Hi, Anastasia This is trac-all.local-copy from 1 subject. Thank you! 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 ********************************************************************** 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: > > Hi Anri - This may be a bug that was fixed at some point. Can you send me > the scripts/trac-all.local-copy from one of your subjects? Thanks! > > a.y > > On Mon, 11 Jul 2016, Anri WATANABE wrote: > > Hi Anastasia,There is an error in .log files of left corticospinal tract >> in cvs template and I attached one >> >> of file. In addition .log files of right corticospinal tract in cvs >> template doesn't exist. >> 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 >> ********************************************************************** >> >> 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu>: >> >> Hi Anri - Is there an error in the stats/*.log files for the >> different tracts? >> >> a.y >> >> On Tue, 5 Jul 2016, Anri WATANABE wrote: >> >> Dear Anastasia, >> >> I use TRACULA to obtain diffusion measures at each voxel in a >> certain pathway for >> group analysis, but >> there aren't stats/*.path.mean.txt files. I found .log files >> (<tract>_PP.avg33_mni_bbr.log) which exist >> 1 file per 1 tract, except corticospinal tract which has 2 >> .log files. >> >> 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 >> >> >> I attached dmrirc.example (configuration file) and >> <subjd>/scripts/trac-all.log. >> >> >> 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 >> >> ********************************************************************** >> >> 2016-06-03 9:51 GMT+09:00 Anri WATANABE < >> z2aa...@koto.kpu-m.ac.jp>: >> 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 < >> ayend...@nmr.mgh.harvard.edu>: >> >> 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 >> <ayend...@nmr.mgh.harvard.edu>: >> >> 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 >> <ayend...@nmr.mgh.harvard.edu>: >> >> 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 >> <ayend...@nmr.mgh.harvard.edu>: >> >> 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 >> >> 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 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 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 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 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 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. > >
trac-all.local-copy
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.
