Re: [Freesurfer] hippocampus volume normalization question
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] hippocampus volume normalization question
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" 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] hippocampus volume normalization question
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 0.1 --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" 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" 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
Re: [Freesurfer] hippocampus volume normalization question
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" 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 0.1 --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" 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" > 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 c
Re: [Freesurfer] hippocampus volume normalization question
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" 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" >>> 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 0.1 --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" > 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" >>> 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 > > > > -- