RE: [Freesurfer] Cluster on Demand

hat 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 (fr

RE: [Freesurfer] Cluster on Demand

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

RE: [Freesurfer] libXmu error on cluster

ssage- 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. clu

[Freesurfer] libXmu error on cluster

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

[Freesurfer] Error on Spline Cubic Set

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

RE: [Freesurfer] statistics in aparc.stats

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

[Freesurfer] Freesurfer Citation in Paper

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, Pe

RE: [Freesurfer] Mac Pro Benchmark

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] M

RE: [Freesurfer] Problem: 'source'

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

RE: [Freesurfer] FreeSurfer on SUN Linux machines

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 insta

RE: [Freesurfer] recon-all times

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 tim

RE: [Freesurfer] where is the patient information in the mgz files

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

RE: [Freesurfer] Regarding QDEC Figure

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:

Re: [Freesurfer] Regarding QDEC Figure

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 t

[Freesurfer] Two questions regarding Matlab

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 ___

[Freesurfer] ENC: Re: Optimizing FreeSurfer

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

RE: [Freesurfer] recon-all Flirt Error

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 install

RE: [Freesurfer] About Gaussian Random Field Theory on fsaverage

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.ha

RE: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans

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 o

Re: [Freesurfer] reprocessing on FS4.0 takes much longer for some scans

pace. 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 Pa

RE: [Freesurfer] equipment

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:

[Freesurfer] Freesurfer FAQ

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

RE: [Freesurfer] freesurfer help

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 Hell

[Freesurfer] Cerebellum Segmentation

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 parc

RE: [Freesurfer] intrasubject segmentation variance

. 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

RE: [Freesurfer] Version 4.1 questions

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 o

RE: [Freesurfer] hyperthreading

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 r

RE: [Freesurfer] problems

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

RE: [Freesurfer] Displaying cortical thickness

lease 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 H

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

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 ou

RE: [Freesurfer] TkmEdit message

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]

RE: [Freesurfer] problems

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.harva

[Freesurfer] Some methodological questions

thickness 0.6mm and other with 0.8mm. Thanks in advance, Pedro Paulo Oliveira Jr. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all in background

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: 23/09/2

RE: [Freesurfer] pictures from the freesurfer digest

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

RE: [Freesurfer] thickness and curvature

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: free

RE: [Freesurfer] Switch hemispheres

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] Sw

[Freesurfer] Doubts regarding maximum thickness

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 ___ Freesurfer mailing