Re: [Freesurfer] fsaverage triangle mesh data

take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br

Re: [Freesurfer] Recon-all in 7 hours

Richard, In FreeSurfer 5.1 can we expect to have CUDA support on OSX? thanks PPJ - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http

[Freesurfer] Recon-all in 7 hours

in one day if you can afford it :) cheers PPJ - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

[Freesurfer] GPU CUDA on Snow Leopard

Is there a plan to release the FreeSurfer CUDA Binaries for Snow Leopard? Thanks PPJ - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http

Re: [Freesurfer] A question about VirtualBox version of FreeSurfer Ver 5.0

I think version 5.0 VDI was generated by Krish. You should check how he attached the VDI disk to Ubuntu (Sata, IDE, etc..) - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom

Re: [Freesurfer] longitudinal processing

Hi Bruce, What's the ETA for 5.1? thanks - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Mon, Oct 18

Re: [Freesurfer] password for windows ubuntu to share folders:

It's in the README As far as I remember is brain2009 - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

Re: [Freesurfer] memory needed to run a freesurfer stream

- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Thu, Oct 7, 2010 at 13:06, Allison Stevens astev...@nmr.mgh.harvard.eduwrote: Nathan, You can find

[Freesurfer] pericalcarine cortex - subdivision

Jr - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile ___ Freesurfer

Re: [Freesurfer] pericalcarine cortex - subdivision

. Or you could draw it in fsaverage and just map the labels to your subjects. Calcarine aligns so well that this method would probably be fine On Fri, 24 Sep 2010, Douglas N Greve wrote: will mris_divide_parcellation do the trick? Pedro Paulo de Magalhães Oliveira Junior wrote: I have a fMRI

[Freesurfer] iPhone and IPad FreeSurfer based atlas

are welcome. Cheers Pedro Paulo Jr. -- via iPhone iOS4 - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

Re: [Freesurfer] iPhone and IPad FreeSurfer based atlas

http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8 The download link for United States -- via iPhone iOS4 Em 22/09/2010, às 20:50, Nick Schmansky ni...@nmr.mgh.harvard.edu escreveu: On Wed, 2010-09-22 at 19:17 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote: More news

Re: [Freesurfer] RAM question

Wow. I think you are in a dangerous direction. FreeSurfer will work in PPC only in older MacOSX version. The 4GB will not help you so much. I would suggest a new computer. - Pedro Paulo de Magalhães Oliveira Junior Diretor de

Re: [Freesurfer] Notes on CUDA Acceleration

Jacek, A 465 will do well, try to grab as much memory as possible in de video board. AFAIK, FreeSurfer will return to compute capabilities 1.1 so you won't need a fermi architeture. cheers - Pedro Paulo de Magalhães Oliveira

[Freesurfer] iPhone and IPad FreeSurfer based atlas

Some weeks ago Bruce announced the first version of the free brain atlas app for IPhone using FreeSurfer aseg. Today we have a major upgrade and now the app has a native IPad interface. Also Bruce provided high resolution mri segmented so IPhone and IPod touch users will benefit too

Re: [Freesurfer] CUDA error

Hi. The 8500GT has CUDA compute capabilities 1.1 so probably it won't work for now. - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http

Re: [Freesurfer] CUDA Error in file '/space/freesurfer/build/minerva/stable/dev/include/volumegpu_impl.hpp'

8500GT is Cuda Compute Capability 1.1 (It won't probably work in this version of FreeSurfer) - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http

Re: [Freesurfer] program error: Exec format error. Wrong Architecture

Maybe you are using the 32bit version in a 64bit Linux or vice versa -- via iPhone iOS4 Em 23/08/2010, às 14:17, Prisciandaro, James J prisc...@musc.edu escreveu: Hello list, I recently installed freesurfer on a dell laptop running centos 5.5. After installing successfully, I ran the

Re: [Freesurfer] program error: Exec format error. Wrong Architecture

? - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile 2010/8/23 Prisciandaro, James J prisc...@musc.edu Thanks for your reply. Probably just a reflection of my ignorance, but when I

