Hi Anastasia, Thank you! It seems work well!! I have another question. Are ROIs for automatic tractography in TRACULA the same ROIs presented in Wakana et al. 2007?
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 ********************************************************************** 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: > > Hi Anri - The problem is in this line: > > set cmd = ($cmd --ref $cvstempdir/$cvstemp) > > It should be changed to this: > > set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz) > > For this to take effect, you need to run "which trac-all" and make the > change in the trac-all file that the which commands shows you. > > Hope this helps, > > a.y > > On Fri, 15 Jul 2016, Anri WATANABE wrote: > > Hi, AnastasiaThis 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. 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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. > >
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