Re: [Freesurfer] Taking a measure of cluster width and length on flat surface
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 3
2]),'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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Re: [Freesurfer] Taking a measure of cluster width and length on flat surface
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Taking a measure of cluster width and length on flat surface
Hi Sarah I don't think we have anything for ellipsoid fitting, although Oliver Hinds did some in his paper on V1. Should be straightforward enough in matlab. The data are in 2D mm coords cheers Bruce On Tue, 12 May 2015, Sarah Finnegan wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Taking a measure of cluster width and length on flat surface
Hi Sarah the unfolding tries very hard to preserve exactly this - the metric properties. If you cut off the occipital third of cortex and flatten it (after introducing some cut along the axis of the cone) you should be able to get to around 10% distortion or below, which I assume is good enough. cheers Bruce On Mon, 11 May 2015, Sarah Finnegan wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Taking a measure of cluster width and length on flat surface
Hi Bruce, Is there some way to know when cuts have been made correctly so that distortion can be minimized? (Or conversely, some way to know when a given patch has or will undergo too much distortion during flattening? Thanks! Michael On Mon, May 11, 2015 at 12:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Sarah the unfolding tries very hard to preserve exactly this - the metric properties. If you cut off the occipital third of cortex and flatten it (after introducing some cut along the axis of the cone) you should be able to get to around 10% distortion or below, which I assume is good enough. cheers Bruce On Mon, 11 May 2015, Sarah Finnegan wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
