Coordinates in TRACULA group analysis

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Anri WATANABE

18 May 2016 18 May '16

5:39 a.m.

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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Anastasia Yendiki

20 May 20 May

5:48 p.m.

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

Anri WATANABE

26 May 26 May

10:44 p.m.

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

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

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.

Anastasia Yendiki

27 May 27 May

9:57 a.m.

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
        **********************************************************************
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.

Anri WATANABE

8:49 p.m.

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

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
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.

Anastasia Yendiki

31 May 31 May

9:55 a.m.

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
                    **********************************************************************


        _______________________________________________
        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.

Anri WATANABE

1 Jun 1 Jun

1:24 a.m.

Hi Anastasia, This is a <subjid>/scripts/trac-all.log of one subject of the group.

Thanks, Anri

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
        _______________________________________________
        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.
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.

Anastasia Yendiki

2:03 p.m.

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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                    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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        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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Anri WATANABE

2 Jun 2 Jun

8:51 p.m.

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.

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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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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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.

Anri WATANABE

5 Jul 5 Jul

4:44 a.m.

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

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
                    _______________________________________________
                    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.

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.

Anastasia Yendiki

7 Jul 7 Jul

7:12 a.m.

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,

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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                    _______________________________________________
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                    The information in this e-mail is intended only for the
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                    addressed. If you believe this e-mail was sent to you in
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        The information in this e-mail is intended only for the person to whom it
        is
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        e-mail
        contains patient information, please contact the Partners Compliance
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Anri WATANABE

11 Jul 11 Jul

4:12 a.m.

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

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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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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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.

Anastasia Yendiki

12 Jul 12 Jul

5:16 p.m.

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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Anri WATANABE

14 Jul 14 Jul

6:29 p.m.

Hi, Anastasia This is trac-all.local-copy from 1 subject. Thank you!

Anri

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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Anastasia Yendiki

27 Jul 27 Jul

12:17 a.m.

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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Anri WATANABE

31 Jul 31 Jul

12:09 a.m.

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

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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Anastasia Yendiki

12:22 a.m.

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 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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        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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                    addressed. If you believe this e-mail was sent
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                                            you in error
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                    contains patient information, please contact
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                                            Partners
                                                        Compliance
                    HelpLine at
                                                                   
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                                                        to you in error
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                    does not contain patient information,
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                                            contact the
                                                        sender and
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                    _______________________________________________
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                    mailing list
                                                       
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        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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                                            error and the e-mail
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Anri WATANABE

12:34 a.m.

Thanks, Anastasia I 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

2016-07-31 13:22 GMT+09:00 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu:

...

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 < 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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Anastasia Yendiki

9:49 a.m.

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 ayendiki@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
        <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



                                                                         
                 
                                       
                                                                   
                                                       
                               
                   
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                                        京都府立医科大学附属病院
                                                                         
                 
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                                        Anri WATANABE, M.D.
                                                                         
                 
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Anri WATANABE

3 Aug 3 Aug

7:19 a.m.

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

2016-07-31 22:49 GMT+09:00 Anastasia Yendiki ayendiki@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 < ayendiki@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
        <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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Anastasia Yendiki

10:15 a.m.

That's correct!

On Wed, 3 Aug 2016, Anri WATANABE wrote:

...

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 ayendiki@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 <ayendiki@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
                    <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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[クリップしたメッセージ] _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Anri WATANABE

6:42 p.m.

Thanks so much!!

2016-08-03 23:15 GMT+09:00 Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu:

...

That's correct!

On Wed, 3 Aug 2016, Anri WATANABE wrote:

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 < ayendiki@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 <
ayendiki@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
                    <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
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