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 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 ayend...@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 zkauf...@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 zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@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 zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.__harvard.edu mailto:zkauf...@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 ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.__harvard.edu mailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.
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 zkauf...@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 zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.**harvard.edu zkauf...@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 zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.** harvard.edu zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.__har**vard.edu http://harvard.edu mailto:zkauf...@nmr.mgh.**harvard.eduzkauf...@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 ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.__har**vard.eduhttp://harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh. mailto:ayend...@nmr.mgh.__ha**r__vard.eduhttp://har__vard.edu http://harvard.edu mailto:ayend...@nmr.mgh.__har**vard.eduhttp://harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@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.manzo...@gmail.com mailto:a.h.manzo...@gmail.com** mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com**__ mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com** mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@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 ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.__har**vard.eduhttp://harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh. mailto:ayend...@nmr.mgh.__ha**r__vard.eduhttp://har__vard.edu http://harvard.edu mailto:ayend...@nmr.mgh.__har**vard.eduhttp://harvard.edu
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 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 zkauf...@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 zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@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 zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.__harvard.edu mailto:zkauf...@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 ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.__harvard.edu mailto:ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh. mailto:ayend...@nmr.mgh.__har__vard.edu http://harvard.edu mailto:ayend...@nmr.mgh.__harvard.edu mailto:ayend...@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.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com__ mailto:a.h.manzo...@gmail.com mailto:a.h.manzo...@gmail.com
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 zkauf...@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.htmlhttps://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 mailto:ayend...@nmr.mgh.**harvard.eduayend...@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.manzo...@gmail.com mailto:a.h.manzo...@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 ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@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 ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@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 ayend...@nmr.mgh.harvard.edu mailto:ayend...@nmr.mgh.**harvard.eduayend...@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.**harvard.edu/fswiki/FsTutorial/**Traculahttp://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
Re: [Freesurfer] bvecs error from Tracula
Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/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.manzo...@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 ayend...@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 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 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 your original bvecs/bvals in 3-row format instead of 3-column format? 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: 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/**compliancelinehttp://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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
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_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.manzo...@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 ayend...@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 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 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 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 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 . 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
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 - 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.manzo...@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 ayend...@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 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 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 your original bvecs/bvals in 3-row format instead of 3-column format? 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: 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/**compliancelinehttp://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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the
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 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 your original bvecs/bvals in 3-row format instead of 3-column format? 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: 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/**compliancelinehttp://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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
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 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 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 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 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 . 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
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 your original bvecs/bvals in 3-row format instead of 3-column format? 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: 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/**compliancelinehttp://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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
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 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@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 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 . 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 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.586792 -0.376583 -0.716841 0.894195 0.022917 0.447091 0.729281 -0.410970 0.547041 -0.154251 0.964369 -0.214941 0.117136 0.773539 -0.622830 -0.407575 -0.414994 -0.813427 0.211330 0.753738 0.622269 0.095375 -0.969517 0.225700 -0.135450 -0.033490 -0.990218 -0.142125 -0.750521 -0.645383 -0.637009 0.746109 -0.193757 0.080563 0.971669 0.222192 0.106871 -0.021213 0.994047 0.298747 0.387214 0.872247 -0.207492 -0.803432 0.558072 0.331125 -0.040337 -0.942724 -0.805294 -0.589494 -0.063231 0.337278 -0.749774 -0.569282 0.592396 -0.761390 0.263348 -0.088979 -0.465650 0.880485 -0.527982 -0.430927 0.731803 -0.369111 -0.927082 0.065397 0.311914 0.926381 -0.211018 -0.684511 0.439336 -0.581746 -0.030114 -0.966623 -0.254425 -0.337568 0.744654 -0.575794 -0.574804 0.024806 -0.817915 0.271135 -0.747834 0.605996 -0.935185 0.185421 0.301743 0.889083 0.309665 -0.337104 -0.884343 0.033574 -0.465629 0.545045 0.586317 -0.599298 -0.350774 -0.016274 0.936319 0.416158 -0.900528 -0.125943 -0.732654 0.003250 0.680593 -0.739209 0.611423 0.282368 -0.256353 0.406875 -0.876776 -0.919023 0.372522 -0.128933 -0.257293 0.765486 0.589773 -0.589833 0.433953 0.681016 0.891136 -0.185957 -0.413881 0.679067 0.142105 -0.720190 -0.879811 -0.309554 0.360705 -0.621609 -0.697195 0.357102 0.897050 -0.430209 0.101102 -0.163347 0.417893 0.893691 -0.507183 -0.778309 -0.370136 0.107015 -0.446398 -0.888412 0.883485 0.435264 0.173205 0.598171 0.029843 0.800812 0.696192 0.698104 -0.167236 -0.393556 0.900808 0.183464 -0.761088 -0.402897 -0.508350 0.210324 0.396164 -0.893766 0.376032 -0.378955 0.845572 0.735763 -0.611461 -0.291148 -0.987214 -0.145866 -0.064273 0.529212 0.807365 0.260953 0.662918 0.472672 0.580621 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
[Freesurfer] bvecs error from Tracula
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 bvals Description: Binary data bvecs Description: Binary data dwi_orig.mghdti.bvals Description: Binary data dwi_orig.mghdti.bvecs Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
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 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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.
