24 Jul
2013
24 Jul
'13
11:42 a.m.
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? If so, why?
-Zeke
On 07/24/2013 11:28 AM, amirhossein manzouri wrote:
Kindly find attached the recon-all.log
On Wed, Jul 24, 2013 at 4:50 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: 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 <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> <mailto:zkaufman@nmr.mgh.__harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>>> 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 04:23 PM, amirhossein manzouri wrote: 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 <https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/019392.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html>> Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: 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_leopard.tar.__gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri <a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__>__>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@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 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: 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 <http://surfer.nmr.mgh.__harva__rd.edu/fswiki/FsTutorial/____Tracula <http://harvard.edu/fswiki/FsTutorial/__Tracula> <http://surfer.nmr.mgh.__harvard.edu/fswiki/FsTutorial/__Tracula <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 flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/______complianceline <http://www.partners.org/____complianceline> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline>> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline> <http://www.partners.org/__complianceline <http://www.partners.org/complianceline>>> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___________________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.__harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.____edu/mailman/listinfo/____freesurfer <https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> -- Best regards, Amirhossein Manzouri-- Best regards, Amirhossein Manzouri
25 Jul
25 Jul
2:33 a.m.
New subject: 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" zkaufman@nmr.mgh.harvard.edu 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? If so, why?
-Zeke
On 07/24/2013 11:28 AM, amirhossein manzouri wrote:
Kindly find attached the recon-all.log
On Wed, Jul 24, 2013 at 4:50 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.**harvard.edu zkaufman@nmr.mgh.harvard.edu>> wrote:
Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__**scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: 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 <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.**harvard.edu zkaufman@nmr.mgh.harvard.edu> <mailto:zkaufman@nmr.mgh.__har**vard.edu http://harvard.edu <mailto:zkaufman@nmr.mgh.**harvard.eduzkaufman@nmr.mgh.harvard.edu>>> 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 04:23 PM, amirhossein manzouri wrote: 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
<https://mail.nmr.mgh.harvard.**__edu/pipermail//freesurfer/__**2011-July/019392.html <https://mail.nmr.mgh.harvard.**edu/pipermail//freesurfer/** 2011-July/019392.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html
Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh.__har**vard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu><<mailto:ayendiki@nmr.mgh.__har**vard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu>>>>>wrote:
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_leopard.tar.__gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri <a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com**> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com**>__> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com**> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com**>__>__>> wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should bein three columns as you have mentioned before.
On Wed, Jul 17, 2013 at 5:11 PM, AnastasiaYendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.eduayendiki@nmr.mgh.harvard.edu
<mailto:ayendiki@nmr.mgh.__har**vard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu><<mailto:ayendiki@nmr.mgh.__har**vard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu>>>>>wrote:
Good to hear! Can you please share with all of us what was wrong with your original files? It mayhelp 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__har**vard.eduhttp://harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.eduayendiki@nmr.mgh.harvard.edu
<mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu><<mailto:ayendiki@nmr.mgh.__har**vard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@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 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__har**vard.eduhttp://harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.eduayendiki@nmr.mgh.harvard.edu
<mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu><<mailto:ayendiki@nmr.mgh.__har**vard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu>wrote: 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
<http://surfer.nmr.mgh.__harva**__rd.edu/fswiki/FsTutorial/___**_Tracula http://harva__rd.edu/fswiki/FsTutorial/____Tracula <http://harvard.edu/fswiki/**FsTutorial/__Traculahttp://harvard.edu/fswiki/FsTutorial/__Tracula
<http://surfer.nmr.mgh.__harva**rd.edu/fswiki/FsTutorial/__**Tracula http://harvard.edu/fswiki/FsTutorial/__Tracula <http://surfer.nmr.mgh.**harvard.edu/fswiki/FsTutorial/**Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: DearExperts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval.
