Re: [Freesurfer] dmri_train malloc error

Hi Anastasia, Having the same issue, I was wondering if it's possible to recompile only tracula from the source code ? If yes could you give some hints ? Thanks a lot, Dr. David Coynel Division of Cognitive Neuroscience University of Basel Birmannsgasse 8 4055 Basel - Switzerland david.coy...@un

[Freesurfer] convert .annot file to lable

Hi all: Are there some FS commands that can convert .annot file to lable file? Thanks!_

Re: [Freesurfer] convert .annot file to lable

Try mri_annotation2label doug ZhiLiangLong wrote: Hi all: Are there some FS commands that can convert .annot file to lable file? Thanks! ___ Freesurfer mailing list Freesurfer@

Re: [Freesurfer] mri_segment optional flags problem

Hi Bruce- Is this fix going to be put on the site as a patch/fix download (e.g., ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/) or distributed on a per-user need? Thanks, Wil William Irwin | Brain Imaging Coordinator UCSF |

[Freesurfer] Error in preprocessing

Hi, I am using stable5.0-env. I have run the pre[processing command: preproc-sess -s 1411_MC -surface fsaverage lhrh -mni305 -fwhm 5 -per-run I got this ERROR message: /autofs/space/shimshon_002/users/eiran/contproc/1411_MC RunList: 005 006 007 --- ** --- --

[Freesurfer] Nvidia upgrade considerations

Dear freesurfer team I'm currently investigating how to tweak 2 2 year old Dell 7400 Xeon machine's to run a large batch of fs jobs. Upgrading to Nehalem won't work, since it will require a new motherboard as well. However, we can replace our old non-fermi quadro card with a C2050. As an alternat

Re: [Freesurfer] skull stripping and gcut error

Yes, I think this may help a lot, if possible. Thanks, Jacquie Jacquelynn N. Copeland, M.A. Doctoral Candidate Medical/Clinical Psychology Program Department of Psychology University of Alabama at Birmingham Email:jcopel...@uab.edu From: Bruce Fischl [fis.

Re: [Freesurfer] Error in preprocessing

You will need the AFNI 3dvolreg command. This is the only AFNI command you'll need, but you may need to download and install AFNI to get it. doug Eiran Vadim Harel wrote: > Hi, > I am using stable5.0-env. > I have run the pre[processing command: > > preproc-sess -s 1411_MC -surface fsaverage lh

Re: [Freesurfer] Nvidia upgrade considerations

In my experience you'll have the benefit of using two cards simultaneously. That means you can run two recon-all with gpu acceleration simultaneously. The SLI is more important for graphics (cad, gaming) than for CUDA. So, I'd go for 2 GTX580 PPJ --

Re: [Freesurfer] Error in preprocessing

Hi, is this true for FSFAST vs. 5.1 as well? -Tapsya > > You will need the AFNI 3dvolreg command. This is the only AFNI command > you'll need, but you may need to download and install AFNI to get it. > > doug > > Eiran Vadim Harel wrote: >> Hi, >> I am using stable5.0-env. >> I have run the pre[p

Re: [Freesurfer] Nvidia upgrade considerations

2011/8/5 Pedro Paulo de Magalhães Oliveira Junior : > In my experience you'll have the benefit of using two cards simultaneously. > That means you can run two recon-all with gpu acceleration simultaneously. > The SLI is more important for graphics (cad, gaming) than for CUDA. So, I'd > go for 2 GTX

Re: [Freesurfer] Error in preprocessing

yes tap...@nmr.mgh.harvard.edu wrote: > Hi, is this true for FSFAST vs. 5.1 as well? -Tapsya > > >> You will need the AFNI 3dvolreg command. This is the only AFNI command >> you'll need, but you may need to download and install AFNI to get it. >> >> doug >> >> Eiran Vadim Harel wrote: >> >

Re: [Freesurfer] mri_segment optional flags problem

Hi Wil we can certainly post it if there is enough interest. cheers Bruce On Fri, 5 Aug 2011, Irwin, William wrote: Hi Bruce- Is this fix going to be put on the site as a patch/fix download (e.g., ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_64/) or distribu

Re: [Freesurfer] Nvidia upgrade considerations

Hi pedro and Richard, Thank you for the responses! The T7400 has just one gpu slot, so I'll probably just buy the single 590, which itself is a dual card. The 2050 doesn't seem to be worth it on these older systems (ddr2, etc). For my supervisor, what kind of performance increase should I expect

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 2011/8/5

Re: [Freesurfer] mri_segment optional flags problem

Bruce, Until it is determined if there is enough interest, how do I obtain it for centos4_x86_64? Thanks much, Wil |-Original Message- |From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] |Sent: Friday, August 05, 2011 12:10 PM |To: Irwin, William |Cc: Christopher Luna; freesurfer@nm

[Freesurfer] tksurfer and viewing eccentricity data

Dear Freesurfers, Is this the correct command for viewing eccentricity data using tksurfer: tksurfer-sess -a rtopy.self.lh -s sj09 -map eccen Thanks. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] tksurfer and viewing eccentricity data

No, to view the angle: tksurfer-sess -a rtopy.self.lh -s sj09 -map angle This will bring up an overlay with two time points. The first time point is eccen, the 2nd is polar. These are unmasked angles in radians (I think). For masked use (masked by p<.01) tksurfer-sess -a rtopy.self.lh -s sj09

Re: [Freesurfer] Nvidia upgrade considerations

2011/8/5 Andries R. Van Der Leij : > For my supervisor, what kind of performance increase should I expect > if we buy a newer nehalem system? Freesurfer as a whole is quite keen on the improved memory subsystem offered by Nehalem. A figure of 2x (CPU only stream) is floating in my mind, but I don

Re: [Freesurfer] mri_segment optional flags problem

Thanks for your help! Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT On Fri, Aug 5, 2011 at 3:22 PM, Irwin, William wrote: > Bruce, > > Until it is determined if there is enough

Re: [Freesurfer] tksurfer and viewing eccentricity data

Hi Doug and Freesurfers, How does one look at each time point separately to view the eccen and polar maps? Thanks. Michelle Quoting Douglas N Greve : > No, to view the angle: > tksurfer-sess -a rtopy.self.lh -s sj09 -map angle > > This will bring up an overlay with two time points. The first t

Re: [Freesurfer] tksurfer and viewing eccentricity data

View->Configure->Functional Overlay this will bring up a control window that you can use to change the time point being viewed doug Michelle Umali wrote: > Hi Doug and Freesurfers, > How does one look at each time point separately to view the eccen and > polar maps? > > Thanks. > Michelle > > Q

[Freesurfer] Using FreeSurfer with 6-14 year olds

Dear FreeSurfer experts, I'm starting to recon-all the MPRAGE volumes of a large sample of 6-14 year olds So far I haven't had any errors (only 15 subjects runned so far) My questions are: - Should I make a template from the subjects of my whole sample, considering their age range? - Or FreeSurfe

[Freesurfer] reference on co-registration of functional brain areas?

Hi all, I'm looking for a reference showing how the functional areas differ when individual brains are co-registered. Thanks, Zeynep. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer