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" <gr...@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" <gr...@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" <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 >>>> >>>> >>>> >>>> >>> ________________________________ >>> >>> 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
