[Freesurfer] FreeSurfer 6

Hey Guys, Sorry if this is a frequently asked question. Do we have an updated ETA for version 6 of Freesurfer? We are planning on upgrading our 1024-node cluster and version 6 is a big deal for us. Best Pedro Paulo Jr. - Pedro

Re: [Freesurfer] Amazon EC2 for FreeSurfer 5.3

Yes. CerebralVol.com does it - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 15, 2015 at

[Freesurfer] Head motion during MRI acquisition reduces gray matter volume and thickness estimates

The paper Martin Reuter and the FS group wrote was featured in an article of Discover Magazine by Neuroskeptic. http://blogs.discovermagazine.com/neuroskeptic/2014/12/19/head-motion-structural-scans/#.VJhYkBSACk Reuter M, Tisdall MD, Qureshi A, Buckner RL, van der Kouwe AJ, & Fischl B (2014). Hea

Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview

. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Nov 5, 2014 at 8:03 PM, Bruce Fischl wrote: > Hi PPJ > > I'm not sure it i

Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview

This server cannot run any X11 for security reasons. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On

[Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview

Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id

Re: [Freesurfer] Freesurfer course 2015 Brazil

We don't have a date yet. An estimate would be March/April - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id

Re: [Freesurfer] recon-all subject folder size

300mb is fine. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Mon, Feb 24, 2014 at 3:01 PM, D

Re: [Freesurfer] longer run time on 5.3 versus 5.2 ?

I saw this issue too. The total running time went from an average of 16.3h to 20.4h - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.co

[Freesurfer] [Release] - iSurf BrainView 4.1.0

redesigned to take advantage of new iOS device GPU - Aseg from FreeSurfer 5.2 As usual suggestions and feedback are welcome. The link for download is: http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8 - Pedro Paulo de

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

n 5.1 - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Apr 11, 2013 at 2:47 PM, Yang, Daniel wrote: > Hi PPJ and

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

Ok, I'll try to put together a stat from aparc too. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

no visible difference in terms of cortical thickness, volumes, etc. If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test. ----- Pedr

[Freesurfer] iSurf BrainView now available for Windows 8 {Disarmed}

uman Brain Mapping 2011, 2011." --------- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com <http://www.netfilter.com.br> ___ Freesurfe

[Freesurfer] Error in Talairach transform version 5.2

I'm having some recon-all errors like this: mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.3505/src.mnc transforms/talairach.auto.xfm Use of uninitialized value $path in join or string at /usr/local/freesurfer/

Re: [Freesurfer] Freesurfer problem on Amazon EC2

The micro instance won't work. You'll need at least one m1.medium instance. I don't want to advertise it again but have you considered using http://cerebralvol.com that runs EC2 instances --------- Pedro Paulo de Mag

Re: [Freesurfer] FS 5.2-beta run-times on Amazon Web services (AWS)

a large amount of data I believe our 1024-core m1.medium is the best cost benefit. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/ar

Re: [Freesurfer] FreeSurfer problem on VirtualBox Linux

Unfortunately Windows XP SP3 is no longer Tier-1 supported for VirtualBox. I suggest you to try it on Windows 7 or Windows 8. cheers PPJ - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Tel

Re: [Freesurfer] mri_cc segfault

Bruce found that the data had the direction cosine wrong. I have fixed the direction and I'm running it again. I've put the data in the ftp ----- Pedro Paulo de Magalhães Oliveira Junior Netfilter & Spe

[Freesurfer] mri_cc segfault

hanks PPJ ----- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ Freesurfer mailing list Freesurfer@nmr.mgh.har

[Freesurfer] Public Supercomputing service to process FreeSurfer data

on at https://www.cerebralvol.com/about.html also you can find information regarding HIPAA at https://www.cerebralvol.com/hipaa.html Signup for free at: https://www.cerebralvol.com We strongly appreciate any suggestions and feedback. Pedro Paulo

Re: [Freesurfer] Freesurfer on Mac Os X 10.8

Yes it works. But for the X11 stuff you need to download X11 (ML doesn't include X11 anymore) http://support.apple.com/kb/HT5293?viewlocale=en_US&locale=en_US ----- Pedro Paulo de Magalhães Oliveira Junior Netfilter &a

Re: [Freesurfer] slanted

No! Do you have a dropbox account? Copy there and send the link to them. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfi

