I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure?
Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance,
Nathan
Hello all, I sent this a couple of weeks ago but it must have slipped through the cracks:
I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure?
Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance,
Nathan
Hi Nathan,
the "unknown" label is intended to be non-cortical regions such as the callosum, and should be ignord. I think total white matter volume is generated by default, but maybe Nick or Doug can correct me (although Nick is out of the country)
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all, I sent this a couple of weeks ago but it must have slipped through the cracks:
I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure?
Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance,
Nathan
Bruce,
In that case, is there a way to have freesurfer output average cortical thickness throughout the entire cortex? In terms of total volumes, I noticed measures labeled IntraCranialVol and BrainSegVol in the wmparc and aseg stats files. I assume intracranial volume includes everything, even non-cortical regions? If that is so, is BrainSegVol a measure of total cortical volume? I also noticed that the values in BrainSegVol differ greatly between the two stats files. Your help is greatly appreciated,
Nathan
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 3/11/2009 12:47 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aparcstats question
Hi Nathan,
the "unknown" label is intended to be non-cortical regions such as the callosum, and should be ignord. I think total white matter volume is generated by default, but maybe Nick or Doug can correct me (although Nick is out of the country)
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all, I sent this a couple of weeks ago but it must have slipped through the cracks:
I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure?
Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance,
Nathan
Hi Nathan,
I think we do output the total cortical volume in one of the stats files,but I don't remember where it is. Doug, Nick or Krish: do any of you know?
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Bruce,
In that case, is there a way to have freesurfer output average cortical
thickness throughout the entire cortex? In terms of total volumes, I noticed measures labeled IntraCranialVol and BrainSegVol in the wmparc and aseg stats files. I assume intracranial volume includes everything, even non-cortical regions? If that is so, is BrainSegVol a measure of total cortical volume? I also noticed that the values in BrainSegVol differ greatly between the two stats files. Your help is greatly appreciated,
Nathan
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 3/11/2009 12:47 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aparcstats question
Hi Nathan,
the "unknown" label is intended to be non-cortical regions such as the callosum, and should be ignord. I think total white matter volume is generated by default, but maybe Nick or Doug can correct me (although Nick is out of the country)
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all, I sent this a couple of weeks ago but it must have slipped through the cracks:
I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure?
Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance,
Nathan
Actually, I don't think we do. ?h.aparc.stats has total cortical area and aseg.stats has surface-based white matter volume. You can get it with something like:
mri_segstats --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --sum lh.cortex.stats --i $SUBJECTS_DIR/subject//lh.volume
Then multiply the "Mean" by the number of vertices.
We'll have to add a better method to mris_anatomical_stats.
Bruce Fischl wrote:
Hi Nathan,
I think we do output the total cortical volume in one of the stats files,but I don't remember where it is. Doug, Nick or Krish: do any of you know?
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Bruce,
In that case, is there a way to have freesurfer output average cortical
thickness throughout the entire cortex? In terms of total volumes, I noticed measures labeled IntraCranialVol and BrainSegVol in the wmparc and aseg stats files. I assume intracranial volume includes everything, even non-cortical regions? If that is so, is BrainSegVol a measure of total cortical volume? I also noticed that the values in BrainSegVol differ greatly between the two stats files. Your help is greatly appreciated,
Nathan
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 3/11/2009 12:47 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aparcstats question
Hi Nathan,
the "unknown" label is intended to be non-cortical regions such as the callosum, and should be ignord. I think total white matter volume is generated by default, but maybe Nick or Doug can correct me (although Nick is out of the country)
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all, I sent this a couple of weeks ago but it must have slipped through the cracks:
I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure?
Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Nathan, If you want stats related to the ?h.cortex.label (e.g., average cortical thickness) you can do the following:
mris_anatomical_stats -l {$hemi}h.cortex.label -f $id/stats/{$hemi}h.cortex.stats $id {$hemi}h
The resulting ?h.cortex.stats file will contain all the same measures (e.g., NumVert, SurfArea, GrayVol, ThickAvg, etc) as ? h.aparc.stats, but the values will be specific to (overall) cortex (as defined by ?h.cortex.label).
