Thanks so much!!
**
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
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
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
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
Thanks, Anastasia
I 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
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,
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
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
Hi, Anastasia
This 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,
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
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
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
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
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 /scripts/trac-all.log of one subject of the
group.
Thanks,
Anri
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
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
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,
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
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?
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