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 <ayend...@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
<ayend...@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
<ayend...@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
<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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