It is whole-brain minus cerebellum and brain stem. But the current release has a bug and should not be trusted. See the email I sent out last week or look at the Release Notes page on our wiki for how to download a patch and regenerate the results. doug
Rashmi Singh wrote:
Thanks so much Doug, Just a last question. Is supratentorial volume present in the aseg.stat file anyway related to the whole brain volume? Thanks, Rashmi.
On 2/29/12 10:33 AM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
You'll have to run it on each subject. Easy to do with a script. You can then cat the data into one fine (they are just text files). doug
Rashmi Singh wrote:
Thanks Doug, Do I need to run the following for each subject or can is there a way to run it with input for all my subjects in one go to get the brain volume of all my subject in one output file. Thanks,
On 2/29/12 10:15 AM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
oh, sorry, I do remember now that we took that out (I think we put it back in for the next release). The work-around is to run
mri_binarize --i brain.mgz --min 0.00001 --count count.dat --o junk.mgh
You can delete junk.mgh. The file count.dat will have info about the number of voxels in the brain. It will have 4 numbers: #voxels in brain, brain volume (mm3), total # voxels in volume, and brain volume as a percent of total volume in the 3d a field of view.
doug
Rashmi Singh wrote:
Hello doug, In the asegstats. Txt ( that got as in the table format with information on all subjects grouped together in a single .Xls file) I found information on Total Gray vol but I don't see whole Brain volume. Can you please suggest me where to get the whole brain volume. Thanks, Rashmi.
On 2/28/12 3:22 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
In the aseg.stats file there is a value for the whole brain volume. doug
Rashmi Singh wrote:
> I would like know how can I get the sub-cortical volumes normalized > it > to > the whole brain. > Thanks, > Rashmi. > > On 2/28/12 3:14 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu > wrote: > > > > > >> No, it does not. All volumes are volumes in native anatomical >> space. >> doug >> >> Rashmi Singh wrote: >> >> >> >> >>> Hello. >>> I am using FreeSurfer to generate subcortical volumes and >>> cortical >>> thickness for my subjects. >>> Does FreeSurfer normalizes the subcortical volumes to the whole >>> brain >>> volume for each subjects. >>> Let me know. >>> For among subjects comparison I am assuming that the sub >>> cortical >>> volumes generated for each subject are normalized to its own whole >>> brain volume. >>> >>> Thank you, >>> Rashmi. >>> >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------- >>> -- >>> -- >>> - >>> >>> This document may contain information covered under the Privacy >>> Act, 5 >>> USC 552(a), and/or the Health Insurance Portability and >>> Accountability >>> Act (PL 104-191) and its various implementing regulations and must >>> be >>> protected in accordance with those provisions. Healthcare >>> information >>> is personal and sensitive and must be treated accordingly. If this >>> correspondence contains healthcare information it is being >>> provided >>> to >>> you after appropriate authorization from the patient or under >>> circumstances that don't require patient authorization. You, the >>> recipient, are obligated to maintain it in a safe, secure and >>> confidential manner. Redisclosure without additional patient >>> consent >>> or as permitted by law is prohibited. Unauthorized redisclosure or >>> failure to maintain confidentiality subjects you to application of >>> appropriate sanction. If you have received this correspondence in >>> error, please notify the sender at once and destroy any copies you >>> have made. >>> >>> >>> >>> ------------------------------------------------------------------- >>> -- >>> -- >>> - >>> >>> _______________________________________________ >>> 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 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> 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. >> >> >> >> >> > ________________________________ > > This document may contain information covered under the Privacy > Act, 5 > USC 552(a), and/or the Health Insurance Portability and > Accountability > Act (PL 104-191) and its various implementing regulations and must > be > protected in accordance with those provisions. Healthcare > information > is > personal and sensitive and must be treated accordingly. If this > correspondence contains healthcare information it is being provided > to > you after appropriate authorization from the patient or under > circumstances that don't require patient authorization. You, the > recipient, are obligated to maintain it in a safe, secure and > confidential manner. Redisclosure without additional patient consent > or > as permitted by law is prohibited. Unauthorized redisclosure or > failure > to maintain confidentiality subjects you to application of > appropriate > sanction. If you have received this correspondence in error, please > notify the sender at once and destroy any copies you have made. > > > > >
>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve