I think you want to use flat.[xyz], but I'm not that familiar with the
patch function
cheers
Bruce
On Wed, 13 May 2015, Sarah Finnegan
wrote:
Hi Bruce,
Thanks thats great to know, I have an ellipsoid fitting function ready for
the job.
I've started the process of getting the occipital flatpatch into MATLAB
following some forums posts, the best route seems to be as follows but i'm
getting an error message.
I can't find anyone posting a solution, can I ask where I'm going wrong?
Thanks
Sarah
>> flat=read_patch_asc('lh.occip.patch.flat.asc');
>> vertices=flat.vertices;
>> faces=flat.faces;
faces is a 91532x3 matrix and vertices is a 46120x1 array, I then shift
everything by 1 as MATLAB starts there rather than 0 and attempt to
visualise the patch using
>> p=patch('faces',faces(:,[1
32]),'vertices',vertices,'facecolor','flat','edgecolor','none','facealpha',1
);
Error using patch
Vertices array must have at least 2 and at most 3 columns (or be empty)
____________________________________________________________________________
From: Sarah Finnegan
Sent: 12 May 2015 10:51
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: Taking a measure of cluster width and length on flat surface
Hi Bruce
Thanks for the information on the flat patch, thats great that the
relationships are preserved!
With that in mind do you know if freesurfer has any inbuilt functions to
take the kind of measurements that I was describing? Or will my MATLAB based
proposal be the best option do you think?
Thanks again!
Sarah
____________________________________________________________________________
From: Sarah Finnegan
Sent: 11 May 2015 17:13
To: Freesurfer support list [freesurfer@nmr.mgh.harvard.edu]
Subject: Taking a measure of cluster width and length on flat surface
Dear all,
I am looking to take two measures within the visual cortex.
1) A measure of width and length for each activation cluster overlaid onto
the flattened cortical surface.
2) A measure of spacing between each cluster
I can find how to take measures of area but I specifically want to know the
width and length separately to correlate this to potential stripe systems.
My plan was to fit an oval to each of these clusters and measure length
through the cardinal axis and width through the minor, spacing would be
calculated from a line fit to the minor axis of each cluster. Unfortunately
I think the unfolding process will have changed the spacing relationships
between clusters to make this inappropriate.
I wonder if there is a command or established pipeline to take such
measures?
Thanks for your help!
Sarah
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