Re: [Freesurfer] bvecs error from Tracula

Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts,  I am running trac-all -prep -c dmrirc on my DWI data. After fli

Re: [Freesurfer] bvecs error from Tracula

Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Amirhossein - Are

Re: [Freesurfer] bvecs error from Tracula

Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia,  I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul

Re: [Freesurfer] bvecs error from Tracula

Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Amirhossein - I'm attaching sample files. > > a.y > > > On Tue, 16 Jul 2013, amirhossein manzouri wrote: > > Hi Anastasia, >> I have tried both , 3-row and 3-column form

Re: [Freesurfer] bvecs error from Tracula

Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia,  IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki

Re: [Freesurfer] bvecs error from Tracula

The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Good to hear! Can you please share with all of us w

Re: [Freesurfer] bvecs error from Tracula

Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the

Re: [Freesurfer] bvecs error from Tracula

Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia,  I am trying to download the dmri_5.1_snow_

Re: [Freesurfer] bvecs error from Tracula

Hi, Yes I am getting the memory error with version 5.3, exactly the one that is reported in this link: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Amirhossein

Re: [Freesurfer] bvecs error from Tracula

Hi, The content is : freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Can it help? On Mon, Jul 22, 2013 at 10:31 PM, Z K wrote: > Hello Amirhossein, > > Can you please provide me with the contents of build-stamp.txt in the > /Applications/freesurfer directory? > > -Zeke > > > On 07/22/2013

Re: [Freesurfer] bvecs error from Tracula

Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR On Jul 24, 2013 5:42 PM, "Z K" wrote: > Hello Amir, > > According to the log file you've attached, recon-all finished to > completion without any errors. Are you sure you are encountering a memory > error?

Re: [Freesurfer] bvecs error from Tracula

Hi Amirhossein - If your error happens when bbregister is run, then it's not the error that the dmri_5.1_snow_leopard.tar.gz fix was meant to address. In any case that fix is not relevant to you b/c you're using 5.3 and not 5.1. Can you please send your trac-all.log to establish where exactly

Re: [Freesurfer] bvecs error from Tracula

Hi Amirhossein - The memory error doesn't occur when bbregister is running, but when dmri_train is running and loading the atlas data. You seem to have the snow leopard version of freesurfer installed, based on your build stamp (freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0). What ve