Hi,
after running recon-all on many datasets without any manual
intervention, it looks like I finally have to.
As you can see in :
https://dl.dropboxusercontent.com/u/2140486/Screen%20Shot%202013-08-28%20at%2013.16.52.png
the CSF is segmented as gray matter while white+gray matters are merged.
Hi Doug,
Thanks! I actually thought I only had to demean variables that were not of
interest.
But this was indeed the problem, it now works!
Thank you very much!
Best
Heidi
Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life S
Dear all,
Is there available a function that, given a certain ROI, returns per vertex
thickness (not the average thickness)?
Thanks
Cheers
Giusy Chinnici
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Hi Alex
that's pretty bad! You could start by specifying some expert options about
the ranges of gray and white matter intensities to mri_segment and
mris_make_surfaces. Hopefully someone will chime in with the syntax, as I
don't remember it. You can also check the recon-all.log to see what ran
you mean only within that ROI? I don't think so, but this would be pretty
easy in matlab
On Wed, 28 Aug 2013, Giusy Chinnici wrote:
> Dear all,
>
> Is there available a function that, given a certain ROI, returns per vertex
> thickness (not the average thickness)?
>
> Thanks
> Cheers
>
> Giusy C
Giusy,
You can access vertex level info in Matlab with MRIread('SUBJECT.FILENAME').
Avram
On Wed, Aug 28, 2013 at 8:42 AM, Giusy Chinnici wrote:
> Dear all,
>
> Is there available a function that, given a certain ROI, returns per
> vertex thickness (not the average thickness)?
>
> Thanks
> Che
In general, you should not need to demean. For the interaction, you need
to demean before computing the interaction.
doug
On 08/28/2013 07:54 AM, Jacobs H (NP) wrote:
> Hi Doug,
>
> Thanks! I actually thought I only had to demean variables that were not of
> interest.
> But this was indeed th
Question regarding longitudinal processing pipeline.
Is there a way to force the -long procedure to use an individual base template
for a time point not used to create the base in the first place?
David F. Tate, Ph.D.
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JoJo,
I have not tried to recreate your issues on machine running Ubuntu 13.04
but have tried to run the commands on Ubuntu 12.04. To summarize:
1) Regarding your first issue... this is standard output to the terminal
on certain OS's including Ubuntu. I got it when I tested your command
but th
I see some reports of license failures, and seem to be having a similar
problem. Our installations of 4.5 and 5.1 work normally, but with 5.3 I had
a mysterious error in unpacksdcmdir that ultimately traced to a license
error in mri_convert. I can reproduce the error like so:
*mri_convert $FREESUR
Hello,
I am having a few issues with editing the pial surface in freeview. It appears
as though the edits I make to the brainmask are not being taken into account
when I re-run recon-all. I work on a MacBook Pro and have been using
"shift+click" to delete voxels at a brush value of 1 and then s
Are you saying that edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are not showing up as affecting the actual pial surfaces themselves?
I would focus on whether the pial surfaces are fixed, not whether edits to brain.finalsurfs.manedit.mgz are "back-propagated" to brainmask.mgz. (I
you can use read_label and the first column (+1) for the indices
Bruce
On Wed, 28
Aug 2013, Giusy Chinnici wrote:
Thanks all,
I opened the file subj/surf/?h.thickness with MATLAB using the function
read_curv(subj/surf/lh.thickness). I obtained a vector with dimensions
nverticesX1, but I need
Dear colleagues,
I wanted to draw your attention on the upcoming Brainhack 2013, which is
being held from October 23-26 at the Centre International d'Études
Pédagogiques, Sèvres, France (just outside of Paris).
Brainhack 2013 is a unique workshop with the goals of fostering
interdisciplinary coll
If you're following the instructions of the tutorial, then I don't know why your edits to brain.finalsurfs.manedit.mgz wouldn't be reflected in the pial surface.
Perhaps one of the FS developers will have a thought as to what is going wrong.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Thanks all,
I did it :)
Cheers
Giusy
Inviato da iPhone
Il giorno 28/ago/2013, alle ore 18:40, Avram Holmes ha
scritto:
> check the .vol values I think they should match those from read_curv.
>
> Avram
>
>
> On Wed, Aug 28, 2013 at 11:37 AM, Giusy Chinnici
> wrote:
>> Thanks all,
>>
>> I
Dear all,
I am interested in looking at developmental changes in the brain during
adolescence period in normal subjects and also comparing our controls to our
clinical patients. Examples in the longitudinal processing stream tutorial have
only mentioned volume and thickness, so I was wondering
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