Hi there
I have generated some anatomical probabilistic maps as overlays on the fsaverage pial surface. Is there a way to automatically find the vertex coordinates of the vertex with the highest probability of overlap? Or does this have to be done manually in Freeview?
Many thanks
Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
hmmm, should be pretty easy in matlab, no? On Mon, 15 May 2017, Trisanna Sprung-Much wrote:
Hi there I have generated some anatomical probabilistic maps as overlays on the fsaverage pial surface. Is there a way to automatically find the vertex coordinates of the vertex with the highest probability of overlap? Or does this have to be done manually in Freeview?
Many thanks
Trisanna
Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
Hi Bruce
I would not know where to start (not an avid matlab user) - what input would be needed to be fed into matlab?
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
hmmm, should be pretty easy in matlab, no? On Mon, 15 May 2017, Trisanna Sprung-Much wrote:
Hi there I have generated some anatomical probabilistic maps as overlays on the fsaverage pial surface. Is there a way to automatically find the vertex coordinates of the vertex with the highest probability of overlap? Or
does
this have to be done manually in Freeview?
Many thanks
Trisanna
Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
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what format is your map of p-values in? On Mon, 15 May 2017, Trisanna Sprung-Much wrote:
Hi Bruce I would not know where to start (not an avid matlab user) - what input would be needed to be fed into matlab?
Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: hmmm, should be pretty easy in matlab, no? On Mon, 15 May 2017, Trisanna Sprung-Much wrote:
> Hi there > I have generated some anatomical probabilistic maps as overlays on the > fsaverage pial surface. Is there a way to automatically find the vertex > coordinates of the vertex with the highest probability of overlap? Or does > this have to be done manually in Freeview? > > Many thanks > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ 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 Bruce
The maps are .mgz format and are % overlap (across 40 subjects). They were generated using
-labels turned into surface overlay using mri_vol2surf -then registered to fsaverage using mri_surf2surf -then averaged within fsaverage space using mri_concat and then mris_fwhm to smooth.
Best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Mon, May 15, 2017 at 2:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what format is your map of p-values in? On Mon, 15 May 2017, Trisanna Sprung-Much wrote:
Hi Bruce I would not know where to start (not an avid matlab user) - what input
would
be needed to be fed into matlab?
Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
wrote: hmmm, should be pretty easy in matlab, no? On Mon, 15 May 2017, Trisanna Sprung-Much wrote:
> Hi there > I have generated some anatomical probabilistic maps as overlays on the > fsaverage pial surface. Is there a way to automatically find the vertex > coordinates of the vertex with the highest probability of overlap? Or does > this have to be done manually in Freeview? > > Many thanks > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ 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
you can do something like
a = MRIread('map1.mgz');
b = MRIread('map2.mgz');
c = MRIread('map3.mgz');
d = (a.vol > thresh + b.vol > thresh + d.vol> thresh)/3;
[mm ii] = max(d);
Then the vertex number will be ii-1 (need to convert from 1-based to 0-based)
On 5/15/17 3:34 PM, Trisanna Sprung-Much wrote:
Hi Bruce
The maps are .mgz format and are % overlap (across 40 subjects). They were generated using
-labels turned into surface overlay using mri_vol2surf -then registered to fsaverage using mri_surf2surf -then averaged within fsaverage space using mri_concat and then mris_fwhm to smooth.
Best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Mon, May 15, 2017 at 2:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
what format is your map of p-values in? On Mon, 15 May 2017, Trisanna Sprung-Much wrote: > Hi Bruce > I would not know where to start (not an avid matlab user) - what input would > be needed to be fed into matlab? > > Trisanna > > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > wrote: > hmmm, should be pretty easy in matlab, no? > On Mon, 15 May 2017, Trisanna > Sprung-Much wrote: > > > Hi there > > I have generated some anatomical probabilistic maps as > overlays on the > > fsaverage pial surface. Is there a way to automatically find > the vertex > > coordinates of the vertex with the highest probability of > overlap? Or does > > this have to be done manually in Freeview? > > > > Many thanks > > > > Trisanna > > -- > > Ph.D. CandidateMcGill University > > Integrated Program in Neuroscience > > Psychology > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thanks Doug! I will give this a shot!
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Mon, May 15, 2017 at 9:56 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
you can do something like
a = MRIread('map1.mgz');
b = MRIread('map2.mgz');
c = MRIread('map3.mgz');
d = (a.vol > thresh + b.vol > thresh + d.vol> thresh)/3;
[mm ii] = max(d);
Then the vertex number will be ii-1 (need to convert from 1-based to 0-based)
On 5/15/17 3:34 PM, Trisanna Sprung-Much wrote:
Hi Bruce
The maps are .mgz format and are % overlap (across 40 subjects). They were generated using
-labels turned into surface overlay using mri_vol2surf -then registered to fsaverage using mri_surf2surf -then averaged within fsaverage space using mri_concat and then mris_fwhm to smooth.
Best Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
On Mon, May 15, 2017 at 2:53 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what format is your map of p-values in? On Mon, 15 May 2017, Trisanna Sprung-Much wrote:
Hi Bruce I would not know where to start (not an avid matlab user) - what input
would
be needed to be fed into matlab?
Trisanna
-- Ph.D. CandidateMcGill University Integrated Program in Neuroscience Psychology
On Mon, May 15, 2017 at 12:52 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
wrote: hmmm, should be pretty easy in matlab, no? On Mon, 15 May 2017, Trisanna Sprung-Much wrote:
> Hi there > I have generated some anatomical probabilistic maps as overlays on the > fsaverage pial surface. Is there a way to automatically find the vertex > coordinates of the vertex with the highest probability of overlap? Or does > this have to be done manually in Freeview? > > Many thanks > > Trisanna > -- > Ph.D. CandidateMcGill University > Integrated Program in Neuroscience > Psychology > > > > _______________________________________________ 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Trisanna Sprung-Much