-- Bestregards,
Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/______**complianceline<http://www.partners.org/______complianceline> <http://www.partners.org/____**complianceline<http://www.partners.org/____complianceline><http://www.partners.org/____**complianceline<http://www.partners.org/____complianceline> <http://www.partners.org/__**complianceline<http://www.partners.org/__complianceline><http://www.partners.org/____**complianceline<http://www.partners.org/____complianceline> <http://www.partners.org/__**complianceline<http://www.partners.org/__complianceline><http://www.partners.org/__**complianceline<http://www.partners.org/__complianceline> <http://www.partners.org/**complianceline<http://www.partners.org/complianceline>>>>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ______________________________**_____________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.__h**arvard.edu<http://harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard._**___edu/mailman/listinfo/____**freesurfer
<https://mail.nmr.mgh.harvard.**__edu/mailman/listinfo/__**freesurfer<https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Best regards, Amirhossein Manzouri-- Best regards, Amirhossein Manzouri
12:25 p.m.
New subject: 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 the error is happening?
Thanks, a.y
On Thu, 25 Jul 2013, amirhossein manzouri wrote:
Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR
On Jul 24, 2013 5:42 PM, "Z K" zkaufman@nmr.mgh.harvard.edu 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? If so, why? -Zeke On 07/24/2013 11:28 AM, amirhossein manzouri wrote: Kindly find attached the recon-all.log On Wed, Jul 24, 2013 at 4:50 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> wrote: Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: 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 <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> <mailto:zkaufman@nmr.mgh.__harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>>> 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 04:23 PM, amirhossein manzouri wrote: 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/01 9392.html <https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/01939 2.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.ht ml>> Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: 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_leopard.tar.__gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri <a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__>__>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@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 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: 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 <http://surfer.nmr.mgh.__harva__rd.edu/fswiki/FsTutorial/____Tracula <http://harvard.edu/fswiki/FsTutorial/__Tracula> <http://surfer.nmr.mgh.__harvard.edu/fswiki/FsTutorial/__Tracula <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 flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/______complianceline <http://www.partners.org/____complianceline> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline>> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline> <http://www.partners.org/__complianceline <http://www.partners.org/complianceline>>> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___________________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.__harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.____edu/mailman/listinfo/____freesurfer <https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri
29 Jul
29 Jul
3 a.m.
New subject: bvecs error from Tracula
Hi, Kindly find attched the trac-all.log !
On Thu, Jul 25, 2013 at 6:25 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
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 the error is happening?
Thanks, a.y
On Thu, 25 Jul 2013, amirhossein manzouri wrote:
Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR
On Jul 24, 2013 5:42 PM, "Z K" zkaufman@nmr.mgh.harvard.edu 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? If so, why? -Zeke On 07/24/2013 11:28 AM, amirhossein manzouri wrote: Kindly find attached the recon-all.log On Wed, Jul 24, 2013 at 4:50 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.**harvard.edu<zkaufman@nmr.mgh.harvard.edu>>>wrote:
Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__**scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: 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 <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.**harvard.edu<zkaufman@nmr.mgh.harvard.edu><mailto:zkaufman@nmr.mgh.__har**vard.edu<http://harvard.edu> <mailto:zkaufman@nmr.mgh.**harvard.edu<zkaufman@nmr.mgh.harvard.edu>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 04:23 PM, amirhossein manzouri wrote: 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/01 9392.html
<https://mail.nmr.mgh.**harvard.<https://mail.nmr.mgh.harvard.>__edu/pipermail//**freesurfer/__2011-July/01939 2.html <https://mail.nmr.mgh.**harvard.edu/pipermail//** freesurfer/2011-July/019392.hthttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.ht ml>> Thanks,
On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu>wrote: 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_leopard.tar.__**gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri <a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com**> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com**>__> <mailto:a.h.manzouri@gmail.**com<a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com**> <mailto:a.h.manzouri@gmail.**com<a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com**>__>__>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu>wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@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 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu>wrote: 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
<http://surfer.nmr.mgh.__harva**__rd.edu/fswiki/FsTutorial/___**_Traculahttp://harva__rd.edu/fswiki/FsTutorial/____Tracula
<http://harvard.edu/fswiki/**FsTutorial/__Tracula<http://harvard.edu/fswiki/FsTutorial/__Tracula><http://surfer.nmr.mgh.__harva**rd.edu/fswiki/FsTutorial/__**Tracula http://harvard.edu/fswiki/FsTutorial/__Tracula
<http://surfer.nmr.mgh.**harvard.edu/fswiki/FsTutorial/**Tracula 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 flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/______**complianceline<http://www.partners.org/______complianceline> <http://www.partners.org/____**complianceline<http://www.partners.org/____complianceline><http://www.partners.org/____**complianceline<http://www.partners.org/____complianceline> <http://www.partners.org/__**complianceline<http://www.partners.org/__complianceline><http://www.partners.org/____**complianceline<http://www.partners.org/____complianceline> <http://www.partners.org/__**complianceline<http://www.partners.org/__complianceline><http://www.partners.org/__**complianceline<http://www.partners.org/__complianceline> <http://www.partners.org/**complianceline<http://www.partners.org/complianceline>>>>. If the e-mail was
sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri _____________________________**______________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.__**harvard.edu<http://harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard._**___edu/mailman/listinfo/____**freesurfer
<https://mail.nmr.mgh.harvard.**__edu/mailman/listinfo/__**freesurfer <https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri
--
Best regards,
Amirhossein Manzouri
1 Aug
1 Aug
6:22 p.m.
