Dear mailing list,
For each of the subjects in our study, we would like to extract the thickness values at each vertex for the surface that has been mapped to fsaverage (so that the number of vertices is identical for all of our subjects). After changing to a specific participants "surf" directory and starting matlab, could I use the following command and file to extract the data I want?:
[thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')
Also, how do I then determine the annotation associated with each vertex for each subject?
Hi Bronwyn
you can use read_annotation.m to read in the parcellation that you want and go from there.
cheers Bruce
On Wed, 14 Oct 2015, Bronwyn Overs wrote:
Dear mailing list,
For each of the subjects in our study, we would like to extract the thickness values at each vertex for the surface that has been mapped to fsaverage (so that the number of vertices is identical for all of our subjects). After changing to a specific participants "surf" directory and starting matlab, could I use the following command and file to extract the data I want?:
[thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')
Also, how do I then determine the annotation associated with each vertex for each subject?
Hi Bruce,
Following up on your comment below, if I am using 'lh.thickness.fwhm10.fsaverage.mgh' for my thickness values, do I read in the lh.aparc.annot file in the subjects directory? I tried doing this for one of my participants, and the vector of thickness values has 163842 columns, while my aparc file has 116407. Or should I be reading in the lh.aparc.annot from fsaverage?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 14/10/2015 11:47 pm, Bruce Fischl wrote:
Hi Bronwyn
you can use read_annotation.m to read in the parcellation that you want and go from there.
cheers Bruce
On Wed, 14 Oct 2015, Bronwyn Overs wrote:
Dear mailing list,
For each of the subjects in our study, we would like to extract the thickness values at each vertex for the surface that has been mapped to fsaverage (so that the number of vertices is identical for all of our subjects). After changing to a specific participants "surf" directory and starting matlab, could I use the following command and file to extract the data I want?:
[thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')
Also, how do I then determine the annotation associated with each vertex for each subject?
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.
Hi Bronwyn
the lh.thickness.fwhm10.fsaverage.mgh has been mapped to fsaverage, so you need to read in the fsaverage parcellations.
cheers Bruce
On Thu, 15 Oct 2015, Bronwyn Overs wrote:
Hi Bruce,
Following up on your comment below, if I am using 'lh.thickness.fwhm10.fsaverage.mgh' for my thickness values, do I read in the lh.aparc.annot file in the subjects directory? I tried doing this for one of my participants, and the vector of thickness values has 163842 columns, while my aparc file has 116407. Or should I be reading in the lh.aparc.annot from fsaverage?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 14/10/2015 11:47 pm, Bruce Fischl wrote:
Hi Bronwyn
you can use read_annotation.m to read in the parcellation that you want and go from there.
cheers Bruce
On Wed, 14 Oct 2015, Bronwyn Overs wrote:
Dear mailing list,
For each of the subjects in our study, we would like to extract the thickness values at each vertex for the surface that has been mapped to fsaverage (so that the number of vertices is identical for all of our subjects). After changing to a specific participants "surf" directory and starting matlab, could I use the following command and file to extract the data I want?:
[thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')
Also, how do I then determine the annotation associated with each vertex for each subject?
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.
Use
thick = MRIread('lh.thickness.fwhm10.fsaverage.mgh'); then thick.vol will be an array of the thickness at each vertex. Remember that matlab uses 1-based when you go to address the vertices
doug
On 10/14/2015 02:59 AM, Bronwyn Overs wrote:
Dear mailing list,
For each of the subjects in our study, we would like to extract the thickness values at each vertex for the surface that has been mapped to fsaverage (so that the number of vertices is identical for all of our subjects). After changing to a specific participants "surf" directory and starting matlab, could I use the following command and file to extract the data I want?:
[thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')
Also, how do I then determine the annotation associated with each vertex for each subject?
--
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bronwyn Overs -
Bruce Fischl -
Douglas N Greve