Re: [Freesurfer] how to expand the disk size if I use VirtualBoxFS45

you can use the Virtual Disk Manager GUI from Virtual Box's File menu - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br

Re: [Freesurfer] CUDA vs. ATI Stream / OpenCL

CUDA won't work on ATI. - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Sun, Aug 22, 2010 at 19:04

Re: [Freesurfer] CUDA vs. ATI Stream / OpenCL

know, but will Freesurfer support ATI Stream and maybe OpenCL in the near future? OpenCL should be something that could run both on ATI and Nvidia GPUs. And then again, is it a good idea to invest money in Nvidia Tesla cards? Cheers, Georg *Von:* Pedro Paulo de Magalhães Oliveira Junior

Re: [Freesurfer] how to expand the disk size if I use VirtualBoxFS45

You can create another virtual disk and attach to your virtual machine -- via iPhone iOS4 Em 22/08/2010, às 16:16, Guang Zeng freesurfer...@hotmail.com escreveu: Hi, there, I am using VirtualBoxFS45 now, everything is fine. But I find that after I load the FSVirtualBox.vdi, the default

Re: [Freesurfer] FreeSurferAlpha Label Volumes

FreeSurferAlpha? Is this a new product? On Fri, Aug 20, 2010 at 15:08, Mona m...@nmr.mgh.harvard.edu wrote: Hello, I'd like to extract hippocampal and PHC volumes from files reconstructed with FreeSurferAlpha. Is there a command for this or would you recommend re-reconstructing to obtain

Re: [Freesurfer] CUDA installation error...

Try running one of CUDA samples from: http://developer.nvidia.com/object/gpucomputing.html I think you have to enable *restricted drivers* at Ubuntu Control Panel and Reboot - Pedro Paulo de Magalhães Oliveira Junior Diretor de

Re: [Freesurfer] CUDA Error - all CUDA-capable devices are busy or unavailable

de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Thu, Aug 19, 2010 at 13:57, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: hello cuda beta users! this problem 'all CUDA-capable devices

Re: [Freesurfer] Curvature of the Corpus Callosum

It's almost flat. So the radius is very large. - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Mon, Aug

Re: [Freesurfer] hippocampus volume

In the aging process there's overall cortical atrophy. Other papers like ours shows that too: https://surfer.nmr.mgh.harvard.edu/pub/articles/Oliveira_JAD2010.pdf Cheers - Pedro Paulo de Magalhães Oliveira Junior Diretor de

Re: [Freesurfer] creation of special image...

You can edit the .thickness files to use this hack. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Thu, Aug 5, 2010 at 12:40

Re: [Freesurfer] creation of special image...

:) - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Thu, Aug 5, 2010 at 12:51, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: the easiest would be to draw a label on the inflated

Re: [Freesurfer] creation of special image...

It's not the same. As you can see in Doug's image the smile is hidden by the sulci and it shows up when you inflate the surface. - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom

[Freesurfer] Exporting FreeSurfer surfaces to Blender

Hi, I just added a quick tutorial on how-to export FreeSurfer surfaces and use it as a render object for Blender http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel If someone has other tutorials I think you can use this new section of User Contributions:

Re: [Freesurfer] cortical thickness more than 5 milimeters...

This answer is in the FAQ: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.3AItseemsthatthereisa5mmthicknessupperlimitinmyvolumes.2Cisitnormal.3FHowcanIchangethis.3F

Re: [Freesurfer] Any update on releasing the source for FreeSurfer?

