Hi Anri - Is there an error in the stats/*.log files for the different
tracts?
a.y
On Tue, 5 Jul 2016, Anri WATANABE wrote:
Dear Anastasia,
I use TRACULA to obtain diffusion measures at each voxel in a certain pathway
for group analysis, but
there aren't stats/*.path.mean.txt files. I found .log files
(<tract>_PP.avg33_mni_bbr.log) which exist
1 file per 1 tract, except corticospinal tract which has 2 .log files.
Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
Error log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35
corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info
ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35
I attached dmrirc.example (configuration file) and <subjd>/scripts/trac-all.log.
Thanks in advance,
Anri
**********************************************************************
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2016-06-03 9:51 GMT+09:00 Anri WATANABE <z2aa...@koto.kpu-m.ac.jp>:
Hi, Anastasia.
There aren't any .log files but text files like
lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text
files complete all pathways and measures.
**********************************************************************
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2016-06-02 3:03 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:
Thanks, Anri. So the previous steps seem to have run fine. Are there any
.log files
created in the stats/ folder, which is created by trac-all -stat?
On Wed, 1 Jun 2016, Anri WATANABE wrote:
Hi Anastasia, This is a <subjid>/scripts/trac-all.log of one
subject of
the group.
Thanks,
Anri
**********************************************************************
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**********************************************************************
2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:
Hi Anri - Can you also send your log file
(scripts/trac-all.log)?
I'll need to see what
exactly was running when the error occurred. Thanks!
a.y
On Sat, 28 May 2016, Anri WATANABE wrote:
Hello Anastasia,sorry for few information and let me
tell you
command and
error log.
Command: trac-all –stat –c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
Error log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35
corRead(): can't open file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info
ERROR: Could not read
/Applications/freesurfer/subjects/cvs_avg35
dmrirc.example (configuration file) is attached to this
e-mail.
Thanks in advance,
Anri
**********************************************************************
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of
Medicine
**********************************************************************
2016-05-27 22:57 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:
Hi Anri - I do not know what command line you ran
and
what your
configuration file looks like, so it is very
hard for me to suggest solutions.
Best,
a.y
On Fri, 27 May 2016, Anri WATANABE wrote:
Hi Anastasia,
Thank you for your answer.
There aren't stats/*.path.mean.txt files and
terminal says 'Could
not read
/Applications/freesurfer/subjects/cvs_avg35.' I
checked
/Application/freesurfer/subjects/cvs_avg35 folder and
couldn't find COR-.info file.
Could you tell me any resolutions, please?
Thanks,
Anri
**********************************************************************
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural
University
of Medicine
**********************************************************************
2016-05-21 6:48 GMT+09:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:
Hi Anri - The FA values are extracted
in
the native space
of each subject, which is why
those are the only
coordinates that you see. If you want
to
display the
results of your analysis on an average
path, after
running trac-all -stat, you can use
the
stats/*.path.mean.txt files (see also the last part
of the TRACULA
tutorial).
Best,
a.y
On Wed, 18 May 2016, Anri WATANABE
wrote:
Dear experts,
I use TRACULA to examine a
measure
(FA) at each voxel
in one pathway.
pathstats.byvoxel.txt files show
coordinates in
native space and after converting
those the new
files don't show any coordinates
which are in MNI
space.
Could you tell me how can I
know MNI
coordinate
values?
Thank you!
Regards,
Anri
**********************************************************************
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**********************************************************************
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto
Prefectural University of
Medicine
**********************************************************************
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