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 <ayend...@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
<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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