
Think you.
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Re: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans

[Pedro Paulo Oliveira Jr]

I'm sure Bruce has much more experience on the subject than me. Also I'm not 
part of Martinos development team.  I'll just add my personal experience: 

1) Your running times seens very high. I never saw 72 hours in my studies. 
Notice that Itanium (and Itanium 2) cpu are far distinct than x86 and x86-64, 
and even running correctly x86 code its performance in fpu falls in my 
experience to 50%. Since FS code is not compiled to Itanium arch I think the 
stated above can explain the problem.

2) Regarding memory my experience is that 1GB usually does fine if you have 
swap space.

3) about 3.0.5 and 4.0.1 differences in running time my data is: 22 hrs vs 31 
hrs average. It depends on the "extended" topological fix 4.0.1 does. 

It would be nice to know your cluster configuration and a sample of your data 
to give you a better advice. 

best regards, 

Pedro Paulo Oliveira Jr.

-- mens. original --
Assunto:Re: [Freesurfer] reprocessing on FS4.0 takes much longer for 
some scans
De: Bruce Fischl <[EMAIL PROTECTED]>
Data:   11/11/2007 21:42

Hi Nicolas,

1. No, sorry, the amount of RAM is sometimes dependent on the 
individual anatomy, and in any case can't be predefine.

2. Not sure about the itaniums. We have no real experience. 72 hours does 
sound pretty long. That's I think about what it used to take on our old 
athlons. Can you extend the time limit?

As for the random stopping of recon-all, we have seen that sometimes as 
well, and are trying to track it down. It seems pretty mysterious, as a 
binary will exit with a nonzero exit code according to the shell even 
though the last printf in the code has been executed and the next statement 
is an exit(0).

Bruce

On 
Mon, 12 Nov 2007, Nicolas Cherbuin wrote:

> Hi,
>
> At the beginning of the year I processed 400 scans on a linux cluster. It had 
> a reported ram limit of 1 Gig but it could cope with the slight excess of FS3 
> and a processing time limit of 48 hours (which was fine for 99% of the 
> scans). Most scans went through autorecon-all without problem.
>
> I am now trying to reprocess the scans with the new version but I am running 
> into a number of problems. On the same linux cluser processing the same 
> scans, some scans (~30%) run without problem. The rest either fail because 
> they exceed the memory limit or because they take much more than 48 hours 
> (the jobs are being killed and the logs report only the left and sometimes 
> part of the right hemisphere being processed).
>
> Since the documentation makes clear that FS works best with 2 Gig of ram, I 
> have switched to an Itinium cluster with 2 Gig ram limit and 48 hours 
> processing time limit. When I compare the logs of the same scans processed on 
> both systems the Itinium cluster seems to take longer and although I am still 
> running tests it appears that for at least some scans autoreconall might take 
> 70+ hours.
>
> Here are my questions:
>
> 1. On the linux cluster can I tell freesurfer not to exceed a certain ram 
> allocation? and if yes how?
>
> 2. Do the problems I have on the Itinium cluster suggest that FS is badly 
> configured on this system? and if yes where should we look? (I don't have 
> access to this system's configuration and I have to feedback to the system 
> managers to fix eventual problems.)
>
> Thank you very much for your help and for sharing these great tools with us.
>
> Nic
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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RE: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans

[Pedro Paulo Oliveira Jr]

one correction: FS does have Itanium version. 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-suse-ia64-stable-pub-v4.0.1-full.tar.gz
 

So my guess for item (1) is check if all code running is for IA64 architecture. 

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Pedro Paulo 
Oliveira Jr
Sent: segunda-feira, 12 de novembro de 2007 06:23
To: Bruce Fischl
Cc: freesurfer@nmr.mgh.harvard.edu; Nicolas Cherbuin
Subject: Re: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans

I'm sure Bruce has much more experience on the subject than me. Also I'm not 
part of Martinos development team.  I'll just add my personal experience: 

1) Your running times seens very high. I never saw 72 hours in my studies. 
Notice that Itanium (and Itanium 2) cpu are far distinct than x86 and x86-64, 
and even running correctly x86 code its performance in fpu falls in my 
experience to 50%. Since FS code is not compiled to Itanium arch I think the 
stated above can explain the problem.