Re: [Freesurfer] TkSurfer and new color table. Mislabelling

-rh-rostralanteriorcingulate 255 40 0 0 6 ctx-rh-superiorparietal 255 48 0 0 7 ctx-rh-frontalpole 255 106 0 0 On Thu, Jul 5, 2012 at 7:14 PM, Douglas N Greve wrote: > Hi Pedro Paulo, it is not quite the right procedure, but I'm surprised > that it gave unknown for all labels. Try >

Re: [Freesurfer] TkSurfer and new color table. Mislabelling

doug > > On 07/05/2012 02:57 PM, Bruce Fischl wrote: > > Hi PPJ, > > > > I think the color lut is embedded in the aparc.annot. If you want to > > change it you have to change the one that's in the .annot. I would do > > it in matlab. > > > > ch

[Freesurfer] TkSurfer and new color table. Mislabelling

e. And the surface is completely mislabeled, there is a 4th ventricle in the surface, putamen in the surface, etc. What am I doing wrong? ----- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter

Re: [Freesurfer] .license file

If FreeSurfer on Mac has been installed on /Applications you may need to type sudo cat > $FREESURFER_HOME/.license and enter your account password when asked ----- Pedro Paulo de Magalhães Oliveira Junior Netfilter & Sp

[Freesurfer] [Release] - iSurf BrainView 4.0.5

ad is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423&mt=8 Note: A version for Windows Phone 7.5 (Nokia Lumia 900, 800, 710, etc) is under development. ----- Pedro Paulo de Magalhães Oliveira Junior

Re: [Freesurfer] OBJ conversion

There's a how-to in the FreeSurfer website: http://surfer.nmr.mgh.harvard.edu/fswiki/HowTo/HowTo Pedro Paulo Jr. On Mon, Feb 20, 2012 at 23:32, Manfred G Kitzbichler < manfr...@nmr.mgh.harvard.edu> wrote: > Hi Darshan, > > as Bruce suggested, you can use mris_convert to g

Re: [Freesurfer] Performance questions

I think IBM has a better compiler. Better than gcc and slightly slower than intel compiler Sent from my iPad On Jan 18, 2012, at 16:09, Nick Schmansky wrote: > Malcolm, > > actually, they (IBM) are looking at openmp (to allow multiple threads to > process for-loops) and SSE3 instructions (bette

[Freesurfer] iSurf Brainview now ported to Mac

ation. You can download it at: http://itunes.apple.com/us/app/isurf-brainview-desktop/id491367143?ls=1&mt=12 As usual, suggestions are welcome. Happy 2012 for everyone. PPJ ----- Pedro Paulo de Magalhães Oliveira Junior Netfilter &a

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

I have restored the image: 060244368407/FREESURFER51 I'll create a web service that can log the number of instances spawned. Is that ok with you? - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedCom

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & Speed

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

Ok. I'll label as private this AMI that has .license file. Maybe we can make a tutorial on how to create an AMI instead. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

Maybe we can set up a web server in the Martinos center and the AMI Image can authenticate in it. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile:

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

I've put together the basic tutorial on getting started using Amazon AWS system: It's in the same place Nick pointed out: https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud ----- Pedro Paulo de Magalhães Olive

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

Tomorrow I'll post a tutorial. It's quite simple ----- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id3653064

Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

No. This is for non GPU instances -- iOS 5.0 Em 09/11/2011, às 22:28, Satrajit Ghosh escreveu: hi pedro, will this work with gpu instances as well? cheers, satra 2011/11/9 Pedro Paulo de Magalhães Oliveira Junior > Some weeks ago I was asked about a public image (AMI) to run in

[Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

Instance. So with the current Amazon cost per Small Instance/Hour you'll have a recon-all for USD 2.04 Amazon request a credit card in order to create an account in http://aws.amazon.com Hope it helps, Pedro Paulo Jr. -

[Freesurfer] Recon-all step estimate

Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?