New subject: 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 version of the operating system do you have on your computer and how much memory?
Thanks, a.y
On Mon, 29 Jul 2013, amirhossein manzouri wrote:
Hi, Kindly find attched the trac-all.log !
On Thu, Jul 25, 2013 at 6:25 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
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 the error is happening? Thanks, a.y On Thu, 25 Jul 2013, amirhossein manzouri wrote: Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR On Jul 24, 2013 5:42 PM, "Z K" <zkaufman@nmr.mgh.harvard.edu> 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? If so, why? -Zeke On 07/24/2013 11:28 AM, amirhossein manzouri wrote: Kindly find attached the recon-all.log On Wed, Jul 24, 2013 at 4:50 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> wrote: Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: 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 <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> <mailto:zkaufman@nmr.mgh.__harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>>> 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 04:23 PM, amirhossein manzouri wrote: 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/0 1 9392.html <https://mail.nmr.mgh.harvard.__edu/pipermail//freesurfer/__2011-July/0193 9 2.html <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.h t ml>> Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: 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_leopard.tar.__gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri <a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__>__>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@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 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>> wrote: 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 <http://surfer.nmr.mgh.__harva__rd.edu/fswiki/FsTutorial/____Tracula <http://harvard.edu/fswiki/FsTutorial/__Tracula> <http://surfer.nmr.mgh.__harvard.edu/fswiki/FsTutorial/__Tracula <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 flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/______complianceline <http://www.partners.org/____complianceline> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline>> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline> <http://www.partners.org/__complianceline <http://www.partners.org/complianceline>>> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___________________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.__harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.____edu/mailman/listinfo/____freesurfer <https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri-- Best regards, Amirhossein Manzouri
6 Aug
6 Aug
8:37 a.m.
New subject: bvecs error from Tracula
Hi, I have Mac OS X Version 10.6.8 - Memory 8 GB 1333 MHz DDR3. I want to add 8 GB more memory and also upgrade my OS. Do you think it can help? BR
On Fri, Aug 2, 2013 at 12:22 AM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:
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 version of the operating system do you have on your computer and how much memory?
Thanks, a.y
On Mon, 29 Jul 2013, amirhossein manzouri wrote:
Hi,
Kindly find attched the trac-all.log !