2) Regarding memory my experience is that 1GB usually does fine if you have 
swap space.

3) about 3.0.5 and 4.0.1 differences in running time my data is: 22 hrs vs 31 
hrs average. It depends on the "extended" topological fix 4.0.1 does. 

It would be nice to know your cluster configuration and a sample of your data 
to give you a better advice. 

best regards, 

Pedro Paulo Oliveira Jr.

-- mens. original --
Assunto:Re: [Freesurfer] reprocessing on FS4.0 takes much longer for 
some scans
De: Bruce Fischl <[EMAIL PROTECTED]>
Data:   11/11/2007 21:42

Hi Nicolas,

1. No, sorry, the amount of RAM is sometimes dependent on the 
individual anatomy, and in any case can't be predefine.

2. Not sure about the itaniums. We have no real experience. 72 hours does 
sound pretty long. That's I think about what it used to take on our old 
athlons. Can you extend the time limit?

As for the random stopping of recon-all, we have seen that sometimes as 
well, and are trying to track it down. It seems pretty mysterious, as a 
binary will exit with a nonzero exit code according to the shell even 
though the last printf in the code has been executed and the next statement 
is an exit(0).

Bruce

On 
Mon, 12 Nov 2007, Nicolas Cherbuin wrote:

> Hi,
>
> At the beginning of the year I processed 400 scans on a linux cluster. It had 
> a reported ram limit of 1 Gig but it could cope with the slight excess of FS3 
> and a processing time limit of 48 hours (which was fine for 99% of the 
> scans). Most scans went through autorecon-all without problem.
>
> I am now trying to reprocess the scans with the new version but I am running 
> into a number of problems. On the same linux cluser processing the same 
> scans, some scans (~30%) run without problem. The rest either fail because 
> they exceed the memory limit or because they take much more than 48 hours 
> (the jobs are being killed and the logs report only the left and sometimes 
> part of the right hemisphere being processed).
>
> Since the documentation makes clear that FS works best with 2 Gig of ram, I 
> have switched to an Itinium cluster with 2 Gig ram limit and 48 hours 
> processing time limit. When I compare the logs of the same scans processed on 
> both systems the Itinium cluster seems to take longer and although I am still 
> running tests it appears that for at least some scans autoreconall might take 
> 70+ hours.
>
> Here are my questions:
>
> 1. On the linux cluster can I tell freesurfer not to exceed a certain ram 
> allocation? and if yes how?
>
> 2. Do the problems I have on the Itinium cluster suggest that FS is badly 
> configured on this system? and if yes where should we look? (I don't have 
> access to this system's configuration and I have to feedback to the system 
> managers to fix eventual problems.)
>
> Thank you very much for your help and for sharing these great tools with us.
>
> Nic
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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RE: [Freesurfer] About Gaussian Random Field Theory on fsaverage

[Pedro Paulo Oliveira Jr]

Hi Jorge,

You can make your own fsaverage. In the QDEC wiki page you can find a quick
howto.

Best regards

Pedro Paulo Jr

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of jorge luis
Sent: terça-feira, 20 de novembro de 2007 08:05
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] About Gaussian Random Field Theory on fsaverage

Thank you Bruce and Moo Chung
I will try with those tools

I have another question:

If I want to use GRFT on smooth thickness spms over
the fsaverage subject , should I use the fsaverage
white matter total surface area which is 70394.7 mm2
or the group average surface area which is 86444.7
mm2?

In advance thank you

Jorge 


   
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RE: [Freesurfer] recon-all Flirt Error

[Pedro Paulo Oliveira Jr]

The FSL library or the path to FSL is missing.

regards,

Pedro Paulo Oliveira Jr.

