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.
So,
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
la
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 received the foll
;
> Hope it helps,
> All the best,
> Barbara
>
>
> 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
it into a unix text editor, it shows up fine.
>
> For row-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
&g
b
>
> with:
> setenv SUBJECTS_DIR /PHShome/my738/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
&g
>> 1. Convert it to 3 columns so you can use it with the 5.3 version of
>> tracula, which requires the gradient table to be formatted in
>> columns
>>
>> OR
>>
>> 2. Download the tracula update that can use gradient tables
>> f
te, and then rerun the -prior and -path steps 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.
tion file.
> Right 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
n Thu, Sep 11, 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
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
>
>
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
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]
lateralorbitofron
an 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
ike
> 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, tha
u 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 thr
ed to run to the end. The good news is
> >> that when we get V6 out you will find it is substantially faster (if
> >> you have a multi-core machine)
> >>
> >> cheers
> >> Bruce
> >> On Wed, 19 Nov 2014, Michele Cavallari wrote:
> >>
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