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