-- mens. original --
Assunto:[Freesurfer] recon-all Flirt Error
De: "Anil Roy" <[EMAIL PROTECTED]>
Data:   26/11/2007 22:38

Hello All,

I wanted to test the Freesurfer installation by running recon-all but I
received an error saying flirt no found. Can someone point me to the cause
of this problem, is it a missing library or some other issue?

I have posted the output from running recon-all on bert below.

Thanks,

Anil.

[EMAIL PROTECTED] freesurfer]# recon-all -s bert -autorecon1
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-rw-1 root root   657949 Aug 18 23:25
/usr/local/freesurfer/subjects/bert/scripts/recon-all.log
Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 i386
GNU/Linux
flirt: Command not found.
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /space/freesurfer/build/pub-releases/freesurfer
#
[EMAIL PROTECTED] MotionCor Mon Nov 26 16:17:47 CST 2007
Found 3 runs
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
#---
/usr/local/freesurfer/subjects/bert


 mri_motion_correct.fsl -o
/usr/local/freesurfer/subjects/bert/mri/rawavg.mgz -wild
/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
/usr/local/freesurfer/subjects/bert/mri/orig/003.mgz


tmpdir is
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009
--
mri_motion_correct.fsl logfile is
/usr/local/freesurfer/subjects/bert/mri/rawavg.mgz.mri_motion_correct.fsl.log
--
-
Converting /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
Mon Nov 26 16:18:28 CST 2007
/usr/local/freesurfer/subjects/bert
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img -odt float
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, -0)
j_ras = (0, 0, -1)
k_ras = (-0, 1, -0)
changing data type from 0 to 3 (noscale = 0)...
writing to
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
1.img...
Analyze Output Matrix
-1.000   0.000  -0.000   134.400;
-0.000   0.000   1.000  -111.000;
-0.000  -1.000  -0.000   129.000;
 0.000   0.000   0.000   1.000;

INFO: set hdr.hist.orient to -1
-
Converting /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
Mon Nov 26 16:18:33 CST 2007
/usr/local/freesurfer/subjects/bert
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img -odt float
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, -0)
j_ras = (0, 0, -1)
k_ras = (-0, 1, -0)
changing data type from 0 to 3 (noscale = 0)...
writing to
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img...
Analyze Output Matrix
-1.000   0.000  -0.000   134.400;
-0.000   0.000   1.000  -111.000;
-0.000  -1.000  -0.000   129.000;
 0.000   0.000   0.000   1.000;

INFO: set hdr.hist.orient to -1
-
Converting /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
Mon Nov 26 16:18:40 CST 2007
/usr/local/freesurfer/subjects/bert
mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
3.img -odt float
$Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $
reading from /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -0, -0)
j_ras = (0, 0, -1)
k_ras = (-0, 1, -0)
changing data type from 0 to 3 (noscale = 0)...
writing to
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
3.img...
Analyze Output Matrix
-1.000   0.000  -0.000   134.400;
-0.000   0.000   1.000  -111.000;
-0.000  -1.000  -0.000   129.000;
 0.000   0.000   0.000   1.000;

INFO: set hdr.hist.orient to -1
-
Motion Correcting
/usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor-
2.img
Mon Nov 26 16:18:45 CST 2007
/usr/local/freesurfer/subjects/bert
fsl_rigid_register

[Freesurfer] ENC: Re: Optimizing FreeSurfer

[Pedro Paulo Oliveira Jr]

Hello,

I have a couple of questions, not so technical.  
 
 A)In your opinion what would be the best measure for comparing number of 
neurons among subjects: Average cortical thickness or Volume of White matter.

B) Automatic parcelation and atlas based segmentation is a valid
approach for patients with severe cortical malformation?

Thanks in advance for your help.

Best Regards

Pedro Paulo Jr.

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[Freesurfer] Two questions regarding Matlab

[Pedro Paulo Oliveira Jr]

Sorry for the stupid questions, I promise to put it on the FAQ after the
answers:

 

1)  Is it possible to use Octave instead Matlab for curv files?

2)  Given a Talairach coordinate how can I get the thickness value in
Matlab?

