Dear All
I'm trying to search for the cortical thickness change associated with the
progression of a neurodegenerative disease.
Each patient may have current age, age of onset, disease duration, and disease
severity score.
To find the cortical areas in which cortical thickness is correlated w
Derin,
You might try importing the surfaces into Caret for this. It seems like
there are two needs:
* flat cartesian grid (Menu bar: Layers: Borders: Create Cartesian Flat
Analysis Grid Borders (see attached capture)
* 3-D scale markers (Toolbar: D/C: Surface Miscellaneous: Surface
Cartesian
Thanks!
Yeah, I forgot this. Now, the results look right now.
> Date: Thu, 25 Mar 2010 16:17:33 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: freesurfer...@hotmail.com
> Subject: RE: [Freesurfer] the thickness of manually selected vertex
>
> are you sure you are using 1-based indices in matla
nope, mris_anatomical_stats will take either (with -l or -a I think)
On Thu,
25 Mar 2010, Guang Zeng wrote:
>
> Do I need convert the .label file to an annotation file before I run
> mris_anatomical_stats?
>
> Could I get the same results if I do something like this:
>
> 1. create the label file
Do I need convert the .label file to an annotation file before I run
mris_anatomical_stats?
Could I get the same results if I do something like this:
1. create the label file, and load it using MATLAB,
2. find the corresponding ID of vertices I clicked.
3. load .thickness file using matlab
4. f
I was wondering if someone could help me answer a relatively simple question:
I set up a paradigm file (called recall.par) as follows:
01
18 2
21 3
27 1
45 2
48 3
and so on...
Where in the right column, condition 1 is blank screen, 2 is a room with a lamp,
and
sorry Derin, I just poked through the tksurfer source and can't find it.
I'll try to look more thoroughly later. I think Mary (Sereno) actually
wrote this code to begin with and I modified it, so you could try pinging
him
On Thu, 25 Mar 2010, Derin Cobia
wrote:
> Don't have the source, but I
That's peculiar. I suppose it's somehow related to my display. I
find that when I zoom in at 110% increments, the bar shrinks until I
reach 177% of the default view, where the bar disappears completely.
After this point, the bar expands. That's pretty strange.
Eric
On Mar 25, 2010, at
Don't have the source, but I could download it. What am I looking for? Do you
think it would it be possible to do this in Matlab or something, and import in
(as an overlay maybe)? New territory for me, I'm sorry too... :(
-Derin
On Mar 25, 2010, at 11:00 AM, Bruce Fischl wrote:
> Hi Derin,
Hi Derin,
you could try this in tksurfer, but it isn't terribly well documented or
supported (or remembered by me). I hacked some stuff together in tksurfer
to get those images, but haven't used it in more than 10 years. Do you have
the source? You're welcome to poke through it, but I'm not sur
Hi Eric,
it doesn't shrink for me, it expands. And I'm pretty sure it's 1cm, not
1mm (which is about the vertex spacing), so the guide must be wrong.
We'll fix it
Bruce
On Thu, 25 Mar 2010, Eric Moulton wrote:
> Thanks Bruce. I just checked the TkSurferGuide and noticed that it says the
> sc
Please refer to this wiki for definitions.
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume
On Thu, 25 Mar 2010, Gonzalo Rojas Costa wrote:
Hi:
What is the definition of the following measures that appears at the
beginning of "aseg.stats" file: "Brain Mask Volume", "Brain Segmentatio
Along these same lines, is it possible to overlay/display a Cartesian grid on
the surface, a la the Neuroimage '99 II paper (Fig 7)? And is it possible to
specify what the 'north pole' of this coordinate system is? For example, if I
wanted it to be at the posterior end of the STS. I'm looking
Hi:
What is the definition of the following measures that appears at the
beginning of "aseg.stats" file: "Brain Mask Volume", "Brain Segmentation
Volume Without Ventricles" (BrainSegVolNotVent), "Brain Segmentation Volume"
(BrainSegVol), "Intracranial Volume" (IntraCranialVol, ICV) ?...
The c
Thanks Bruce. I just checked the TkSurferGuide and noticed that it
says the scale bar is 1mm (which looks about right). However, while
the scale bar at the default zoom looks fine, I find that it's length
behaves strangely (it shrinks) when I zoom into the image. Does the
distance value
Hi Eric,
in tksurfer click view->scale bar to see the 1cm bar.
cheers,
Bruce
On Thu, 25 Mar 2010,
Eric Moulton wrote:
> I was wondering if freesurfer has a way of generating a scale for
> distance, similar to what one would see in the legend of a roadmap.
> I'm thinking of using such a scale fo
I was wondering if freesurfer has a way of generating a scale for
distance, similar to what one would see in the legend of a roadmap.
I'm thinking of using such a scale for a 3-d pial surface-render of an
averaged brain (as generated using make_average_surface). Since it's
a 3-d image, I
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