I have one. I'll give you the link -- iOS 5.0 Em 28/10/2011, às 20:52, Joshua Lee escreveu: Are there any existing Amazon EC2 AMI registered publicly that can be used? I want to analyze a lot of data fast. Thanks, - Joshua Lee ___ Freesurfer mailing

Re: [Freesurfer] cortical thickness asymmetries

e a good explanation though. ----- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Oct 27, 2011 at 10:03, Br

Re: [Freesurfer] implementation on Neurodebian

No. Cuda only runs in NVidia hardware. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Mon, Oc

[Freesurfer] [Major Upgrade] - iSurf Brainview 4.0.0

ng used in the Radiology course. All med students in São Paulo University now have basic MRI neuroanatomy training using iSurf ----- Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilte

Re: [Freesurfer] mris_convert exporting parcellation per vertex

rfer.io.read_annotation). > > If you're just using the io routines, you won't need the somewhat heavy > Mayavi visualization dependencies. You should be able to read in and > manipulate surfaces/annotations just with numpy. > > Best, > Michael > > > 2011/10/

Re: [Freesurfer] mris_convert exporting parcellation per vertex

Yes, but --seg in mri_annotation2label --subject bert --hemi lh --seg saida.mgz produces a volume and not a surface. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mo

Re: [Freesurfer] mris_convert exporting parcellation per vertex

Thanks. It works as I wished. from surfer import io as sIo a = sIo.read_annot('label/lh.aparc.annot') b = sIo.read_geometry('surf/lh.pial') And now I can have each vertex labeled ----- Pedro Paulo de Magal

Re: [Freesurfer] mris_convert exporting parcellation per vertex

. >> >> Hope it helps! >> >> All the best, >> >> Anderson >> >> On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior wrote: >>I need to create a file where I have the parcellation value >> (structure

[Freesurfer] mris_convert exporting parcellation per vertex

file type specified for output: saida.asc Has someone done this before? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/

[Freesurfer] Process monkey data

I have data from 100 monkeys and I need to compare cortical thickness among two groups. In the wiki page there is an entry MonkeyData that has a set of scripts which break-down the steps needed, unfortunately I'm having trouble with this scripts and FS 5.1 Are there an updated version of those pr

Re: [Freesurfer] tksurfer display

I have added this answer to the FAQ: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile:

Re: [Freesurfer] tksurfer display

Can you describe the hardware / video card you are using? - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id36530

Re: [Freesurfer] Renaming a processed subject

You can just rename the directory ABC1234 to Case1 *mv ABC1234 Case1* On Thu, Sep 1, 2011 at 12:01, Irwin, William wrote: > Hi > > ** ** > > For purposes of de-identification, is there an easy way to “rename” all the > contents of data for a processed subject? > > ** ** > > For example

Re: [Freesurfer] FreeSurfer on AWS

I'll try to write a tutorial this weekend -- iOS 5 Em 18/08/2011, às 20:01, Nolan Nichols escreveu: Hi Pedro, I came across your post on the FreeSurfer mailing list and am trying to find the AMI you created ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018272.html). I have

Re: [Freesurfer] Nvidia upgrade considerations

I would go for a complete new PC. You won't benefit much of a GTX590 in an old PC PPJ - Pedro Paulo de Magalhães Oliveira Junior -- check our new iOS app: Cargo<http://itunes.apple.com/app/cargo/id444529879?ls=1&mt=8

Re: [Freesurfer] Nvidia upgrade considerations

TX580 PPJ ----- Pedro Paulo de Magalhães Oliveira Junior -- check our new iOS app: Cargo<http://itunes.apple.com/app/cargo/id444529879?ls=1&mt=8> On Fri, Aug 5, 2011 at 14:28, Andries R. Van Der Leij < a.r.vanderl...@gmail.com> wrote: > Dear freesurfer team &g

Re: [Freesurfer] Re : Book with FreeSurfer chapter

t wishes, Andy Simmons - Date: Fri, 15 Jul 2011 20:36:01 -0300 From: Pedro Paulo de Magalh?es Oliveira Junior Subject: [Freesurfer] Book with FreeSurfer chapter To: Freesurfer Mailing List Message-ID: Content-Type: text/plain; charset="iso-8859-1" Just for information:

[Freesurfer] Book with FreeSurfer chapter

"Automated Volumetric Methods to Detect Alzheimer's Disease" / Pedro Paulo de Magalhães Oliveira Jr. et al. * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The inform