Thanks in advance

 

Pedro Paulo Jr

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Re: [Freesurfer] Regarding QDEC Figure

[Pedro Paulo Oliveira Jr]

I can dig into the code, but do you know how qdec extract the values to that 
graph?

thanks,

Pedro Paulo
on E61

-- mens. original --
Assunto:Re: [Freesurfer] Regarding QDEC Figure
De: Bruce Fischl <[EMAIL PROTECTED]>
Data:   20/12/2007 20:44

Hi Pedro,

the mapping from tal to surface isn't well defined as there will be many 
tal coords that are not on the surface. You could find the closest point 
on the surface to a given coord, but many coords will have the same 
closest point

cheers,
Bruce

On Thu, 20 Dec 2007 [EMAIL PROTECTED] wrote:

> In the attached figure:
>
> The numbers (-28.25, -12.73, -0.57) refer to fsaverage. How can I export
> the Thickness values of the subjects for this cordinates?
>
> The numbers (-28.25, -12.73, -0.57) are in Talairach space?
>
> Thanks,
>
> PPJ

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RE: [Freesurfer] Regarding QDEC Figure

[Pedro Paulo Oliveira Jr]

Hi,

I was wondering in creating another version of mri_glm with some other kind
of tests. Do you think this is useful/feasible?

Best Regards,

PPJ

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bruce Fischl
Sent: quinta-feira, 20 de dezembro de 2007 18:42
To: [EMAIL PROTECTED]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Regarding QDEC Figure

Hi Pedro,

the mapping from tal to surface isn't well defined as there will be many 
tal coords that are not on the surface. You could find the closest point 
on the surface to a given coord, but many coords will have the same 
closest point

cheers,
Bruce

On Thu, 20 Dec 2007 [EMAIL PROTECTED] wrote:

> In the attached figure:
>
> The numbers (-28.25, -12.73, -0.57) refer to fsaverage. How can I export
> the Thickness values of the subjects for this cordinates?
>
> The numbers (-28.25, -12.73, -0.57) are in Talairach space?
>
> Thanks,
>
> PPJ
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RE: [Freesurfer] where is the patient information in the mgz files

[Pedro Paulo Oliveira Jr]

Hello Wang,

 

I don't think MGZ store all Dicom data.

 

I'll look into the source code and tell you.

 

Regards

 

Pedro Paulo Jr

 

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Wang, Xin
Sent: domingo, 23 de dezembro de 2007 18:34
To: freesurfer
Subject: [Freesurfer] where is the patient information in the mgz files

 

Hello, Group,

 

I have a problem to read patient information in the .mgz files. this
information was stored in the header files of dicom files. Could sb. tell me
how to read this information from the .mgz files?

Thank you in advance,

 

Xin Wang 

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RE: [Freesurfer] recon-all times

[Pedro Paulo Oliveira Jr]

Suggestion:

 

Include if possible:

 

HD type (SCSI,SATA,IDE)

Chipset (Intel, VIA, SIS, NVidia)

 

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Thomas Doering
Sent: terça-feira, 15 de janeiro de 2008 09:50
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all times

 

Dear freesurfers,

 

as a suggestion of Mishkin, i would like to expand the freesurfer wiki page
and add some infos about typical reconstruction times of freesurfer.

For this reason, i would like to ask everybody to write me a message
including following informations of your computer:

ex:

  CPU-MODEL:   2 x Intel(R) Xeon(R) CPU X5355


  CPU-FREQ:   2.66GHz 

RAM:   16GB 

 FREESURFER-VERSION TIME:
freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.1

TIME:   20.5 h

 

Thanks in advance for your contribution,

 

Thomas

 

 

 

 

 

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RE: [Freesurfer] FreeSurfer on SUN Linux machines

[Pedro Paulo Oliveira Jr]

Solaris is another OS distinct from Linux.
Freesurfer 4.0 won't run

Pedro Paulo
on E61

-- mens. original --
Assunto:RE: [Freesurfer] FreeSurfer on SUN Linux machines
De: "Iman Aganj" <[EMAIL PROTECTED]>
Data:   18/01/2008 19:28

Dear Nick,

I think it is Solaris. Tcsh is installed, and I am not quite sure about the
processor.

