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] FreeSurfer 6

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.harvard.edu https://mail.nmr.mgh.harvard

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

[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/

[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

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

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

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

[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] 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

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] 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] TkSurfer and new color table. Mislabelling

t. TkSurfer > >> seems to be ignoring > >> FreeSurferColorLUT.txt, but the labels are placed in the right spots. > >> > >> When I try to manually force the FreeSurferColorLUT.txt I'm > >> visualizing an all grey image. And the surface is &

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

modifying the colortable.txt such that the first entry is the name and > color for your first label, etc. > doug > > > On 07/05/2012 03:44 PM, Pedro Paulo de Magalhães Oliveira Junior wrote: > >> Doug, >> >> I did >> >> mri_annotation2label

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] 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

[Freesurfer] Public Supercomputing service to process FreeSurfer data

Oliveira Jr. ----- 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.ha

[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

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

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] 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 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] 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

[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] 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

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

[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] 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] 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] 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] 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] 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] 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:

[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

[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/

Re: [Freesurfer] mris_convert exporting parcellation per vertex

Thanks. I suppose I can't do this without matlab. Right? -- iOS 5.0 Em 08/10/2011, às 19:29, Bruce Fischl escreveu: > there is a write_annotation.m file you can use > On Sat, 8 Oct 2011, Anderson Winkler wrote: > >> ops, it seems the comments inside the dpxwrite.m no longer reflect what it >>

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

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

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/

[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] 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

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] 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

[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 htt

[Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available

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.harvard.edu https://mail.nmr.mgh.ha

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

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

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

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

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

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

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

[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] 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

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 get an STL file which yo

[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

[Freesurfer] Spherical visualization

Sorry for the question but in order to generate the visualization of the spherical mapping of, for instance, cortical thickness we should use which command line in TKSurfer? -- --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfi

Re: [Freesurfer] Spherical visualization

it's spherical map? That would be: > > tksurfer $subject $hemi sphere.reg -overlay > $SUBJECTS_DIR/$subject/surf/$hemi.thickness > > cheers, > Bruce > > > On Mon, 22 Sep 2008, Pedro Paulo de Magalhães Oliveira Junior wrote: > > Sorry for the question but in

Re: [Freesurfer] which computer/server to buy?

Narly, We have recently bought 64 Dell 1950PE With Dual processor Xeon Quad Core 16 Gb RAM I think there are two approaches to the problem: 1) Machine to run recon-all analysis: Maximum performance and memory like the one I put above. 2) Visualization Workstation: I would indicate: AMD Phenon X4

[Freesurfer] A methodological question

Some weeks ago,I have posted here a compilation of the main papers that describe FreeSurfer implementation. I was wondering if someone has researched in comparison between FreeSurfer methodology and other ones. (For instance: doi:10.1016/j.neuroimage.2004.12.056) Best Regards PPJ -- --

Re: [Freesurfer] Voxel resolution impact / skull stripping and bias correction replacement

João, Here is my opinion: I have worked on resolutions distinct than 1mm3 isotropic and usually I have no problem. What do you mean by false negatives in your cohort study? I think you should avoid seeding data with skull striped by other program to the pipeline. Best Regards, PPJ 2008/10/3 J

Re: [Freesurfer] Voxel resolution impact / skull stripping and biascorrection replacement

what about >> data which had been previously bias corrected? >> >> Thank you very much for all you help! >> >> Best, >> >> Joao >> >> -Original Message- >> From: [EMAIL PROTECTED] >> [mailto:[EMAIL PROTECTED] Behalf Of

Re: [Fwd: Re: [Freesurfer] Volume processing question]

I think Douglas can answer better this but I think you can find some help in: http://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats and in: http://wideman-one.com/gw/brain/fs/surfacefileformats.htm 2008/10/6 Tommaso De Marco <[EMAIL PROTECTED]> > Dear Doug Greve, > I have tried to use mri_surf2

Re: [Freesurfer] Permissions Denied (Control Points)

Kellen, I think you could send us the system you use (Linux/Mac) and the FreeSurfer version. PPJ 2008/10/9 Kellen Mobilia <[EMAIL PROTECTED]> > Help- > As a relatively new user to Freesurfer, I have encountered some problems > none that more experienced users have been able to solve until now. E

[Freesurfer] Re: Freesurfer qdec-coord script

my post for more details, but if you have any input (or > scripts) on how to do this, it would be greatly appreciated. > > thanks, > mishkin > > > > On Thu, Oct 2, 2008 at 9:08 PM, Pedro Paulo de Magalhães Oliveira > Junior <[EMAIL PROTECTED]> wrote: > > Sure.