Re: [Freesurfer] muliple fressurfer instance and cuda

Try running only one GPU-assisted recon-all On Fri, Jul 8, 2011 at 10:02, Knut J Bjuland wrote: > Hi > > When I have ran two or more Freesurfer instance in pc with one geforce > gtx 460. I usually get a abort or memory corruption when running two or > more Freesurfer instance. I usually get tro

Re: [Freesurfer] cortical dysplasia

Carolina, We have worked with several cases of MCD (including cortical dysplasia). We have published this paper: https://surfer.nmr.mgh.harvard.edu/pub/articles/jon_372_LR.pdf It may help. But in most cases of cortical dysplasia (not Gray matter heterotopia cases) you'll find a ticker cortex not

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

I usually can run one instance of FreeSurfer with 1GB if I use the -no-gut flag I have a benchmark of 4 recon-all running in a 4 Core AMD with 4GB RAM that took only 10% more time than one recon-all alone. 2011/7/6 John Jan Drozd > Hi Bruce, > > Thanks for pointing this out to me about the RAM.

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide On Tue, Jul 5, 2011 at 13:14, John Drozd wrote: > Hi, > > I am running freesurfer on 64 bit Fedora 10 linux. > I am using version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. > Can anyone point me to a reference web page l

Re: [Freesurfer] Fwd: freesurfer recon error

Have you tried including the flag -cw256 with the recon-all command? On Tue, Jul 5, 2011 at 10:18, Sarah Rappaport - UoB` wrote: > Hi!, > > I am new to FreeSurfer and I am having some difficulty with the T1 > reconstruction. My MRI files were Par Rec and converted to nii. I > successfully conver

Re: [Freesurfer] Difference in hippocampal volume between scanners

This is not normal. Maybe you should check the aseg volume for improper segmentation. On Thu, Jun 23, 2011 at 19:27, Jessica Liu wrote: > Hi everyone! > > I'm currently a summer student working at a lab which uses Freesurfer to > measure hippocampal volumes. I noticed that scanning the same pa

Re: [Freesurfer] How to obtain volume of specific structure

Take a look in aseg.stats file -- iOS 4.3 Em 22/06/2011, às 23:09, ZhiLiangLong escreveu: > Hi all: >After all "recon-all -all" processing has been completed for all subjects > ,I want to obtain volume of specific structure of each subject(e.g., the > volume of Caudate Nucleus). But i ha

Re: [Freesurfer] recon-all -s exited with ERRORS

recon-all -s bert -all -use-gpu -- iOS 4.3 Em 13/06/2011, às 21:30, Leo Souza escreveu: /recon-all -use-gpu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

Re: [Freesurfer] choroid plexus

The volume should be in aseg.stats On Wed, Jun 8, 2011 at 16:45, Tracy Butler wrote: > Is there a good method to segment choroid plexus and calculate volume? I > know it’s an aseg label. > > Thanks, > > Tracy > > ___ > Freesurfer mailing list > Frees

Re: [Freesurfer] FreeSurfer Tutorial and Workshop

I think you should send an e-mail to Allison (astevens) On Fri, May 27, 2011 at 13:34, Eisenstein, Sarah wrote: > Does anyone know how to register for the FreeSurfer Tutorial and Workshop > scheduled for September, 2011? I cannot find a link or a phone number to do > this on the Course Descript

Re: [Freesurfer] FS5.1 for CentOS4 works for CentOS5-like OS?

Yes. It works -- iOS 4.3 Em 25/05/2011, às 10:14, Xinian Zuo escreveu: > Dear FS team, Only see new 5.1 version for CentOS4 in the website. Thanks, XN. > > -- > Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) > ___ > Freesurfer mail

Re: [Freesurfer] Error from cudadetect

5.1 was released yesterday -- iOS 4.3 Em 25/05/2011, às 09:42, R Edgar escreveu: > On Wed, May 25, 2011 at 7:59 AM, Howison, Mark wrote: > >> We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute >> cluster at Brown and are seeing the following error when running >> 'cudadetect': >

Re: [Freesurfer] Running FreeSurfer Remotely

It will probably work. However the experience can be sluggish On Mon, May 23, 2011 at 11:34, wrote: > Hi, > > Will FreeSurfer run remotely using NX Client for OSX or should I employ > VNC only? > > Thanks, > > Gabriel > ___ > Freesurfer mailing list >

Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

seems 'squashed', as if there is a slice gap. do > you know the details of how this was acquired? > > N. > > > > On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães Oliveira > Junior wrote: > > I'm having this error in the recon-all > >

[Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

I'm having this error in the recon-all # #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

[Freesurfer] [Major Upgrade] - iSurf Brainview 3.0.0

e.woa/wa/viewSoftware?id=381072423&mt=8 A personal note: Some residents in Radiology of our med school found the quiz challenging. I think it can be a very good tool to teach neuroanatomy in MRI ----- Pedro Paulo de Magalhães

Re: [Freesurfer] Smaller Virtual Machine

I have distributed another EC2 image. I think you can now start FreeSurfer instances at Amazon EC2 On Tue, May 3, 2011 at 06:25, Fidel wrote: > So... What about this? > > Cheers :) > > El 29/04/2011 16:43, Pedro Paulo de Magalhães Oliveira Junior escribió: > > I&#x

[Freesurfer] [New release] - iSurf Brainview 2.1.1

welcome. Upcoming features should include 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423&mt=8 Cheers Pedro Paulo Jr. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard

Re: [Freesurfer] Smaller Virtual Machine

r do we have to create our own and then, upload it to > Amazon? > > Thanks again. > > Fidel. > > El 29/04/2011 16:25, Pedro Paulo de Magalhães Oliveira Junior escribió: > > Yes. But that machine distributed by FreeSurfer is the one with full GUI to > run under Windows. &

Re: [Freesurfer] Smaller Virtual Machine

Yes. But that machine distributed by FreeSurfer is the one with full GUI to run under Windows. I have a machine for cloud processing in Amazon EC2 (you can look up for FreeSurfer DMI in Amazon EC2) PPJ On Fri, Apr 29, 2011 at 11:15, Fidel wrote: > Hi all, > > I have been trying the virtual di

Re: [Freesurfer] FreeSurfer movie generation recipe

easier. Can you inflate until you get the sphere? 2011/4/28 Bruce Fischl > or you can save snapshots from mris_inflate with > > mris_inflate -w 1 -scale 1 ... > > then render each of the resulting surfaces. > cheers, > Bruce > > > On Thu, 28 Apr 2011, Pedro Paul

[Freesurfer] FreeSurfer movie generation recipe

Some months ago it was asked in this list how to make a Movie of he process of the inflation of the brain. Some hints: Create this tcl script and name it as script.tcl: for {set x 0} {$x<120} {incr x} { set r [expr (round(1.2*$x + 3))] shrink $r redraw save_tiff ${x}-img.tif } exit

Re: [Freesurfer] Unknown label in Parcellation

lh.aparc.stats 2011/4/27 Bruce Fischl > which parcellation are you using? > > > On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: > > In one study we are conducting we found significant difference in cortical >> thickness between the two groups in

[Freesurfer] Unknown label in Parcellation

In one study we are conducting we found significant difference in cortical thickness between the two groups in some areas. One of those areas are lh_unknown. Is this an error or it's a still unlabelled area? thanks Pedro Paulo Jr ___ Frees

Re: [Freesurfer] qdec analysis different scanner

Yes it does. However you can maybe use the scanner as a covariate. On Wed, Apr 27, 2011 at 09:24, John Fredy wrote: > Hello all, > > In voxel based morphometry is not recommended use images from different > scanners. This recommendation also apply in the qdec analysis? > > Thanks in advance > >

Re: [Freesurfer] Fwd: display error

in tcsh try: setenv doublebufferflag 1 in bash it would be export doublebufferflag=1 before running tksurfer Refs: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11049.html http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems On Tue, Apr 26, 2011 at 10:35, Cris Lan

Re: [Freesurfer] Setup configuration error

Freesurfer installation directory is the directory where you installed FreeSurfer In Mac it's usually /Applications/freesurfer -- iOS 4.3 Em 21/04/2011, às 20:57, Jade escreveu: Hi, After I installed FreeSurfer ( freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0.dmg) in my Macbook (Snow Leopar

Re: [Freesurfer] Could I run several freesurfers at the same time?

the figure below show memory consumption for 3 running process (the OS uses 400MB) 2011/4/21 Pedro Paulo de Magalhães Oliveira Junior : > You can set up multicore in VirtualBox or VMWare > > In my experience ( without the gcut) 1GB is enough > > -- iOS 4.3 > > Em 21/04/2011,

Re: [Freesurfer] Could I run several freesurfers at the same time?

