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 <ayend...@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 <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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