Nick, the 5.0 will be non-clinical? -- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile On Tue, Jul 6, 2010 at 16:05, Nick Schmansky

Re: [Freesurfer] heterotopias

Hi Jenifer Although this paper (Cortical thickness reduction of normal appearing cortex in patients with polymicrogyriahttps://surfer.nmr.mgh.harvard.edu/pub/articles/corticalPedroSep08.pdf) is about Polymicrogyria we had plenty of cases of heterotopias and other malformations of cortical

Re: [Freesurfer] Serious failure of surface reconstruction

I guess you should send to the mailing list your recon-all.log -- Sent via iPhone iOS4 Em 25/06/2010, às 05:40, Cindy Eckart cindy.eck...@web.de escreveu: My last email seemed to be too big because of the picture, so I try it without the picture Dear FreeSurfers, after having now

Re: [Freesurfer] computer shut down

Now we entered this in the FAQ: Q. I had a [Power Outage|Computer Failure|Spilled coffee on computer|etc], how can I resume the

Re: [Freesurfer] Across Scanner Comparisons

It's hard to know without the info about scanner type (Manufacturer/Field/Sequence) and FreeSurfer version. I usually see 3-5% difference in measurements. Phillips 3T with common fSPGR. -- Pedro Paulo de M. Oliveira Junior Diretor de

Re: [Freesurfer] Across Scanner Comparisons

With distinct fields/gradients and FS 4.01 I think you can have quite distinct results. My guess: 10% difference. Bruce can give you a more accurate figure. At http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes notice: -norandomness is the the default. The binaries in the recon-all stream

Re: [Freesurfer] retinotopy: MGH vs UCSD

what do you mean by Old FreeSurfer? -- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile On Wed, Jun 9, 2010 at 17:44, francesca strappini

Re: [Freesurfer] version number

try: recon-all -version http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ -- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile On Fri, May

Re: [Freesurfer] Subcortical segmentation

Martin, In my experience I never found any problem in aseg.mgz cheers PPJ -- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile On Thu, May 13, 2010 at

Re: [Freesurfer] Thickness values for every vertex

*Use the 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* Ref: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011618.html You can make search in previous answers of the

Re: [Freesurfer] CUDAEnabling for FreeSurfer 4.5.0

Hi This wiki page is for internal development. The FreeSurfer version that will have a partial support for CUDA is the upcoming 5.0 cheers PPJ On Tuesday, April 20, 2010, wen miao mwinv...@gmail.com wrote: Hello Freesurfer experts. I'm recently woking on CUDA 

Re: [Freesurfer] CUDAEnabling for FreeSurfer 4.5.0

) have work it out perfectly. I just can't wait to try. 2010/4/20 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Hi This wiki page is for internal development. The FreeSurfer version that will have a partial support for CUDA is the upcoming 5.0 cheers PPJ On Tuesday, April

Re: [Freesurfer] Processing of brains with malformations of cortical development

Take a look at this paper of our group: https://surfer.nmr.mgh.harvard.edu/pub/articles/corticalPedroSep08.pdf --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.4

Re: [Freesurfer] Processing of brains with malformations of cortical development

Em 9 de abril de 2010 15:58, Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br escreveu: Take a look at this paper of our group: https://surfer.nmr.mgh.harvard.edu/pub/articles/corticalPedroSep08.pdf --- Pedro Paulo de M

Re: [Freesurfer] extract thickness values for vertex

Maybe I need to change that script. How do you usually run you glmfit analysis? 2010/3/24, Prapti Gautam prapti.gau...@anu.edu.au: Dear FreeSurfers, Is there a way to extract thickness values for individual subjects for a vertex that are obtained after analyses with mri_glmfit? I have seen

Re: [Freesurfer] extract thickness values for vertex

couldn't get the script to run either with qdec or mri_glmfit output directory, so figured it must be a permission issue with fsaverage? -Original Message- From: Pedro Paulo de Magalhães Oliveira Junior [mailto: p...@netfilter.com.br] Sent: Wed 3/24/2010 7:27 PM To: Prapti

Re: [Freesurfer] Performance on brains with tumors

I think the results may be quite unpredictable. It depends on the size of the tumor, the infiltration, the necrosis, etc. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.4

Re: [Freesurfer] Measuring Cortical Volume

You said FS 3.0.5? Probably you should upgrade to current version. Cheers 2010/2/13, Jeff Sadino jsadino.que...@gmail.com: Hello, I want to measure the volume of my groups' cortex, n=139, mostly males. I am using fs 3.0.5. From the aseg.stats file, lh + rh white matter is 548,000 and gray

