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 ayendiki@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 <ayendiki@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 <ayendiki@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 <z2aanri@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 <ayendiki@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 <ayendiki@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 <ayendiki@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 <ayendiki@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
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