I am looking to derive total brain volume measures from the data that I have. Judging by reading previous posts, it seems that BrainSegVol in aseg.stats includes cerebellum and ventricles. Is there any way to eliminate these from the calculation? Is it kosher to subtract the cerebellum/ventricle measures found elsewhere in aseg.stats/wm.parc from BrainSegVol, or are these derived differently from BrainSegVol? Secondly, would merely adding the left-cerebral-cortex to right-cerebral-cortex measures found in aseg.stats give me total brain volume? Thank you in advance,
Nathan
I think this may have slipped through the cracks, so I am posting it again. I apologize if this has been answered already. If the information is available elsewhere and I happened to miss it, please let me know.
-----Original Message----- From: Dankner, Nathan (NIH/NIMH) [F] Sent: Thu 4/9/2009 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] total brain volumes
I am looking to derive total brain volume measures from the data that I have. Judging by reading previous posts, it seems that BrainSegVol in aseg.stats includes cerebellum and ventricles. Is there any way to eliminate these from the calculation? Is it kosher to subtract the cerebellum/ventricle measures found elsewhere in aseg.stats/wm.parc from BrainSegVol, or are these derived differently from BrainSegVol? Secondly, would merely adding the left-cerebral-cortex to right-cerebral-cortex measures found in aseg.stats give me total brain volume? Thank you in advance,
Nathan
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Hi Nate,
sorry, I think we were each waiting for someone else to answer :). I'm not sure about the BrainSegVol. It shouldn't include ventricle in principle, but in practice it might. Probably the easiest thing to do is to use mri_label_volume -a aseg.mgz
which will give you the volume of all the non-zero voxels in the aseg, the use it again to compute the volumes of the structures you want to remove (ventricles, cerebellum, etc...). We'll look into the other question and get back to soon.
cheers Bruce
On Mon, 13 Apr 2009, Dankner, Nathan (NIH/NIMH) [F] wrote:
I think this may have slipped through the cracks, so I am posting it
again. I apologize if this has been answered already. If the information is available elsewhere and I happened to miss it, please let me know.
-----Original Message----- From: Dankner, Nathan (NIH/NIMH) [F] Sent: Thu 4/9/2009 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] total brain volumes
I am looking to derive total brain volume measures from the data that I
have. Judging by reading previous posts, it seems that BrainSegVol in aseg.stats includes cerebellum and ventricles. Is there any way to eliminate these from the calculation? Is it kosher to subtract the cerebellum/ventricle measures found elsewhere in aseg.stats/wm.parc from BrainSegVol, or are these derived differently from BrainSegVol? Secondly, would merely adding the left-cerebral-cortex to right-cerebral-cortex measures found in aseg.stats give me total brain volume? 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
Did you look at the Brain Volume wiki page? To find it, go to our wiki and type in "BrainSegVol" in the search box and hit the "Text" button.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
I think this may have slipped through the cracks, so I am posting it again. I apologize if this has been answered already. If the information is available elsewhere and I happened to miss it, please let me know.
-----Original Message----- From: Dankner, Nathan (NIH/NIMH) [F] Sent: Thu 4/9/2009 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] total brain volumes
I am looking to derive total brain volume measures from the data that I have. Judging by reading previous posts, it seems that BrainSegVol in aseg.stats includes cerebellum and ventricles. Is there any way to eliminate these from the calculation? Is it kosher to subtract the cerebellum/ventricle measures found elsewhere in aseg.stats/wm.parc from BrainSegVol, or are these derived differently from BrainSegVol? Secondly, would merely adding the left-cerebral-cortex to right-cerebral-cortex measures found in aseg.stats give me total brain volume? Thank you in advance,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I've checked out the wiki, and it brings up a couple of other questions. I don't seem to have the BrainSegVolNoVent measure...maybe this is an issue with versions? I ran the mri_label_volume command that Bruce provided. There was roughly a 300,000 mm^3 difference between the output of the mri_label_volume and BrainSegVol (the mri_label_volume output was the smaller value). Is this to be expected? It seems to me that they should be the same, unless I am mistaken?
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 4/13/2009 11:42 AM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] total brain volumes
Did you look at the Brain Volume wiki page? To find it, go to our wiki and type in "BrainSegVol" in the search box and hit the "Text" button.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
I think this may have slipped through the cracks, so I am posting it again. I apologize if this has been answered already. If the information is available elsewhere and I happened to miss it, please let me know.
-----Original Message----- From: Dankner, Nathan (NIH/NIMH) [F] Sent: Thu 4/9/2009 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] total brain volumes
I am looking to derive total brain volume measures from the data that I have. Judging by reading previous posts, it seems that BrainSegVol in aseg.stats includes cerebellum and ventricles. Is there any way to eliminate these from the calculation? Is it kosher to subtract the cerebellum/ventricle measures found elsewhere in aseg.stats/wm.parc from BrainSegVol, or are these derived differently from BrainSegVol? Secondly, would merely adding the left-cerebral-cortex to right-cerebral-cortex measures found in aseg.stats give me total brain volume? 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
Not having BrainSegVolNoVent might just mean that you have an old version. It was added two years ago, but I'm not sure which build that would have gotten into. Not sure about the discrepancy with mri_label_volume.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
I've checked out the wiki, and it brings up a couple of other questions. I don't seem to have the BrainSegVolNoVent measure...maybe this is an issue with versions? I ran the mri_label_volume command that Bruce provided. There was roughly a 300,000 mm^3 difference between the output of the mri_label_volume and BrainSegVol (the mri_label_volume output was the smaller value). Is this to be expected? It seems to me that they should be the same, unless I am mistaken?
