Hi, Anastasia. There aren't any .log files but text files like lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text files complete all pathways and measures.
********************************************************************** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ********************************************************************** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ********************************************************************** 2016-06-02 3:03 GMT+09:00 Anastasia Yendiki <[email protected]>: > > Thanks, Anri. So the previous steps seem to have run fine. Are there any > .log files created in the stats/ folder, which is created by trac-all -stat? > > > On Wed, 1 Jun 2016, Anri WATANABE wrote: > > Hi Anastasia, This is a <subjid>/scripts/trac-all.log of one subject of >> the group. >> >> Thanks, >> Anri >> >> ********************************************************************** >> 京都府立医科大学附属病院 >> 精神科・心療内科 >> 渡辺 杏里 >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> ********************************************************************** >> >> 2016-05-31 22:55 GMT+09:00 Anastasia Yendiki < >> [email protected]>: >> >> Hi Anri - Can you also send your log file (scripts/trac-all.log)? >> I'll need to see what >> exactly was running when the error occurred. Thanks! >> >> a.y >> >> On Sat, 28 May 2016, Anri WATANABE wrote: >> >> Hello Anastasia,sorry for few information and let me tell you >> command and >> error log. >> Command: trac-all –stat –c >> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example >> >> Error log: Loading output reference volume from >> /Applications/freesurfer/subjects/cvs_avg35 >> >> corRead(): can't open file >> /Applications/freesurfer/subjects/cvs_avg35/COR-.info >> >> ERROR: Could not read >> /Applications/freesurfer/subjects/cvs_avg35 >> >> >> dmrirc.example (configuration file) is attached to this >> e-mail. >> >> Thanks in advance, >> Anri >> >> >> >> >> ********************************************************************** >> 京都府立医科大学附属病院 >> 精神科・心療内科 >> 渡辺 杏里 >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> >> ********************************************************************** >> >> 2016-05-27 22:57 GMT+09:00 Anastasia Yendiki < >> [email protected]>: >> >> Hi Anri - I do not know what command line you ran and >> what your >> configuration file looks like, so it is very >> hard for me to suggest solutions. >> >> Best, >> a.y >> >> On Fri, 27 May 2016, Anri WATANABE wrote: >> >> Hi Anastasia, >> Thank you for your answer. >> There aren't stats/*.path.mean.txt files and >> terminal says 'Could >> not read >> /Applications/freesurfer/subjects/cvs_avg35.' I >> checked >> /Application/freesurfer/subjects/cvs_avg35 folder and >> couldn't find COR-.info file. >> Could you tell me any resolutions, please? >> >> Thanks, >> Anri >> >> >> >> ********************************************************************** >> 京都府立医科大学附属病院 >> 精神科・心療内科 >> 渡辺 杏里 >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University >> of Medicine >> >> >> ********************************************************************** >> >> 2016-05-21 6:48 GMT+09:00 Anastasia Yendiki >> <[email protected]>: >> >> Hi Anri - The FA values are extracted in >> the native space >> of each subject, which is why >> those are the only >> coordinates that you see. If you want to >> display the >> results of your analysis on an average >> path, after >> running trac-all -stat, you can use the >> stats/*.path.mean.txt files (see also the last part >> of the TRACULA >> tutorial). >> >> Best, >> a.y >> >> On Wed, 18 May 2016, Anri WATANABE wrote: >> >> Dear experts, >> I use TRACULA to examine a measure >> (FA) at each voxel >> in one pathway. >> pathstats.byvoxel.txt files show >> coordinates in >> native space and after converting >> those the new >> files don't show any coordinates >> which are in MNI >> space. >> Could you tell me how can I know MNI >> coordinate >> values? >> >> Thank you! >> >> >> Regards, >> Anri >> >> >> >> >> >> ********************************************************************** >> 京都府立医科大学附属病院 >> 精神科・心療内科 >> 渡辺 杏里 >> >> >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto >> Prefectural University of >> Medicine >> >> >> ********************************************************************** >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> >> 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 mailing list >> [email protected] >> 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 mailing list >> [email protected] >> 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 mailing list > [email protected] > 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 mailing list [email protected] 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.