[Freesurfer] RES: Re: how to QC hippocampal measurement

In our AD paper (Journal of Alzheimer's disease) has some standard values for AD and non-demented -- @mobile -Msg original- De: Nick Schmansky Enviado: 04/02/2010 17:07:02 Para: Guang Zeng Cc: freesurfer@nmr.mgh.harvard.edu Assunto: Re: [Freesurfer] how to QC hippocampal measurement a

[Freesurfer] ANN - SVM, Alzheimer's Disease and FreeSurfer

Hi, We have published another paper using FreeSurfer, maybe you can add it to the Article page in the Wiki http://iospress.metapress.com/content/r1533322r7481q35/?p=2cecbdd44e114a5fbff200e3feee3ad0pi=12

Re: [Freesurfer] bbregister: 6 or 12 DOF ?...

Is there some feature like the fast fluid registration in the dev pipeline? --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

Re: [Freesurfer] Ubuntu FreeSurf VirtualBox root password

The password is in the README file. I think it's brain2009 cheers --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

[Freesurfer] RES: How can I install freesurfer for Windows(XP, 32bit)?

In the dowload section there's a version for Virtualbox Use it with Virtualbox for Windows Enviado do meu celular Nokia -Msg original- De: So-young Choe Enviado: 29/12/2009 00:35:01 Para: freesurfer@nmr.mgh.harvard.edu Assunto: [Freesurfer] How can I install freesurfer for

Re: [Freesurfer] colin27 skullstrip problem

Also the ch2 dataset that comes with MRICro suffers from the same problem. It's the averaging of several acquisition from one brain. Is it possible to infer that too many acquisitions is worse than one acquisition? -- PPJ 2009/11/30 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Mishkin, yes,

Re: [Freesurfer] problems on virtual machine

The password is brain2009 2009/11/27 liyari5018 liyari5...@163.com Dear freesurfer users: I don't know how to read my data in virtual system. When I tried to mount the local disk into virtual system, it asked for root authentication. Do you guys know about the password for root? LJ

Re: [Freesurfer] (no subject)

Probably something wrong in your contrast files. It's hard to tell just from this msg --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter

Re: [Freesurfer] Skull Stripping Free surfer

Using FreeSurfer just for Skull Striping is like killing an ant with an MP5 :) Are you sure you just want to skull strip? 2009/11/3 Ribes Delphine delphine.ri...@epfl.ch Dear Users, I've just started using FreeSurfer. I would like to use it for skull-stripping. I've created a batch file

Re: [Freesurfer] Computer specifications for FreeSurfer

Hi, This IMac is good for running up to 4 simultaneous recon-all You can expect 30 hours for 4 simultaneous cases in this machine you described. PPJ --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom

Re: [Freesurfer] running fs on multi processing computers

I think it would run. But it's hard to tell without knowing the system. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

Re: [Freesurfer] freesurfer in a cluster computer

Depends on your cluster configuration. But if you are using a PBS cluster you can just spawn one recon-all per subject and the queue will take care of them. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm

Re: [Freesurfer] problem display tksurfer in vmware

Have you installed the VirtualBox that comes from the FreeSurfer Wiki? VirtualBox 3.x? --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter

[Freesurfer] Fwd: Re: problem display tksurfer in vmware

-- Forwarded message -- From: Giacomo Mandruzzato giacomo.man...@gmail.com Date: 2009/9/28 Subject: Re: Re: [Freesurfer] problem display tksurfer in vmware To: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br ok.thank for interest. I resolved my problem: -I

Re: [Freesurfer] Getting Started

Try this: cd ~ vi .bashrc You wont see the .bashrc unless you use ls -a --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

Re: [Freesurfer] Something wrong with the display image of tksurfer

Try this: http://www.youtube.com/watch?v=9573UYJxlok -- PPJ 2009/9/16 QQ Liu qqli...@gmail.com Hi all, I have a problem about the tksurfer. When I use tksurfer to show the surface of the cortex. The window of the tksurfer is normal, but the image cannot be seen in the front window.

