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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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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