Hi, I would need to extract multiple labels from the aparc+aseg labelmap.
I am using the mri_extract_label command, but by default all the labels of
the output file are coded with the same number. Would it be possible to
change such behavior, and extract multiple labels while assigning different
Hi there,
I have a couple questions regarding TRACULA results.
When I visualize the probability distributions of all white-matter pathways
simultaneously in some cases the tracts are very small, but by adjusting
the threshold I am able to visualize the tract in its entire (and expected)
path.
that is further than 5mm from cortex. You
can change the threshold so that it labels all of WM regardless of the
distance. Other than that, I don't have much to suggest.
doug
On 11/18/14 6:13 PM, Michele Cavallari wrote:
Hi, I am planning to perform some regional analysis of the frontal white
like
recon-all -s subject -wmparc -expert YourXOptsFile
2. Look in recon-all.log for the mri_aparc2aseg command, cut and paste
it into the terminal, add
--wmparc-dmax 100, and run
On 11/19/2014 11:34 AM, Michele Cavallari wrote:
Hi Douglas, thanks for your reply. Is there a way to rerun only
will find it is substantially faster (if you have a
multi-core machine)
cheers
Bruce
On Wed, 19 Nov 2014, Michele Cavallari wrote:
Hi Douglas, thanks for your reply. Is there a way to rerun only WM
segmentation with the threshold option, without going through the whole
time-consuming FS
it is substantially faster (if
you have a multi-core machine)
cheers
Bruce
On Wed, 19 Nov 2014, Michele Cavallari wrote:
Hi Douglas, thanks for your reply. Is there a way to rerun only WM
segmentation with the threshold option, without going through the whole
time-consuming FS pipeline
Hi, I am planning to perform some regional analysis of the frontal white
matter as a whole, and asking here for suggestions/help.
From the FS output wmparc.mgz I could select and merge the following labels
to define my ROI
parsorbitalis [4019, 3019]
parstriangularis [4020, 3020]
errata corrige: it did work! I had to re-run the whole thing including only
that specific tract...and eventually it worked.
On Fri, Sep 12, 2014 at 11:19 AM, Michele Cavallari
cavallari.mich...@gmail.com wrote:
Tried...unfortunately it didn't improve
On Thu, Sep 11, 2014 at 4:56 PM, Chris
Tried...unfortunately it didn't improve
On Thu, Sep 11, 2014 at 4:56 PM, Chris Watson
christopher.wat...@childrens.harvard.edu wrote:
You can try just re-running trac-prep -prior and trac-paths for the
L uncinate and no other tracts
On 09/11/2014 02:58 PM, Michele Cavallari wrote:
So, I
of trac-all on this
subject.
On Wed, 10 Sep 2014, Michele Cavallari wrote:
uploaded (and activated).Thanks!
On Wed, Sep 10, 2014 at 1:14 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
Hi Michele - The anatomical segmentation does look good, but from
the
screenshot
now it reads the path to your file as a flag, which is of course not
what you want.
Best,
Barbara
On 11/09/2014 17:49, Michele Cavallari wrote:
Hi Anastasia,
I am probably doing something wrong with the syntax of the dmrirc file.
I get this error message
trac-all -prior
/Users
, 2014 at 1:36 PM, Michele Cavallari
cavallari.mich...@gmail.com wrote:
Thanks! it's running...
On Thu, Sep 11, 2014 at 1:31 PM, Barbara Kreilkamp
bakk@googlemail.com wrote:
Hi Michele,
Don't think there is anything wrong with the attached dmrirc.tutorial
file.
You definitely need
the uncinate. It's hard to tell just from one slice.
If you upload all the tracula output directories of this subject (dmri,
dmri.bedpostX, dlabel, dpath) for me here, I'll take a look:
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks!
a.y
On Wed, 10 Sep 2014, Michele Cavallari wrote
-formatted gradient tables, you have to make sure you have the
latest version of tracula, as that option was added more recently:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
Hope this helps,
a.y
On Thu, 28 Aug 2014, Michele Cavallari wrote:
Hi,
I'm having some problems
/FSout
(Or whatever the location of your freesurfer recons is.)
a.y
On Wed, 3 Sep 2014, Michele Cavallari wrote:
Hi Barbara,I checked the path. The folder with the trac-all output is is
the
very same folder of the dwi dicoms.
Attached is the dmrirc file I am using, with all the specs
On 03.09.14 17:31, Michele Cavallari wrote:
Hi Barbara,
thanks again for your help.
I checked the bvecs file using the 'more' command, and (as you pointed
out) there was some extra text. This was likely due to MS-excel formatting,
which I have used to reshape the bvecs file from row to column
the same amount of
volumes as entries in bvec and bval?
Good luck,
Barbara
On 28/08/2014 22:47, Michele Cavallari wrote:
Hi,
I'm having some problems with the first command of the tracula pipeline.
I am using FreeSurfer 5.3 on a mac (OS 10.9).
The problem seems to be related to the bvecs file. I
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