Re: [Freesurfer] Help in Qdec

Answers bellow 2009/9/15 Gergely Orsi gergo.o...@gmail.com 1, I'd like to know what Curv does stand for? Because We have a highly significant difference in Curv among our groups unilaterally. Curv is the curvature of the surface, afaik. 2. Is it possible to list the total brain volume

[Freesurfer] Autoredraw in TKSurfer

Some people asked me how to enable Auto Redraw in TKSurfer in the virtual machine distribution of FreeSurfer. A video tutorial was placed in YouTube: http://www.youtube.com/watch?v=9573UYJxlok --- Pedro Paulo de M. Oliveira Junior Diretor de

Re: [Freesurfer] Fwd: selecting the best structural scan

Hi Sima, I've run 6 versions of the same scan of the same subject I got some differences too. Not so big as you found but still some differences Probably it's the -randomness flag in the recon-all Check: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html

Re: [Freesurfer] Fwd: selecting the best structural scan

these 6 different scans. I need to know how to select the best. any suggestion? Regards, Sima. 2009/9/4 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Hi Sima, I've run 6 versions of the same scan of the same subject I got some differences too. Not so big as you found

Re: [Freesurfer] Windows VirtualBox freesurfer v4.5.0

Thanks Nick! The link to download VirtualBox is: http://www.virtualbox.org/wiki/Downloads --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter

[Freesurfer] VentralDC

Sorry for the question but what is VentralDC? I mean what means the acronym -- Enviado do meu celular --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br ---

Re: [Freesurfer] FreeSurfer Licence for Grid Computing?

Henri, FS will check the license in $FREESURFER_HOME I think It's easy to make it work on the grid. I have done this last year without problems. PPJ 2009/8/19, Henri Vrooman h.vroo...@erasmusmc.nl: Hi there, I have a question about FreeSurfer Licensing. For our image processing

Re: [Freesurfer] installing FS - permission denied

You don't have permission to write in /usr/local Try using sudo before the mv Enviado do meu celular Nokia -Msg original- De: Ahmed, F, Me fah...@sun.ac.za Enviada: 18/08/2009 05:37:54 Para: Freesurfer Mailing List Assunto: [Freesurfer] installing FS - permission denied Hello. I am

Re: [Freesurfer] reinstalling

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 fah...@sun.ac.za

Re: [Freesurfer] installation problems

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

Re: [Freesurfer] installation problems

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 fah...@sun.ac.za fah...@sun.ac.za Ok, how do I get it in there? *From:* Pedro Paulo de Magalhães Oliveira

Re: [Freesurfer] installation problems

I think you should grab some help from you local sys admin or some linux user 2009/8/14 Ahmed, F, Me fah...@sun.ac.za fah...@sun.ac.za 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

Re: [Freesurfer] reinstalling freesurfer

You can simply execute: rm -rf /usr/local/freesurfer If your freesurfer installation is in another directory, change the command above accordingly --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom ---

Re: [Freesurfer] tksurfer display

try: setenv doublebufferflag 1 before running tksurfer --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/8/10

Re: [Freesurfer] tksurfer display

corinna...@gmail.com That didn't work. Corinna 2009/8/10 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br try: setenv doublebufferflag 1 before running tksurfer --- Pedro Paulo de M. Oliveira Junior Diretor de Operações

Re: [Freesurfer] redraw failed: no gl window open problem

setenv doublebufferflag=0tksurfer bert lh inflated --- Pedro Paulo de M. Oliveira Junior 2009/8/5 Guang Zeng freesurfer...@hotmail.com Hi, there, I am running the tksurfer command to view the cortical surface data as *tksurfer bert

Re: [Freesurfer] tksurfer display

Two procedures may help you: 1) setenv doublebufferflag 1 2) If you virtual machine is VirtualBox, upgrade to 3.0 and enable OpenGL --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- New Netfilter

Re: [Freesurfer] Segmentation fault

I think you need to send more info about where it crashed --- Pedro Paulo de M. Oliveira Junior 2009/8/3 Ritobrato Datta rida...@mail.med.upenn.edu Hello All, I got this error when I ran recon-all -all. I changed machines and the same

Re: [Freesurfer] libtiff.so.3 instalaton error ?...

