Hi,
I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance.
-Derin
Hi Derin,
mris_anatomical_status gives you only cortical gray matter.
cheers, Bruce
On Mon, 10 Jul 2006 derin@conte.wustl.edu wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It is only cortical. And you don't want to use ?h.ribbon.mgz as this is quantized to 1mm^3 and will be less accurate than mris_anatomical stats.
doug
derin@conte.wustl.edu wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Is this true of the aseg files as well? I tried *double-checking* the mris_anatomical_stats by using the aseg file in MatLab (assigning values to the voxel-intensities, counting them up, etc, etc) and the numbers came up different. Is that why? Probably not the best method now that I think about it... Thanks Doug & Bruce.
-Derin
It is only cortical. And you don't want to use ?h.ribbon.mgz as this is quantized to 1mm^3 and will be less accurate than mris_anatomical stats.
doug
derin@conte.wustl.edu wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Yes, it is true for both (and the aparc+aseg.mgz). This puzzled me when I first wrote mri_aparc2aseg (which creates the aparc+aseg.mgz file).
derin@conte.wustl.edu wrote:
Is this true of the aseg files as well? I tried *double-checking* the mris_anatomical_stats by using the aseg file in MatLab (assigning values to the voxel-intensities, counting them up, etc, etc) and the numbers came up different. Is that why? Probably not the best method now that I think about it... Thanks Doug & Bruce.
-Derin
It is only cortical. And you don't want to use ?h.ribbon.mgz as this is quantized to 1mm^3 and will be less accurate than mris_anatomical stats.
doug
derin@conte.wustl.edu wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
the aseg will be different, since it's voxel-based (and typically not as accurate as the surfaces) On Mon, 10 Jul 2006 derin@conte.wustl.edu wrote:
Is this true of the aseg files as well? I tried *double-checking* the mris_anatomical_stats by using the aseg file in MatLab (assigning values to the voxel-intensities, counting them up, etc, etc) and the numbers came up different. Is that why? Probably not the best method now that I think about it... Thanks Doug & Bruce.
-Derin
It is only cortical. And you don't want to use ?h.ribbon.mgz as this is quantized to 1mm^3 and will be less accurate than mris_anatomical stats.
doug
derin@conte.wustl.edu wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Are not the mris_anatomical_stats voxel-based as well? I thought that was what I was measuring in *total gray matter volume*. If the aseg & ribbon files are quantized to 1mm^3, what is the surface? Plus, is there any way to verify the stats I'm getting in mris_anatomical_stats? Thanks.
-Derin
the aseg will be different, since it's voxel-based (and typically not as accurate as the surfaces) On Mon, 10 Jul 2006 derin@conte.wustl.edu wrote:
Is this true of the aseg files as well? I tried *double-checking* the mris_anatomical_stats by using the aseg file in MatLab (assigning values to the voxel-intensities, counting them up, etc, etc) and the numbers came up different. Is that why? Probably not the best method now that I think about it... Thanks Doug & Bruce.
-Derin
It is only cortical. And you don't want to use ?h.ribbon.mgz as this is quantized to 1mm^3 and will be less accurate than mris_anatomical stats.
doug
derin@conte.wustl.edu wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Derin,
no, they aren't quantized - they are computed from the surfaces, which live in a continuum.
Bruce
On Wed, 12 Jul 2006 derin@conte.wustl.edu wrote:
Are not the mris_anatomical_stats voxel-based as well? I thought that was what I was measuring in *total gray matter volume*. If the aseg & ribbon files are quantized to 1mm^3, what is the surface? Plus, is there any way to verify the stats I'm getting in mris_anatomical_stats? Thanks.
-Derin
the aseg will be different, since it's voxel-based (and typically not as accurate as the surfaces) On Mon, 10 Jul 2006 derin@conte.wustl.edu wrote:
Is this true of the aseg files as well? I tried *double-checking* the mris_anatomical_stats by using the aseg file in MatLab (assigning values to the voxel-intensities, counting them up, etc, etc) and the numbers came up different. Is that why? Probably not the best method now that I think about it... Thanks Doug & Bruce.
