Dear Freesurfers,
We are trying to subdivide the cortical surface of our average subject into a set of small and compact regions of similar area. Please have a look to the attached file (taken from Hagmann et al. (2008) in PLoS Biol) to have a better idea what I would like to get. We tried it hard by using different strategies, but results were not as expected. Could anybody give me some insights about how to approach this problem by using Freesurfer or Matlab code?
Thank you very much in advance.
Best, Jose
--- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/es/
Hi Jose,
this looks pretty much correct. We have another utility, called mris_make_face_parcellation that can be used to generate parcellation units of mostly uniform area over the surface of the cortex. If you tell us your hardware/software environment we can give you a beta.
cheers, Bruce
On Mon, 2 Mar 2009, Jose Luis Cantero Lorente wrote:
Dear Freesurfers,
We are trying to subdivide the cortical surface of our average subject into a set of small and compact regions of similar area. Please have a look to the attached file (taken from Hagmann et al. (2008) in PLoS Biol) to have a better idea what I would like to get. We tried it hard by using different strategies, but results were not as expected. Could anybody give me some insights about how to approach this problem by using Freesurfer or Matlab code?
Thank you very much in advance.
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/es/
Jose,
mris_make_face_parcellation is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc
for three of the supported platforms.
Nick
On Mon, 2009-03-02 at 13:23 -0500, Bruce Fischl wrote:
Hi Jose,
this looks pretty much correct. We have another utility, called mris_make_face_parcellation that can be used to generate parcellation units of mostly uniform area over the surface of the cortex. If you tell us your hardware/software environment we can give you a beta.
cheers, Bruce
On Mon, 2 Mar 2009, Jose Luis Cantero Lorente wrote:
Dear Freesurfers,
We are trying to subdivide the cortical surface of our average subject into a set of small and compact regions of similar area. Please have a look to the attached file (taken from Hagmann et al. (2008) in PLoS Biol) to have a better idea what I would like to get. We tried it hard by using different strategies, but results were not as expected. Could anybody give me some insights about how to approach this problem by using Freesurfer or Matlab code?
Thank you very much in advance.
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/es/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Nick
Is it possible to refer the "faces" I got with the command below to the labels from an annotation file?
[Macintosh-10:subjects/fsaverage_fineparc_uniformareas/surf] diana% mris_make_face_parcellation rh.inflated /Applications/freesurfer/lib/bem/ic4.tri rh.ic4.annot
I would like to run the following commands from the .annot file I generated with the mris_make_face_parcellation in order to get a txt-file with, for example, the cortical thickness information in each face:
mri_surf2surf mris_anatomical_stats aparcstats2table
With this procedure I would lose the precise site of a face and its associated anatomical label.
Thank you very much for your help! Diana
On Mon, 02 Mar 2009 14:44:54 -0500 Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Jose,
mris_make_face_parcellation is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc
for three of the supported platforms.
Nick
On Mon, 2009-03-02 at 13:23 -0500, Bruce Fischl wrote:
Hi Jose,
this looks pretty much correct. We have another utility, called mris_make_face_parcellation that can be used to generate parcellation units of mostly uniform area over the surface of the cortex. If you tell us your hardware/software environment we can give you a beta.
cheers, Bruce
On Mon, 2 Mar 2009, Jose Luis Cantero Lorente wrote:
Dear Freesurfers,
We are trying to subdivide the cortical surface of our average subject
into a set of small and compact regions of similar area. Please have a look to the attached file (taken from Hagmann et al. (2008) in PLoS Biol) to have a better idea what I would like to get. We tried it hard by using different strategies, but results were not as expected. Could anybody give me some insights about how to approach this problem by using Freesurfer or Matlab code?
Thank you very much in advance.
Best, Jose
Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- Spain -
Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor@upo.es http://www.upo.es/neuroaging/es/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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
All,
I have generated a mask of the cingulate regions for each of my participants from their aparc+aseg.mgz files (see attached image) and I would like see how these masks overlay with the group average brain I have generated for my study. Is there a simple way to transform a mask from an individual subjects space to the group average volume space? I made my group average with the make_average_subject command.
In a related question is it possible to generate a group average aparc+aseg.mgz file? I can see the surface labels in the average and the aseg.mgz cortical labels. However, I don't know of a way to generate the aparc+aseg.mgz file.
Thanks for any help you can offer, Avram
On Sun, 22 Mar 2009, Avram Holmes wrote:
All,
I have generated a mask of the cingulate regions for each of my participants from their aparc+aseg.mgz files (see attached image) and I would like see how these masks overlay with the group average brain I have generated for my study. Is there a simple way to transform a mask from an individual subjects space to the group average volume space? I made my group average with the make_average_subject command.
You can create a mask of the cingulate with mri_binarize --match XXX, then convert that into the average space with mri_vol2vol (for command-line ops see how the aseg is done in make_average_subject), then concatenate all of your masks together with mri_concat, adding --mean to compute the mean. The value at each voxel will then be the fraction of your subjects that had a cingualte mask at that voxel. You can display this as an overlay, or you can threshold it to turn it back into a mask.
In a related question is it possible to generate a group average aparc+aseg.mgz file? I can see the surface labels in the average and the aseg.mgz cortical labels. However, I don't know of a way to generate the aparc+aseg.mgz file.
I did write software to do this, but it turned into a real mess. Cortex is so thin and the location of the indivdual cortical regions so variable, that the final map ended up with all kinds of strange holes (a good advertisement against talairach!). If you just want it for display, you should be able to run "mri_aparc2aseg --s avgsubject --volmask", but this won't reflect the actual labels from your group of subjects.
doug
Thanks for any help you can offer, Avram
Doug,
I'm having some trouble tracking down the command line that you suggest I find (where teh aseg file is transformed in make_average_subject). Do you think you could give me a pointer in the right direction? Once again I'm trying to convert individual subjects cingulate masks into the group average space.
Thanks, Avram
On 3/22/2009 3:34 PM, Doug Greve wrote:
On Sun, 22 Mar 2009, Avram Holmes wrote:
All,
I have generated a mask of the cingulate regions for each of my participants from their aparc+aseg.mgz files (see attached image) and I would like see how these masks overlay with the group average brain I have generated for my study. Is there a simple way to transform a mask from an individual subjects space to the group average volume space? I made my group average with the make_average_subject command.
You can create a mask of the cingulate with mri_binarize --match XXX, then convert that into the average space with mri_vol2vol (for command-line ops see how the aseg is done in make_average_subject), then concatenate all of your masks together with mri_concat, adding --mean to compute the mean. The value at each voxel will then be the fraction of your subjects that had a cingualte mask at that voxel. You can display this as an overlay, or you can threshold it to turn it back into a mask.
In a related question is it possible to generate a group average aparc+aseg.mgz file? I can see the surface labels in the average and the aseg.mgz cortical labels. However, I don't know of a way to generate the aparc+aseg.mgz file.
I did write software to do this, but it turned into a real mess. Cortex is so thin and the location of the indivdual cortical regions so variable, that the final map ended up with all kinds of strange holes (a good advertisement against talairach!). If you just want it for display, you should be able to run "mri_aparc2aseg --s avgsubject --volmask", but this won't reflect the actual labels from your group of subjects.
doug
Thanks for any help you can offer, Avram
Hi Avram,
I think mri_label2label should do the trick.
cheers, Bruce On Sat, 4 Apr 2009, Avram Holmes wrote:
Doug,
I'm having some trouble tracking down the command line that you suggest I find (where teh aseg file is transformed in make_average_subject). Do you think you could give me a pointer in the right direction? Once again I'm trying to convert individual subjects cingulate masks into the group average space.
Thanks, Avram
On 3/22/2009 3:34 PM, Doug Greve wrote:
On Sun, 22 Mar 2009, Avram Holmes wrote:
All,
I have generated a mask of the cingulate regions for each of my participants from their aparc+aseg.mgz files (see attached image) and I would like see how these masks overlay with the group average brain I have generated for my study. Is there a simple way to transform a mask from an individual subjects space to the group average volume space? I made my group average with the make_average_subject command.
You can create a mask of the cingulate with mri_binarize --match XXX, then convert that into the average space with mri_vol2vol (for command-line ops see how the aseg is done in make_average_subject), then concatenate all of your masks together with mri_concat, adding --mean to compute the mean. The value at each voxel will then be the fraction of your subjects that had a cingualte mask at that voxel. You can display this as an overlay, or you can threshold it to turn it back into a mask.
In a related question is it possible to generate a group average aparc+aseg.mgz file? I can see the surface labels in the average and the aseg.mgz cortical labels. However, I don't know of a way to generate the aparc+aseg.mgz file.
I did write software to do this, but it turned into a real mess. Cortex is so thin and the location of the indivdual cortical regions so variable, that the final map ended up with all kinds of strange holes (a good advertisement against talairach!). If you just want it for display, you should be able to run "mri_aparc2aseg --s avgsubject --volmask", but this won't reflect the actual labels from your group of subjects.
doug
Thanks for any help you can offer, Avram
that's in make_average_volume
doug
Avram Holmes wrote:
Doug,
I'm having some trouble tracking down the command line that you suggest I find (where teh aseg file is transformed in make_average_subject). Do you think you could give me a pointer in the right direction? Once again I'm trying to convert individual subjects cingulate masks into the group average space.
Thanks, Avram
On 3/22/2009 3:34 PM, Doug Greve wrote:
On Sun, 22 Mar 2009, Avram Holmes wrote:
All,
I have generated a mask of the cingulate regions for each of my participants from their aparc+aseg.mgz files (see attached image) and I would like see how these masks overlay with the group average brain I have generated for my study. Is there a simple way to transform a mask from an individual subjects space to the group average volume space? I made my group average with the make_average_subject command.
You can create a mask of the cingulate with mri_binarize --match XXX, then convert that into the average space with mri_vol2vol (for command-line ops see how the aseg is done in make_average_subject), then concatenate all of your masks together with mri_concat, adding --mean to compute the mean. The value at each voxel will then be the fraction of your subjects that had a cingualte mask at that voxel. You can display this as an overlay, or you can threshold it to turn it back into a mask.
In a related question is it possible to generate a group average aparc+aseg.mgz file? I can see the surface labels in the average and the aseg.mgz cortical labels. However, I don't know of a way to generate the aparc+aseg.mgz file.
I did write software to do this, but it turned into a real mess. Cortex is so thin and the location of the indivdual cortical regions so variable, that the final map ended up with all kinds of strange holes (a good advertisement against talairach!). If you just want it for display, you should be able to run "mri_aparc2aseg --s avgsubject --volmask", but this won't reflect the actual labels from your group of subjects.
doug
Thanks for any help you can offer, Avram
freesurfer@nmr.mgh.harvard.edu
-
Avram Holmes -
Bruce Fischl -
Diana Wotruba -
Doug Greve -
Douglas N Greve
-
Jose Luis Cantero Lorente -
Nick Schmansky