Thanks,
Iman

-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED] 
Sent: Thursday, January 17, 2008 9:49 PM
To: Iman Aganj
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer on SUN Linux machines

Iman,

What OS is installed on the system?  What processor does it use?  Do all
the freesurfer commands give that error?  Is tcsh installed?

Nick


> Hello everybody,
>
>
>
> I am trying to install FreeSurfer on SUN Linux machines, and I am not sure
> which platform to choose. I have already tried CentOS 4, but when I try
> for
> example "tkmedit bert orig.mgz", I get the Invalid argument error. I will
> appreciate any help.
>
>
>
> Thanks a lot.
>
>
>
> Best,
>
> Iman
>
>
>
> ___
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RE: [Freesurfer] Problem: 'source'

[Pedro Paulo Oliveira Jr]

Henrique.

Are you sure that freesurfer is at /Applications/freesurfer?

Execute ls -l /Applications/freesurfer

Regards

PPJ

-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Henrique
Fernandes
Sent: terça-feira, 19 de fevereiro de 2008 08:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Problem: 'source'

Dear collegues,


I had a problem during the installation of Freesurfer on my computer.
I have a Mac Intel, and since the shell I'm using is the bash, I've  
entered those two lines written in the installation instructions:

export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

The problem is that when I wrote the second line I received an error  
message like the one above:

bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
bash: /Applications/freesurfer/SetUpFreeSurfer.sh: No such file or  
directory

What would you recommend me to do? I would prefer to continue the  
installation only after solving this problem, since it is recommended  
by you to "perform the setup described at this point in the time".


Hope you can solve my problem, and I'll be able to use your program  
very soon,


Best regards,


Henrique Fernandes
_
Researcher in Medical Imaging
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RE: [Freesurfer] Mac Pro Benchmark

[Pedro Paulo Oliveira Jr]

You won't gain 8 times in one analysis. But you can run 8 analysis in
roughly the same time you would do one.

 

From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Dabbs (Kevin)
Sent: quinta-feira, 21 de fevereiro de 2008 13:43
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Mac Pro Benchmark

 

 

Been running Freesurfer on Linux 2.0 GHz machines.  I like the results but
need to increase through-put for a 500 subject run.  Got the money for a Mac
Pro with 8 cores and 16 GB ram.  Is it likely that I will get an eight times
gain in through-put?  Just need some kind of benchmark to determine a
reasonable schedule for this job.

Thanks for any comments;
Kevin Dabbs
Dept. Neurology
Univ. Wisconsin-Madison
  

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[Freesurfer] Freesurfer Citation in Paper

[Pedro Paulo Oliveira Jr]

Is correct the statement below?

FreeSurfer implementation of cortical surface-based analysis is distinct
from other surface-based algorithms and conventional volume based
morphometry with atlas mapping, as it does not necessarily depend on
smoothing or matching to an atlas.

Thanks in advance,

Pedro Paulo Jr

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RE: [Freesurfer] statistics in aparc.stats

[Pedro Paulo Oliveira Jr]

Aaron,

My opinion is that you are right, but maybe the folding index should be taken 
into account.

When we reach a conclusion about this I think is a good question to put in the 
faq.

best regards,

Pedro Paulo
on E61

-- mens. original --
Assunto:[Freesurfer] statistics in aparc.stats
De: "Goldman, Aaron (NIH/NIMH) [C]" <[EMAIL PROTECTED]>
Data:   28/02/2008 22:23

Hi, I just had a question regarding the statistics in ?h.aparc.stats.
I'm interested in calculating average thicknesses for several labels
combined, and wanted to verify how to do that correctly. The way the
stat files are calculated, would it be valid to simply take an average
of the listed average thicknesses, weighted by the listed surface areas?

Thanks,

-Aaron-

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[Freesurfer] Error on Spline Cubic Set

[Pedro Paulo Oliveira Jr]

Anyone can shed a light? FS 4.0.2 i386 CentOS

 

Fri Mar 21 20:11:45 EDT 2008

talairach_avi done

#

[EMAIL PROTECTED] Talairach Failure Detection Fri Mar 21 20:11:46 EDT 2008

/b/03/netfi01/freesurfer/subjects/neliseoliveira/mri

 

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

 

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2855,
pval=0.0254 >= threshold=0.0050)

 

 awk -f /b/03/netfi01/freesurfer/bin/extract_talairach_avi_QA.awk
/b/03/netfi01/freesurfer/subjects/neliseoliveira/mri/transforms/talairach_av
i.log

 

TalAviQA: 0.97187

z-score: -1

#

[EMAIL PROTECTED] Intensity Normalization Fri Mar 21 20:11:46 EDT 2008

/b/03/netfi01/freesurfer/subjects/neliseoliveira/mri

 

 mri_normalize -g 1 nu.mgz T1.mgz

 

using max gradient = 1.000

reading from nu.mgz...

normalizing image...

talairach transform

 1.157   0.025  -0.069  -0.036;

 0.081   0.971   0.642   1.728;

 0.091  -0.685   1.159  -15.320;

 0.000   0.000   0.000   1.000;

INFO: Modifying talairach volume c_(r,a,s) based on average_305

 

SPLINE_CUBIC_SET - Fatal error!

  The number of data points N must be at least 2.

  The input value is 1.

Linux n122128 2.6.18-1.2798.fc6 #1 SMP Mon Oct 16 14:54:20 EDT 2006 i686
athlon i386 GNU/Linux

 

recon-all exited with ERRORS at Fri Mar 21 20:11:51 EDT 2008

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[Freesurfer] libXmu error on cluster

[Pedro Paulo Oliveira Jr]

Hi,

 

I ran 40 process and all finished with 

 

/b/03/netfi01/freesurfer/subjects/rodiguespierinam/scripts/recon-all.log:mri
s_volmask.bin: error while loading shared libraries: libXmu.so.6: cannot
open shared object file: No such file or directory

 

But in /usr/lib there is a libXmu.so.6

 

My questions are:

 

1)  Anybody know why it failed?

2)  If I fix this how can I run recon-all from this point?

 

Thanks

 

PPJ

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RE: [Freesurfer] libXmu error on cluster

[Pedro Paulo Oliveira Jr]

Nick,

 Thanks for the hint. I already solved the problem.

 We are testing a Cluster-on demand, pay-per-hour-used service in US and
seems pretty good. I ran 100 recon-all in 33 hours!!!

 When I finish my tests I'll send a message to the list indicating this
service.

PPJ

-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED] 
Sent: segunda-feira, 24 de março de 2008 12:53
To: Pedro Paulo Oliveira Jr
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] libXmu error on cluster

Pedro,

You have encountered the achilles heel of freesurfer running on a
cluster.  clusters often don't have the X-Windows libs (like libXmu)
installed, because they dont need them.  But mris_volmask is the one
binary in the recon-all stream that is built against VTK, and VTK builds
against X-Windows (at least on Linux, and our default distribution).
I'd like to eliminate this dependency, but haven't had the time.

You have three options:

 1) copy the necessary X libs to your cluster (run ldd mris_volmask.bin
to see them).

 2) or use the -nocortribbon flag to skip that step (no downstream steps
depend on the ?h.ribbon.mgz files)

 3) or build freesurfer from source, based on a VTK which is built
without an X Windows dependency.

Nick




On Sat, 2008-03-22 at 22:51 -0300, Pedro Paulo Oliveira Jr wrote:
> Hi,
> 
>  
> 
> I ran 40 process and all finished with 
> 
>  
> 
> /b/03/netfi01/freesurfer/subjects/rodiguespierinam/scripts/recon-
> all.log:mris_volmask.bin: error while loading shared libraries:
> libXmu.so.6: cannot open shared object file: No such file or directory
> 
>  
> 
> But in /usr/lib there is a libXmu.so.6
> 
>  
> 
> My questions are:
> 
>  
> 
> 1) Anybody know why it failed?
> 
> 2) If I fix this how can I run recon-all from this point?
> 
>  
> 
> Thanks
> 
>  
> 
> PPJ
> 
> 
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RE: [Freesurfer] Cluster on Demand

[Pedro Paulo Oliveira Jr]

Yes. That was the value. But it was waived because I requested a trial.