Re: [Freesurfer] recon-all : in a raw or parallel?

If you have a dual core machine it's better run two patients at same time. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom 2008/10/14 asaf achiron <[EMAIL PROTECTED]> > dear all, > > i would like to

Re: [Freesurfer] Philips DICOM Files

Hi, We also have a Philips 3.0T and unfortunately the images from this scanners are not Dicom 3 compliant. We have wrote a patch and we are pressing Philips to fix this. Best Regards PPJ --- Pedro Paulo de M. Oliveira Junior Diretor de Opera

Re: [Freesurfer] Philips DICOM Files

s PPJ --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom 2008/10/20 Pedro Paulo de Magalhães Oliveira Junior <[EMAIL PROTECTED]> > Hi, > We also have a Philips 3.0T and unfortunately the images from this scanners > are not Dicom 3 compliant. We

Re: [Freesurfer] Philips DICOM Files

ything i can do about it or probably i just go > another way to unpack my data??. > > thank you > > Atae > > - Mensaje original > De: Pedro Paulo de Magalhães Oliveira Junior <[EMAIL PROTECTED]> > Para: ATAE AKHRIF <[EMAIL PROTECTED]> > CC: freesurfer

Re: [Freesurfer] shell choice

I think tcsh are recommended for historical reasons. However you can use bash. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom On Fri, Nov 28, 2008 at 12:02, Jared Price <[EMAIL PROTECTED]> wrote: >

Re: [Freesurfer] group analysis

Hi, Freesurfer do present thickness in mm. Also the p-Value is from the GLM model used in QDEC (mri_glmfit) --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom On Mon, Dec 22, 2008 at 09:50, b9403208

[Freesurfer] [recon-all] [MacOS Leopard] Global Region of the brain empty

Hi, I'm running 100 cases in a MacPro with 8 core and in all cases I'm receiving this message in skull strip step: GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073732725 RIGHT_CERCSF_MIN=1, CSF_intensity=2, CSF_MAX=218 , nb = -1073752790 LEFT_CER CSF_MIN=0, CSF_inten

Re: [Freesurfer] 3D graphics card and blade systems

Hi Anderson, I don't remember if I showed you here in Sao Paulo our Freesurfer processing. I think you could have a cluster or for better power consumption a Blade Server to run several recon-all at same time (don't forget to reserve at least 1GB Ram per core) To visualize your data you can use a

Re: [Freesurfer] 3D graphics card and blade systems

ers are looking forward to: any idea on when GPU might become a > requirement, or how essential it might become? > That's because what is going to a brand new system may quickly become > obsolete for FreeSurfer if the GPU stuff comes along soon. > > Thanks a lot! > > Anderso

[Freesurfer] FreeSurfer Tutorial and Workshop in Sao Paulo, Brazil

The FreeSurfer Development Team is hosting a two-day course for beginner and experienced users of FreeSurfer . Day 1 will be an introduction toFreeSurfer

[Freesurfer] Adding papers to the Wiki

Hi, Can you add this paper to the Wiki page? "Cortical thickness reduction of normal appearing cortex in patients with polymicrogyria" - Oliveira Jr, Pedro Paulo; Leite, Claudia; Valente, Kette; Shergill, Sukhwinder; Amaro Jr, Edson; - Journal of Neuroimaging - 2008 - In Press Tks PPJ ---

Re: [Freesurfer] problem with tksurfer:no open gl window

Besides what Krish told you, you should disable effects in Ubuntu preferences->appearance. Otherwise you'll have a window without border. Also, you should turn on Auto redraw in TKSurfer. Notice that setenv is for csh, if you are using bash you should do export doublebufferflag=1 tksurfer ---

Re: [Freesurfer] FDR correction

Some links that may be helpful: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis http://surfer.nmr.mgh.harvard.edu/fswiki/MultipleComparisons Hope it helps. PPJ ---

Re: [Freesurfer] extracting data used in QDEC scatterplots

Yes. Use the script in UserContributions section of the Wiki http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/ppaulo/qdec-coord --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- No

[Freesurfer] recon-all finished with errors

There is a researcher here who is getting this error in version 4.2.0, I have uploaded the 001.mgz to the ftp: TEMPLATE DEFORMATION second estimation of the COG coord: x=150,y=117, z=145, r=8362 iterations GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4

Re: [Freesurfer] Error in MRI resample?