On Thu, Jul 25, 2013 at 6:25 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
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 the error is happening? Thanks, a.y On Thu, 25 Jul 2013, amirhossein manzouri wrote: Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR On Jul 24, 2013 5:42 PM, "Z K" <zkaufman@nmr.mgh.harvard.edu> 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? If so, why? -Zeke On 07/24/2013 11:28 AM, amirhossein manzouri wrote: Kindly find attached the recon-all.log On Wed, Jul 24, 2013 at 4:50 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.**harvard.edu<zkaufman@nmr.mgh.harvard.edu>wrote: Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/__**scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: 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 <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.**harvard.edu<zkaufman@nmr.mgh.harvard.edu><mailto:zkaufman@nmr.mgh.__har**vard.edu <http://harvard.edu> <mailto:zkaufman@nmr.mgh.**harvard.edu<zkaufman@nmr.mgh.harvard.edu>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 04:23 PM, amirhossein manzouri wrote: 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.<https://mail.nmr.mgh.harvard.>____edu/pipermail//**freesurfer/____2011-July/0 1 9392.html
<https://mail.nmr.mgh.**harvard.<https://mail.nmr.mgh.harvard.>__edu/pipermail//**freesurfer/__2011-July/0193 9 2.html <https://mail.nmr.mgh.** harvard.edu/pipermail//**freesurfer/2011-July/019392.hhttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.h t ml>> Thanks,
On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu>wrote: 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_leopard.tar.__**gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri <a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com**> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com**>__> <mailto:a.h.manzouri@gmail.**com <a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com**> <mailto:a.h.manzouri@gmail.**com <a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com**>__>__>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu>wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@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 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu><mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__ha**rvard.edu<http://harvard.edu> <mailto:ayendiki@nmr.mgh.**harvard.edu<ayendiki@nmr.mgh.harvard.edu>wrote: 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
<http://surfer.nmr.mgh.__harva**__rd.edu/fswiki/FsTutorial/___**_Traculahttp://harva__rd.edu/fswiki/FsTutorial/____Tracula
<http://harvard.edu/fswiki/**FsTutorial/__Tracula<http://harvard.edu/fswiki/FsTutorial/__Tracula><http://surfer.nmr.mgh.__harva**rd.edu/fswiki/FsTutorial/__**Tracula http://harvard.edu/fswiki/FsTutorial/__Tracula
<http://surfer.nmr.mgh.**harvard.edu/fswiki/FsTutorial/**Tracula 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 flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/______**complianceline<http://www.partners.org/______complianceline> <http://www.partners.org/____**complianceline<http://www.partners.org/____complianceline><http://www.partners.org/____**complianceline<http://www.partners.org/____complianceline> <http://www.partners.org/__**complianceline<http://www.partners.org/__complianceline><http://www.partners.org/____**complianceline<http://www.partners.org/____complianceline> <http://www.partners.org/__**complianceline<http://www.partners.org/__complianceline><http://www.partners.org/__**complianceline<http://www.partners.org/__complianceline> <http://www.partners.org/**complianceline<http://www.partners.org/complianceline>>>>. If
the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri _____________________________**______________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.__**harvard.edu<http://harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard._**___edu/mailman/listinfo/____**freesurfer
<https://mail.nmr.mgh.harvard.**__edu/mailman/listinfo/__**freesurfer
<https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri-- Best regards, Amirhossein Manzouri
--
Best regards,
Amirhossein Manzouri
11:38 a.m.
New subject: bvecs error from Tracula
Amir,
It appears from your trac-all.og file that the SnowLeopard machine you are on is booted in 64bit mode, but running the 32bit version of freesurfer.
Oddly, the recon-all.log file you sent a couple weeks back was either run on a different machine or it was the same machine booted in 32bit mode.
To fix the error you are getting you either need to reboot your Mac into 32bit mode (this is usually the default, but you can guarantee it by holding the 3 and 2 keys during startup) or if you prefer to be running in 64bit mode than install the 64bit (10.7 64b Intel) version of freesurfer from the following page:
http://surfer.nmr.mgh.harvard.edu/fswiki/Download
Best of luck.