I think if he forgot the root password there's no way to do this --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business

Re: [Freesurfer] problems with qdec

Paula, You must add at least two levels in each .levels file. Ex: in the gender file: *gender.**levels* Female Male --- Pedro Paulo de M. Oliveira Junior 2009/7/23 Paula Diniz paula.rej...@gmail.com Hello I`m problems with the levels

Re: [Freesurfer] continue from a specific stage of autorecon2

It would be: recon-all -s YOUR_SUBJ -make all --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- Em breve Netfilter Small Business 2009/7/22 Gonzalo Rojas

Re: [Freesurfer] from dicom to mgz

Pablo This Dicom you attached comes from a Philips scanner. We had a bug in 3 Philips scanners with their DICOM files not being compliant with DICOM standard. In your header there's DICOM 4.0 MR datadefs - that's the problem with Philips: Dicom current standard is 3. Take a look of this thread:

Re: [Freesurfer] from dicom to mgz

Because Philips Dicoms are not true Dicoms At least here in Brazil they told us they are aware of the problem and suggest we export in nii format --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo

Re: [Freesurfer] making subject directory

chmod 755 is not the solution since it gives writing permission only to the owner of the directory. Use: chmod 777 $SUBJECTS_DIR Or chown YOUR_USERNAME $SUBJECTS_DIR 2009/7/15, Barnali Basu barnali.b...@gmail.com: Experts I am stuck up with a real basic issue, which I have done easily

Re: [Freesurfer] asegstats2tabel, ICV

I have a Python script to do this. I don't know how to make this using asegatats2table, let's wait if somebody answer, otherwise I'll send you this script. --- Pedro Paulo de M. Oliveira Junior CIO Latam Netfilter SpeedComm Telecom ---

Re: [Freesurfer] problem starting qdec

You need an X Server (http://www.straightrunning.com/XmingNotes/) - I think this one is free However, X Server are usually very slow! --- Pedro Paulo de M. Oliveira Junior CIO Latam Netfilter SpeedComm Telecom --- New Netfilter 3.0

[Freesurfer] Surface based volumetry vs Voxel based morphometry

It's more a methodological question, and I have asked this before, but I think it could be better discussed in the FreeSurfer community. Several times people ask me what's the advantage of Surface based methods like the ones used in FreeSurfer over VBM in estimating volumetric parameters of

[Freesurfer] Re: Surface based volumetry vs Voxel based morphometry

such as putamen, pallidum, etc cheers, Bruce On Thu, 9 Jul 2009, Pedro Paulo de Magalhães Oliveira Junior wrote: It's more a methodological question, and I have asked this before, but I think it could be better discussed in the FreeSurfer community. Several times people ask me what's

Re: [Freesurfer] How to remove defects from inflated surface

Some bumps are normal. I think you should post a screenshot. 2009/7/8, pcrai...@cc.hut.fi pcrai...@cc.hut.fi: Hello, I have run recon-all for my images but the resulting inflated surface has a lot of bumps on it even after first hand edits to the brainmask and wm volumes. I have tried

[Freesurfer] Citing FreeSurfer in Papers - GLM - Thickness Analysis

I'm co-writing a paper using FreeSurfer and reading the Wiki page regarding how to cite FreeSurfer: http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitationWhen we cite the mri_glmfit we usually use as reference: Fischl

Re: [Freesurfer] building from source

I have one AIX version. Is it x86? --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br 2009/6/24 Michael Scheel msch...@eyecarecentre.org I have the

Re: [Freesurfer] building from source

x86 was a typo. I mean POWER5 --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br 2009/6/24 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br I

Re: [Freesurfer] error message

Fatima, Try this simple procedure to get started. 1) Convert your dicom files to 001.mgz recon-all -i DICOM_FILE_DIR -o 001.mgz 2) Inside your subjects_dir create a subdirectory like this: mkdir -p $SUBJECTS_DIR/test01/mri/orig 3) copy your 001.mgz into that dir cp 001.mgz

<    1   2   3   >