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. 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lh.cst_AS.avg33_cvs_bbr.log
Description: Binary data
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