-Zeke
On 08/06/2013 08:37 AM, amirhossein manzouri wrote:
Hi, I have Mac OS X Version 10.6.8 - Memory 8 GB 1333 MHz DDR3. I want to add 8 GB more memory and also upgrade my OS. Do you think it can help? BR
On Fri, Aug 2, 2013 at 12:22 AM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu mailto:ayendiki@nmr.mgh.harvard.edu> wrote:
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 version of the operating system do you have on your computer and how much memory? Thanks, a.y On Mon, 29 Jul 2013, amirhossein manzouri wrote: Hi, Kindly find attched the trac-all.log ! On Thu, Jul 25, 2013 at 6:25 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> wrote: 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 the error is happening? Thanks, a.y On Thu, 25 Jul 2013, amirhossein manzouri wrote: Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR On Jul 24, 2013 5:42 PM, "Z K" <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> 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? If so, why? -Zeke On 07/24/2013 11:28 AM, amirhossein manzouri wrote: Kindly find attached the recon-all.log On Wed, Jul 24, 2013 at 4:50 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> <mailto:zkaufman@nmr.mgh.__harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>>> wrote: Hello Amir, Thanks for that... could you also please provide the recon-all.log file? It will be located in $SUBJECT_DIR/subject_name/____scripts/recon-all.log -Zeke On 07/24/2013 03:01 AM, amirhossein manzouri wrote: 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 <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> <mailto:zkaufman@nmr.mgh.__harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> <mailto:zkaufman@nmr.mgh. <mailto:zkaufman@nmr.mgh.>__har__vard.edu <http://harvard.edu> <mailto:zkaufman@nmr.mgh.__harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>>>> 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 04:23 PM, amirhossein manzouri wrote: 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. <https://mail.nmr.mgh.harvard.>____edu/pipermail//__freesurfer/____2011-July/0 1 9392.html <https://mail.nmr.mgh.__harvard. <https://mail.nmr.mgh.harvard.>__edu/pipermail//__freesurfer/__2011-July/0193 9 2.html <https://mail.nmr.mgh.__harvard.edu/pipermail//__freesurfer/2011-July/019392.h <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.h> t ml>> Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha__rvard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>> <mailto:ayendiki@nmr.mgh <mailto:ayendiki@nmr.mgh>. <mailto:ayendiki@nmr.mgh <mailto:ayendiki@nmr.mgh>.>__ha__r__vard.edu <http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha__rvard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>>> wrote: 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_leopard.tar.____gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri <a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__>__> <mailto:a.h.manzouri@gmail.__com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__> <mailto:a.h.manzouri@gmail.__com <mailto:a.h.manzouri@gmail.com> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com>__>__>__>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha__rvard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>> <mailto:ayendiki@nmr.mgh <mailto:ayendiki@nmr.mgh>. <mailto:ayendiki@nmr.mgh <mailto:ayendiki@nmr.mgh>.>__ha__r__vard.edu <http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha__rvard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>>> wrote: 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha__rvard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>> <mailto:ayendiki@nmr.mgh <mailto:ayendiki@nmr.mgh>. <mailto:ayendiki@nmr.mgh <mailto:ayendiki@nmr.mgh>.>__ha__r__vard.edu <http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha__rvard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@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 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 <ayendiki@nmr.mgh.harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha__rvard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>> <mailto:ayendiki@nmr.mgh <mailto:ayendiki@nmr.mgh>. <mailto:ayendiki@nmr.mgh <mailto:ayendiki@nmr.mgh>.>__ha__r__vard.edu <http://har__vard.edu> <http://harvard.edu> <mailto:ayendiki@nmr.mgh. <mailto:ayendiki@nmr.mgh.>__ha__rvard.edu <http://harvard.edu> <mailto:ayendiki@nmr.mgh.__harvard.edu <mailto:ayendiki@nmr.mgh.harvard.edu>>>>> wrote: 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 <http://surfer.nmr.mgh.__harva____rd.edu/fswiki/FsTutorial/______Tracula <http://harva__rd.edu/fswiki/FsTutorial/____Tracula> <http://harvard.edu/fswiki/__FsTutorial/__Tracula <http://harvard.edu/fswiki/FsTutorial/__Tracula>> <http://surfer.nmr.mgh.__harva__rd.edu/fswiki/FsTutorial/____Tracula <http://harvard.edu/fswiki/FsTutorial/__Tracula> <http://surfer.nmr.mgh.__harvard.edu/fswiki/FsTutorial/__Tracula <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 flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/________complianceline <http://www.partners.org/______complianceline> <http://www.partners.org/______complianceline <http://www.partners.org/____complianceline>> <http://www.partners.org/______complianceline <http://www.partners.org/____complianceline> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline>>> <http://www.partners.org/______complianceline <http://www.partners.org/____complianceline> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline>> <http://www.partners.org/____complianceline <http://www.partners.org/__complianceline> <http://www.partners.org/__complianceline <http://www.partners.org/complianceline>>>> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri _____________________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.__harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh. <mailto:Freesurfer@nmr.mgh.>____harvard.edu <http://harvard.edu> <mailto:Freesurfer@nmr.mgh.__harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard.______edu/mailman/listinfo/______freesurfer <https://mail.nmr.mgh.harvard.____edu/mailman/listinfo/____freesurfer <https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri-- Best regards, Amirhossein Manzouri
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amirhossein manzouri -
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