Hi Anastasia, Thank you for your kind explanation. I can be understanding how TRACULA tracts white matter pathways. At each position (in training subjects, not in new subjects of my data) probability that next goes for which direction to every labels in the aparc+aseg (not with setting a certain ROI) is computed with use of training subjects. The prior probabilities are made from training subjects (your publication in 2011) and they are based on manual labeling (the manual labeling tracts are referred to Wakana et al. 2007). Then when white matter pathways are reconstructed in my subjects, TRACULA computes anatomical priors in each subjects in my data in pre-processing and probability distributions from anatomical priors and by fitting ball-and-stick model. Is this comprehension ok?
Best 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 ********************************************************************** 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: > > Hi Anri - Instead of hard-coding some ROIs in the white matter that the > tract is forced to go through, TRACULA uses information like "what is the > probability that this tract goes lateral/anterior/etc to XXX", where XXX > any of the labels in the aparc+aseg. TRACULA computes these prior > probabilities from a set of training subjects, where the tracts have been > labeled manually. So it knows how likely a tract is to go through a certain > aparc+aseg label, or to he left, right, anterior, etc of a certain > aparc+aseg label. This is computed separately at each position along the > tract. It's computed from the training subjects, and then used when > reconstructing the tract in the new subject that you run TRACULA on. > > Hope this helps, > a.y > > On Sun, 31 Jul 2016, Anri WATANABE wrote: > > Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if >> ROIs are not >> >> set how determine the origin and the end of a certain tract? I think that >> the first we >> have to determine the origin and the end of the tract, the second it >> constructs possible >> pathway not with the deterministic way (only 1 direction / 1 voxel) but >> with the >> probabilistic way (considering which direction should be next to). Is >> this comprehension >> wrong? >> 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 >> ********************************************************************** >> >> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu>: >> >> Hi Anri - TRACULA does not use deterministic ROIs. It uses a >> probabilistic >> model of how likely each tract is to go through or next to each of >> the labels >> of the freesurfer subcortical segmentation and cortical >> parcellation, as a >> function of position along the trajectory of the tract. >> >> Best, >> a.y >> >> On Sun, 31 Jul 2016, Anri WATANABE wrote: >> >> 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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