Re: [Freesurfer] Problems with hippocampus subfields segmentation

2013-05-14 Thread zkauf...@nmr.mgh.harvard.edu
Hello Luke, A patch was released to fix this problem. In order to fix this issue please follow these instruction: 1) Download the file "kvl.zip" from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/kvl.zip 2) Overwrite the existing kvl files in your /Application/fr

Re: [Freesurfer] Loading V5.2 on Virtualbox

2013-05-06 Thread zkauf...@nmr.mgh.harvard.edu
Hello Will, Clicking the "Terminal" icon on the desktop will load Freesurfer. From that point on its just a matter of typing the appropriate commands. -Zeke On 05/04/2013 09:27 AM, will brown wrote: > I am endeavouring to install FreeSurfer on a windows 8 PC. Virtualbox is > installed along wit

Re: [Freesurfer] Problems visualizing hippocampal subfields

2013-04-26 Thread zkauf...@nmr.mgh.harvard.edu
The "invalid drawable" are warning messages and are normal. No need to worry about them. -Zeke On 04/26/2013 04:58 PM, Erin Walsh wrote: > Hi Eugenio and Zeke, > > I attempted to enter the command line in again (re-copying/pasting) from > the website. Perhaps I had entered in an error somewhere

Re: [Freesurfer] Problems with freesurfer after an upgrade to fedora 18

2013-04-03 Thread zkauf...@nmr.mgh.harvard.edu
Did you try running the freesurfer CentOS6 version on the upgraded version of Fedora? -Zeke On 04/03/2013 08:09 AM, Sidy Fall wrote: > After doing an upgrade from fedora 17 to fedora 18,I am trying to > execute the installation tests, I can't start "$tkmedit", tksurfer or > mri_convert. But free

Re: [Freesurfer] Libray/tool used to read license file - cannot checkout source code

2013-04-02 Thread zkauf...@nmr.mgh.harvard.edu
I am > using > > cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot > checkout -P dev > > Seems I'm out of luck with FS these days! > > Thanks > > Nicola > > On 4/2/2013 11:53 AM, zkauf...@nmr.mgh.harvard.edu wrote: >> Nicola, >>

Re: [Freesurfer] Libray/tool used to read license file - cannot checkout source code

2013-04-02 Thread zkauf...@nmr.mgh.harvard.edu
Nicola, Perhaps it is worth getting a new license file: https://surfer.nmr.mgh.harvard.edu/registration.html As to checking out the source code, I too received that error during checkout and by simply reissuing the checkout command I was able to get the checkout finish to completion. (It even

Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd)

2013-03-27 Thread zkauf...@nmr.mgh.harvard.edu
with FS v5.2 > . If you scroll down the log file, you will see the > "/Application/freesurfer", which is the v5.2 where it crashed. > > Anyhow I have attached the log file of another subject run by FS 5.2, > both recon-all and trac-all. > > Thanks. > p

[Freesurfer] Fwd: Re: memory allocation errors on Snow Leopard running dmri_train (fwd)

2013-03-27 Thread zkauf...@nmr.mgh.harvard.edu
Ping, According to line 9 of the log file you sent to Anastasia, are running freesurfer version v5.1. Not version 5.2. -Zeke Original Message Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd) Date: Wed, 27 Mar 2013 15:17:34 -0400 (ED

Re: [Freesurfer] hippo subfield

2013-03-22 Thread zkauf...@nmr.mgh.harvard.edu
Stefano, In order to fix this issue please follow these instruction exactly: 1) Download the file "kvl.zip" from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ 2) Overwrite the existing kvl files in /Application/freesurfer/bin with the files in kvl.zip I was abl

Re: [Freesurfer] R: Re: R: Re: hippo subfield

2013-03-22 Thread zkauf...@nmr.mgh.harvard.edu
He's on a Mac, so the command would be: otool -L kvlApplyTransform and the output will be: kvlApplyTransform: libITKCommon.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITKIO.3.16.dylib (compatibility version 3.16.0, current version 3.16.0) libITK

Re: [Freesurfer] installation problem

2013-03-21 Thread zkauf...@nmr.mgh.harvard.edu
I believe you are correct, that the poor card is the most likely culprit. The Matrox G200 range are not good at anything graphically intensive. If you have adequate permission you could try updating the drivers. (http://www.matrox.com/graphics/en/support/drivers/latest/) Also, try running 'glxi