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.edu<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.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<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 >> <mailto:ayend...@nmr.mgh.**harvard.edu<ayend...@nmr.mgh.harvard.edu> >> > >> <mailto:ayend...@nmr.mgh.__har**vard.edu<http://harvard.edu> >> <mailto:ayend...@nmr.mgh.**harvard.edu<ayend...@nmr.mgh.harvard.edu> >> >> >> <mailto:ayend...@nmr.mgh. >> <mailto:ayend...@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu>< >> http://harvard.edu> >> >> <mailto:ayend...@nmr.mgh.__har**vard.edu<http://harvard.edu> >> >> <mailto:ayend...@nmr.mgh.**harvard.edu<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**> >> >> <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.edu<ayend...@nmr.mgh.harvard.edu> >> > >> <mailto:ayend...@nmr.mgh.__har**vard.edu<http://harvard.edu> >> <mailto:ayend...@nmr.mgh.**harvard.edu<ayend...@nmr.mgh.harvard.edu> >> >> >> <mailto:ayend...@nmr.mgh. >> <mailto:ayend...@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu>< >> http://harvard.edu> >> >> <mailto:ayend...@nmr.mgh.__har**vard.edu<http://harvard.edu> >> >> <mailto:ayend...@nmr.mgh.**harvard.edu<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 <mailto:ayend...@nmr.mgh.** >> harvard.edu <ayend...@nmr.mgh.harvard.edu>> >> <mailto:ayend...@nmr.mgh.__har**vard.edu<http://harvard.edu> >> <mailto:ayend...@nmr.mgh.**harvard.edu<ayend...@nmr.mgh.harvard.edu> >> >> >> <mailto:ayend...@nmr.mgh. >> <mailto:ayend...@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu>< >> http://harvard.edu> >> >> <mailto:ayend...@nmr.mgh.__har**vard.edu<http://harvard.edu> >> <mailto:ayend...@nmr.mgh.**harvard.edu<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 <mailto:ayend...@nmr.mgh.** >> harvard.edu <ayend...@nmr.mgh.harvard.edu>> >> <mailto:ayend...@nmr.mgh.__har**vard.edu<http://harvard.edu> >> <mailto:ayend...@nmr.mgh.**harvard.edu<ayend...@nmr.mgh.harvard.edu> >> >> >> <mailto:ayend...@nmr.mgh. >> <mailto:ayend...@nmr.mgh.>__ha**r__vard.edu<http://har__vard.edu>< >> http://harvard.edu> >> >> <mailto:ayend...@nmr.mgh.__har**vard.edu<http://harvard.edu> >> <mailto:ayend...@nmr.mgh.**harvard.edu<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 >> >> >> >> <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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.__h**arvard.edu<http://harvard.edu> >> >> <mailto:freesur...@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 >> >> >>
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