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of U. Hasson
Sent: quarta-feira, 26 de março de 2008 13:08
To: Pedro Paulo Oliveira Jr
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] Cluster on Demand

You might consider applying for a (free) Teragrid account with which
you can relatively easily obtain  30 thousand CPU hours in a
Development Allocation. We're using a few allocations for neuroimaging
analysis workflows including FreeSurfer.  Just to understand, would
they have charged you 33*100*0.75 ($2475) dollars for this?

See:
http://www.teragrid.org/userinfo/getting_started.php


On Wed, Mar 26, 2008 at 10:33 AM, Pedro Paulo Oliveira Jr
<[EMAIL PROTECTED]> wrote:
>
>
>
>
> Dear Freesurfers
>
>
>
> I was testing a Cluster-on demand, pay-per-hour-used service US based and
it
> seems pretty good. I ran 100 recon-all in 33 hours!!!
>
>
>
> The cost of one hour of CPU is USD 0.77
>
>
>
> The quote I received is a package of 200.000 hours / month with an hour
> priced as USD 0.25 cents
>
>
>
> This figure represents 5500 Freesurfer recon-all per month.
>
> If many people in the list are interested in sharing the expenses I think
it
> would be a quick way to process tons of brains.
>
>
>
> The info I received is that this cluster is based in Florida and have 300
> cpus
>
>
>
> Hope this helps,
>
>
>
> PPJ
>
>
>
>
>
>
> ___
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>


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RE: [Freesurfer] Cluster on Demand

[Pedro Paulo Oliveira Jr]

Hi,

I entered Teragrid web and I saw this info:

" To qualify for an award, the principal investigator (PI) must be a
researcher or educator at a U.S. academic or non-profit research
institution. A qualified advisor may apply for an allocation for his or her
class, but a high school, undergraduate or graduate student may not be a PI.
A postdoctoral researcher can also be a PI. (After receiving an award, PIs
can request that students be granted accounts to use the PI’s allocation.)

In general, TeraGrids follow the guidelines outlined in the current NSF
Grant Proposal Guide. However, investigators with support from any funding
source, not just NSF, are encouraged to apply. If your institution is not a
university or a 2- or 4-year college, special rules may apply. Contact
[EMAIL PROTECTED] for details."

Since I'm outside US I believe I'm not elegible. Is that right?

Tks

PPJ

-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of U. Hasson
Sent: quarta-feira, 26 de março de 2008 13:08
To: Pedro Paulo Oliveira Jr
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] Cluster on Demand

You might consider applying for a (free) Teragrid account with which
you can relatively easily obtain  30 thousand CPU hours in a
Development Allocation. We're using a few allocations for neuroimaging
analysis workflows including FreeSurfer.  Just to understand, would
they have charged you 33*100*0.75 ($2475) dollars for this?

See:
http://www.teragrid.org/userinfo/getting_started.php


On Wed, Mar 26, 2008 at 10:33 AM, Pedro Paulo Oliveira Jr
<[EMAIL PROTECTED]> wrote:
>
>
>
>
> Dear Freesurfers
>
>
>
> I was testing a Cluster-on demand, pay-per-hour-used service US based and
it
> seems pretty good. I ran 100 recon-all in 33 hours!!!
>
>
>
> The cost of one hour of CPU is USD 0.77
>
>
>
> The quote I received is a package of 200.000 hours / month with an hour
> priced as USD 0.25 cents
>
>
>
> This figure represents 5500 Freesurfer recon-all per month.
>
> If many people in the list are interested in sharing the expenses I think
it
> would be a quick way to process tons of brains.
>
>
>
> The info I received is that this cluster is based in Florida and have 300
> cpus
>
>
>
> Hope this helps,
>
>
>
> PPJ
>
>
>
>
>
>
> ___
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