Re: [Freesurfer] Coordinates in TRACULA group analysis

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.

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京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里

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Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine

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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

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京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里

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Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine

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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

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        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
                                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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