You can set up multicore in VirtualBox or VMWare In my experience ( without the gcut) 1GB is enough -- iOS 4.3 Em 21/04/2011, às 13:53, "Richard G. Edgar" escreveu: > > On Thu, 2011-04-21 at 09:48 -0700, Rongxiang Tang wrote: >> >> I was wondering if I can run several freesurfers in my virtual

Re: [Freesurfer] Fedora 14

Yes. It works. -- iOS 4.3 Em 18/04/2011, às 21:13, "roger@yale.edu" escreveu: > Hi all, > Quick question: will the latest Linux 32-bit install work with Fedora 14? > Please let me know if there are known issues. > Thanks, > Roger > ___ > Freesurfe

[Freesurfer] Course FreeSurfer - São Paulo, Brazil

Just to inform we still have two spots available for the course in São Paulo next week http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Brazil2011CourseSchedule If there's anyone interested write me for more details. cheers Pedro Pau

Re: [Freesurfer] recommende pc and cuda

Maybe a NVidia GTX590 (it's a dual GPU) On Mon, Apr 4, 2011 at 08:13, Knut J Bjuland wrote: > Hi > > I am in the process of acquiring a new computer to run freesurfer on.  I am > currently think about buying a PC with a geforce 4X0 and a Tesla card along > with a two screen setup running either

Re: [Freesurfer] data preparation for SVM classification

Sorry for the advertisement :) I wrote a paper using this technique: Use of SVM methods with surface-based cortical and volumetric subcortical measurements to detect Alzheimer's disease. Oliveira PP Jr, Nitrini R, Busatto G, Buchpiguel C, Sato JR, Ama

Re: [Freesurfer] single subject versus a group map in qdec

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 On Wed, Mar 23, 2011 at 14:21, Emily Rogalski wrote:

[Freesurfer] [New release] - iSurf Brainview 2.1.0

://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423&mt=8 Cheers Pedro Paulo Jr. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mai

Re: [Freesurfer] Mac Pro with 12cores

That's without GPU? On Thu, Mar 10, 2011 at 11:17, Richard G. Edgar wrote: > > On Thu, 2011-03-10 at 08:27 -0500, Bruce Fischl wrote: > > If you have enough memory! Maybe Richard can post current CPU recon > > times with the latest hardware and optimizations. I think they are > > much shorter th

Re: [Freesurfer] Mac Pro with 12cores

You can run 12 recon-all in parallel. You'll have 12 patients processed in each day approximately - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.

Re: [Freesurfer] Newbie - problems compiling project tree

libnetcdf-dev or netcdf-dev will do the trick On Tue, Mar 8, 2011 at 19:42, Shay Ohayon wrote: > Hi All, > > I am having some problems compiling freesurfer . > I checked out the recent development version from the CVS, ran > "setup_configure" successfully, but upon "./configure", I end up with

Re: [Freesurfer] CUDA comparable to non-CUDA?

We assume that. On Tue, Mar 8, 2011 at 09:58, Marcus N Schmidt wrote: > Hi FreeSurfer Experts, > > Just a quick question: Generally speaking, assuming everything else remains > the same, are subjects run through a CUDA-enabled recon-all comparable to > subjects run through recon-all without CUDA

[Freesurfer] Freesurfer Tutorial and Workshop April 16-18 in Sao Paulo, Brazil

tion about arranging payment for the course, accommodations,course location, as well traveling issues please contact me in the e-mail above. Regards, Pedro Paulo Oliveira Jr. ----- Pedro Paulo de Magalhães Oliveira Junior Diretor de

[Freesurfer] aparc+aseg.mgz and aparc.a2009s+aseg.mgz

14999) 2) There are many areas in FreeSurferColorLUT.txt that don't appear neither in aparc+aseg nor in aparc.a2009s+aseg My main concern is with the out of range values, which structure they map to? thanks - Pedro Pau

Re: [Freesurfer] parellizing Freesurfer

files > and run the analysis separately and then merge back the output volumes. Has > anyone done something like that or nicer? > > Thanks! > > Pablo > > 2011/2/26 Pedro Paulo de Magalhães Oliveira Junior > > Yes. Take a look at: >> http://surfe

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