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 4/13/2009 11:42 AM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] total brain volumes
Did you look at the Brain Volume wiki page? To find it, go to our wiki and type in "BrainSegVol" in the search box and hit the "Text" button.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
I think this may have slipped through the cracks, so I am posting it again. I apologize if this has been answered already. If the information is available elsewhere and I happened to miss it, please let me know.
-----Original Message----- From: Dankner, Nathan (NIH/NIMH) [F] Sent: Thu 4/9/2009 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] total brain volumes
I am looking to derive total brain volume measures from the data that I have. Judging by reading previous posts, it seems that BrainSegVol in aseg.stats includes cerebellum and ventricles. Is there any way to eliminate these from the calculation? Is it kosher to subtract the cerebellum/ventricle measures found elsewhere in aseg.stats/wm.parc from BrainSegVol, or are these derived differently from BrainSegVol? Secondly, would merely adding the left-cerebral-cortex to right-cerebral-cortex measures found in aseg.stats give me total brain volume? Thank you in advance,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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probably partial volume correction, which is a good thing to do. On Mon, 13 Apr 2009, Douglas N Greve wrote:
Not having BrainSegVolNoVent might just mean that you have an old version. It was added two years ago, but I'm not sure which build that would have gotten into. Not sure about the discrepancy with mri_label_volume.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
I've checked out the wiki, and it brings up a couple of other questions. I don't seem to have the BrainSegVolNoVent measure...maybe this is an issue with versions? I ran the mri_label_volume command that Bruce provided. There was roughly a 300,000 mm^3 difference between the output of the mri_label_volume and BrainSegVol (the mri_label_volume output was the smaller value). Is this to be expected? It seems to me that they should be the same, unless I am mistaken?
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 4/13/2009 11:42 AM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] total brain volumes Did you look at the Brain Volume wiki page? To find it, go to our wiki and type in "BrainSegVol" in the search box and hit the "Text" button.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
I think this may have slipped through the cracks, so I am posting it again. I apologize if this has been answered already. If the information is available elsewhere and I happened to miss it, please let me know.
-----Original Message----- From: Dankner, Nathan (NIH/NIMH) [F] Sent: Thu 4/9/2009 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] total brain volumes I am looking to derive total brain volume measures from the data that I have. Judging by reading previous posts, it seems that BrainSegVol in aseg.stats includes cerebellum and ventricles. Is there any way to eliminate these from the calculation? Is it kosher to subtract the cerebellum/ventricle measures found elsewhere in aseg.stats/wm.parc from BrainSegVol, or are these derived differently from BrainSegVol? Secondly, would merely adding the left-cerebral-cortex to right-cerebral-cortex measures found in aseg.stats give me total brain volume? Thank you in advance,
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ok, sorry to be a bother, but I just want to be sure I'm getting accurate volumes here. Using the mri_label_volume method on one particular scan, the output volume is 500,000 mm^3 less than that of BrainSegVolNotVent (which is approx 1.2 million mm^3). Bruce, I know you mentioned that this is likely due to partial volume correction. However, the wiki indicates that the BrainSegVolNotVent also uses the partial volume correction, so it seems unusual that the two measures would be so vastly different. The wiki does indicate that BrainSegVolNotVent is probably what should be used, but I just want to make sure. If indeed BrainSegVolNotVent is the one to use, can I subtract cerebellum from it as I would with the mri_label_volume output? Once again, your help is very much appreciated.
Nathan
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Mon 4/13/2009 2:42 PM To: Douglas N Greve Cc: Dankner, Nathan (NIH/NIMH) [F]; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] total brain volumes
probably partial volume correction, which is a good thing to do. On Mon, 13 Apr 2009, Douglas N Greve wrote:
Not having BrainSegVolNoVent might just mean that you have an old version. It was added two years ago, but I'm not sure which build that would have gotten into. Not sure about the discrepancy with mri_label_volume.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
I've checked out the wiki, and it brings up a couple of other questions. I don't seem to have the BrainSegVolNoVent measure...maybe this is an issue with versions? I ran the mri_label_volume command that Bruce provided. There was roughly a 300,000 mm^3 difference between the output of the mri_label_volume and BrainSegVol (the mri_label_volume output was the smaller value). Is this to be expected? It seems to me that they should be the same, unless I am mistaken?
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Mon 4/13/2009 11:42 AM To: Dankner, Nathan (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] total brain volumes Did you look at the Brain Volume wiki page? To find it, go to our wiki and type in "BrainSegVol" in the search box and hit the "Text" button.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
I think this may have slipped through the cracks, so I am posting it again. I apologize if this has been answered already. If the information is available elsewhere and I happened to miss it, please let me know.
-----Original Message----- From: Dankner, Nathan (NIH/NIMH) [F] Sent: Thu 4/9/2009 1:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] total brain volumes I am looking to derive total brain volume measures from the data that I have. Judging by reading previous posts, it seems that BrainSegVol in aseg.stats includes cerebellum and ventricles. Is there any way to eliminate these from the calculation? Is it kosher to subtract the cerebellum/ventricle measures found elsewhere in aseg.stats/wm.parc from BrainSegVol, or are these derived differently from BrainSegVol? Secondly, would merely adding the left-cerebral-cortex to right-cerebral-cortex measures found in aseg.stats give me total brain volume? Thank you in advance,
Nathan
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freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Dankner, Nathan (NIH/NIMH) [F] -
Douglas N Greve