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" <gr...@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" <gr...@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 >>>> gr...@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 >> gr...@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 gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