I think you have a problem in the voxel size. *The physical sizes are (280.00 mm, 280.00 mm, **492.00 mm**), which cannot fit in 256^3 mm^3 volume.* --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom ---

Re: [Freesurfer] GM

I think you mean FreeSurfer? You can find this in aseg.stats inside stats directory in each subject. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br On Fri

Re: [Freesurfer] tksurfer error

If you are using tcsh setenv doublebufferflag 1 in bash export doublebufferflag=1 --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br On Wed, Apr 1, 2009 a

Re: [Freesurfer] tksurfer error

sage: > surfer: ### redraw failed: no gl window open > > Is there anything else that you would suggest to try? > > Thank you in advance, > Elisa > > 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior > > If you are using tcsh >> >> setenv doublebu

Re: [Freesurfer] tksurfer error

r your time and patience. > > Elisa > > 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior > >> It seems that you are using running this Centos inside a VMWare. >> TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in >> current vmware >>

Re: [Freesurfer] Sulcal depth and width

This paper may help you:http://www.jneurosci.org/cgi/reprint/25/34/7840.pdf And also this threads: http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2005-December/002092.html

Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

If you are using tcsh setenv doublebufferflag 1 in bash export doublebufferflag=1 --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br On 1 de abril de 2009

Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

Can you post the output of dmesg command? Are you using vmware? TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in current vmware. If you are using it I suggest you to migrate your virtual machine to VirtualBox: http://www.virtualbox.org/ Have you tried setting the autoredraw o

Re: [Freesurfer] Talairach

Can you try converting directly Dicom to mgz? --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br 2009/4/2 Kelly Silva > We started with DICOM. After we hav

Re: [Freesurfer] tksurfer error

in 5.0 seconds = 1677.716 FPS > 8520 frames in 5.0 seconds = 1701.086 FPS > 8021 frames in 5.1 seconds = 1587.792 FPS > > thanks, > > Elisa > > > 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior > >> Try running glxgears >> >> Can you post the out

Re: [Freesurfer] ventricles labeled as white matter in hydrocephalus brain

Dana, I have done some recon-all in NPH patients and didn't have any problems with NPH with large ventricles. Best Regards PPJ --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 w

Re: [Freesurfer] 3d reconstruction of the hippocampus or thalamus

You can use slicer 3 --- Pedro Paulo de M. Oliveira Junior 2009/4/18 asaf achiron > hi group, > > Is there a way to reconstruct in 3d the hippocampus or thalamus > segmentation in Freesurfer? > this is for verification of the automatic

Re: RES: [Freesurfer] Individual thickness data extraction from plot

2009/4/23 > Hi Pedro Paulo, > > I tried to use your script (qdec-coord) to extract individual thickness > data from my plot in qdec, but I have a couple of questions: > > - I found the output from the instruction in a file called* lh.l.asc *in my > working directory (.../qdec/FolderOfTheSpecificA

Re: [Freesurfer] tkmedit error

Probably you updated the kernel (or the OS did by himself) and the restricted drivers (ATI/NVidia) are not enabled by default. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.

Re: [Freesurfer] tkmedit error

oore > Thanks for the quick responses. Is there an easy way to enable these > drivers? (We unfortunately don't have an IT linux expert here). > > > At 03:38 PM 4/23/2009, Pedro Paulo de Magalhães Oliveira Junior wrote: > > Probably you updated the kernel (or the OS di

Re: Re: RES: [Freesurfer] Individual thickness data extraction from plot

#!/bin/bash cd #your directory where qdec data are stored. set numsubject = 17 #your value for i in `seq 1 $numsubject` do mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.mgh mris_convert -c $i.mgh ../../fsaverage/surf/lh.inflated lh.$i.asc done Did you use bash

Re: [Freesurfer] hardware recommendations

Take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br 2009/4/30 Elina Pitri >

Re: [Freesurfer] License Key issue (not recognized)

You should use: ozgun.oza...@gmail.com 7235 *CZag.N9G9Ekc Only three lines in license file --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br 2009/5/14 ozgu

[Freesurfer] FreeSurfer in Multiple Sclerosis some questions

I'm not sure whether the Freesurfer list is the appropriate place for this discussion or not, however I'll place the question here and if somebody has an idea we can discuss by pm. Regarding the paper: Focal thinning of the cerebral cortex in multiple sclerosis ( http://www.nmr.mgh.harvard.edu/~fis

Re: [Freesurfer] licensing question

Software used for clinical purposes need a FDA approval in US. FreeSurfer main target is research. If you use it for clinical purposes you are on your own risk. cheers. PPJ --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter

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