And you can even use 'aparcstats2table' to collect these values if you wish. e.g., aparcstats2table --subjects subj1 <subj2 ...> --h lh --parc cortex -- meas thickness --t avgCortexThickness.txt
cheers, Mike H.
On Wed, 2009-03-11 at 18:25 -0400, Douglas N Greve wrote:
Actually, I don't think we do. ?h.aparc.stats has total cortical area and aseg.stats has surface-based white matter volume. You can get it with something like:
mri_segstats --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --sum lh.cortex.stats --i $SUBJECTS_DIR/subject//lh.volume
Then multiply the "Mean" by the number of vertices.
We'll have to add a better method to mris_anatomical_stats.
Bruce Fischl wrote:
Hi Nathan,
I think we do output the total cortical volume in one of the stats files,but I don't remember where it is. Doug, Nick or Krish: do any of you know?
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Bruce,
In that case, is there a way to have freesurfer output average cortical
thickness throughout the entire cortex? In terms of total volumes, I noticed measures labeled IntraCranialVol and BrainSegVol in the wmparc and aseg stats files. I assume intracranial volume includes everything, even non-cortical regions? If that is so, is BrainSegVol a measure of total cortical volume? I also noticed that the values in BrainSegVol differ greatly between the two stats files. Your help is greatly appreciated,
Nathan
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 3/11/2009 12:47 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aparcstats question
Hi Nathan,
the "unknown" label is intended to be non-cortical regions such as the callosum, and should be ignord. I think total white matter volume is generated by default, but maybe Nick or Doug can correct me (although Nick is out of the country)
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all, I sent this a couple of weeks ago but it must have slipped through the cracks:
I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure?
Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance,
Nathan
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
And just a note that aparcstats2table ( as well as asegstats2table ) has been revamped. http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes See under "Known Issues" on how to get the new version
Re: Mike's command line.. the new version will complain about "--h" option since there are two options starting with --h.. the exact error message is like this : aparcstats2table: error: ambiguous option: --h (--help, --hemi?) You can give --hel or --hem to choose either but "--h" or "--he" are ambiguous. And it'll do the same thing for "--t" too. the 2 possible candidates are --tablefile and --transpose. ( --tr will select the transpose option and --ta will select the tablefile option )
Krish
On Mar 11, 2009, at 10:07 PM, Michael Harms wrote:
Hello Nathan, If you want stats related to the ?h.cortex.label (e.g., average cortical thickness) you can do the following:
mris_anatomical_stats -l {$hemi}h.cortex.label -f $id/stats/{$hemi}h.cortex.stats $id {$hemi}h
The resulting ?h.cortex.stats file will contain all the same measures (e.g., NumVert, SurfArea, GrayVol, ThickAvg, etc) as ? h.aparc.stats, but the values will be specific to (overall) cortex (as defined by ?h.cortex.label).
And you can even use 'aparcstats2table' to collect these values if you wish. e.g., aparcstats2table --subjects subj1 <subj2 ...> --h lh --parc cortex -- meas thickness --t avgCortexThickness.txt
cheers, Mike H.
On Wed, 2009-03-11 at 18:25 -0400, Douglas N Greve wrote:
Actually, I don't think we do. ?h.aparc.stats has total cortical area and aseg.stats has surface-based white matter volume. You can get it with something like:
mri_segstats --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --sum lh.cortex.stats --i $SUBJECTS_DIR/subject//lh.volume
Then multiply the "Mean" by the number of vertices.
We'll have to add a better method to mris_anatomical_stats.
Bruce Fischl wrote:
Hi Nathan,
I think we do output the total cortical volume in one of the stats files,but I don't remember where it is. Doug, Nick or Krish: do any of you know?