-Derin
It is only cortical. And you don't want to use ?h.ribbon.mgz as this is quantized to 1mm^3 and will be less accurate than mris_anatomical stats.
doug
derin@conte.wustl.edu wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bruce,
Sorry, I think I was confusing. Basically I was wondering how the numbers in mris_anatomical_stats are calculated, and if I can independently verify them. Does a paper/article address this? Thanks again for your help.
-Derin
Hi Derin,
no, they aren't quantized - they are computed from the surfaces, which live in a continuum.
Bruce
On Wed, 12 Jul 2006 derin@conte.wustl.edu wrote:
Are not the mris_anatomical_stats voxel-based as well? I thought that was what I was measuring in *total gray matter volume*. If the aseg & ribbon files are quantized to 1mm^3, what is the surface? Plus, is there any way to verify the stats I'm getting in mris_anatomical_stats? Thanks.
-Derin
the aseg will be different, since it's voxel-based (and typically not as accurate as the surfaces) On Mon, 10 Jul 2006 derin@conte.wustl.edu wrote:
Is this true of the aseg files as well? I tried *double-checking* the mris_anatomical_stats by using the aseg file in MatLab (assigning values to the voxel-intensities, counting them up, etc, etc) and the numbers came up different. Is that why? Probably not the best method now that I think about it... Thanks Doug & Bruce.
-Derin
It is only cortical. And you don't want to use ?h.ribbon.mgz as this is quantized to 1mm^3 and will be less accurate than mris_anatomical stats.
doug
derin@conte.wustl.edu wrote:
Hi,
I am attempting to assess (& compare) total cortical gray matter volume in a series of subjects (schiz vs. control), and was wondering if the tabular mris_anatomical_stats gm output consisted of only cortical gm, or included subcortical and other nuclei as well. I've searched the wiki, articles, and listserve archive with not much success; I get the sense that it is, but want to make sure. Additionally, what is shown in the ?h.ribbon.mgz files appears to be exactly what I am looking for. Is there any way to run the mris_anatomical_stats command on these files (use mris_convert maybe)? Thanks in advance.
-Derin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, Diana Rosas' HD paper and Gina Kuperberg schizophrenia paper both have validation studies in them. As does our PNAS thickness paper
On Wed, 12 Jul 2006, Derin Cobia wrote:
Bruce,
Sorry, I think I was confusing. Basically I was wondering how the numbers in mris_anatomical_stats are calculated, and if I can independently verify them. Does a paper/article address this? Thanks again for your help.
-Derin
Hi Derin,
no, they aren't quantized - they are computed from the surfaces, which live in a continuum.
Bruce
On Wed, 12 Jul 2006 derin@conte.wustl.edu wrote:
Are not the mris_anatomical_stats voxel-based as well? I thought that was what I was measuring in *total gray matter volume*. If the aseg & ribbon files are quantized to 1mm^3, what is the surface? Plus, is there any way to verify the stats I'm getting in mris_anatomical_stats? Thanks.
-Derin
the aseg will be different, since it's voxel-based (and typically not as accurate as the surfaces) On Mon, 10 Jul 2006 derin@conte.wustl.edu wrote:
Is this true of the aseg files as well? I tried *double-checking* the mris_anatomical_stats by using the aseg file in MatLab (assigning values to the voxel-intensities, counting them up, etc, etc) and the numbers came up different. Is that why? Probably not the best method now that I think about it... Thanks Doug & Bruce.
-Derin
It is only cortical. And you don't want to use ?h.ribbon.mgz as this is quantized to 1mm^3 and will be less accurate than mris_anatomical stats.
doug
derin@conte.wustl.edu wrote:
> Hi, > > I am attempting to assess (& compare) total cortical gray matter > volume > in > a series of subjects (schiz vs. control), and was wondering if the > tabular > mris_anatomical_stats gm output consisted of only cortical gm, or > included > subcortical and other nuclei as well. I've searched the wiki, > articles, > and listserve archive with not much success; I get the sense that it > is, > but want to make sure. Additionally, what is shown in the > ?h.ribbon.mgz > files appears to be exactly what I am looking for. Is there any way > to > run the mris_anatomical_stats command on these files (use > mris_convert > maybe)? Thanks in advance. > > -Derin > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Derin Cobia -
derin＠conte.wustl.edu
-
Doug Greve