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Bruce,
In that case, is there a way to have freesurfer output average cortical
thickness throughout the entire cortex? In terms of total volumes, I noticed measures labeled IntraCranialVol and BrainSegVol in the wmparc and aseg stats files. I assume intracranial volume includes everything, even non-cortical regions? If that is so, is BrainSegVol a measure of total cortical volume? I also noticed that the values in BrainSegVol differ greatly between the two stats files. Your help is greatly appreciated,
Nathan
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 3/11/2009 12:47 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aparcstats question
Hi Nathan,
the "unknown" label is intended to be non-cortical regions such as the callosum, and should be ignord. I think total white matter volume is generated by default, but maybe Nick or Doug can correct me (although Nick is out of the country)
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all, I sent this a couple of weeks ago but it must have slipped through the cracks:
I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure?
Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance,
Nathan
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you all, this has been very helpful
-----Original Message----- From: Krish Subramaniam [mailto:krish@nmr.mgh.harvard.edu] Sent: Wed 3/11/2009 10:19 PM To: Michael Harms Cc: Doug Greve; Dankner, Nathan (NIH/NIMH) [F]; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aparcstats question
And just a note that aparcstats2table ( as well as asegstats2table ) has been revamped. http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes See under "Known Issues" on how to get the new version
Re: Mike's command line.. the new version will complain about "--h" option since there are two options starting with --h.. the exact error message is like this : aparcstats2table: error: ambiguous option: --h (--help, --hemi?) You can give --hel or --hem to choose either but "--h" or "--he" are ambiguous. And it'll do the same thing for "--t" too. the 2 possible candidates are --tablefile and --transpose. ( --tr will select the transpose option and --ta will select the tablefile option )
Krish
On Mar 11, 2009, at 10:07 PM, Michael Harms wrote:
Hello Nathan, If you want stats related to the ?h.cortex.label (e.g., average cortical thickness) you can do the following:
mris_anatomical_stats -l {$hemi}h.cortex.label -f $id/stats/{$hemi}h.cortex.stats $id {$hemi}h
The resulting ?h.cortex.stats file will contain all the same measures (e.g., NumVert, SurfArea, GrayVol, ThickAvg, etc) as ? h.aparc.stats, but the values will be specific to (overall) cortex (as defined by ?h.cortex.label).
And you can even use 'aparcstats2table' to collect these values if you wish. e.g., aparcstats2table --subjects subj1 <subj2 ...> --h lh --parc cortex -- meas thickness --t avgCortexThickness.txt
cheers, Mike H.
On Wed, 2009-03-11 at 18:25 -0400, Douglas N Greve wrote:
Actually, I don't think we do. ?h.aparc.stats has total cortical area and aseg.stats has surface-based white matter volume. You can get it with something like:
mri_segstats --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --sum lh.cortex.stats --i $SUBJECTS_DIR/subject//lh.volume
Then multiply the "Mean" by the number of vertices.
We'll have to add a better method to mris_anatomical_stats.
Bruce Fischl wrote:
Hi Nathan,
I think we do output the total cortical volume in one of the stats files,but I don't remember where it is. Doug, Nick or Krish: do any of you know?
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Bruce,
In that case, is there a way to have freesurfer output average cortical
thickness throughout the entire cortex? In terms of total volumes, I noticed measures labeled IntraCranialVol and BrainSegVol in the wmparc and aseg stats files. I assume intracranial volume includes everything, even non-cortical regions? If that is so, is BrainSegVol a measure of total cortical volume? I also noticed that the values in BrainSegVol differ greatly between the two stats files. Your help is greatly appreciated,
Nathan
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 3/11/2009 12:47 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Aparcstats question
Hi Nathan,
the "unknown" label is intended to be non-cortical regions such as the callosum, and should be ignord. I think total white matter volume is generated by default, but maybe Nick or Doug can correct me (although Nick is out of the country)
Bruce
On Wed, 11 Mar 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all, I sent this a couple of weeks ago but it must have slipped through the cracks:
I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure?
Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance,
Nathan
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Dankner, Nathan (NIH/NIMH) [F] -
Douglas N Greve -
Krish Subramaniam -
Michael Harms -
Nathan Dankner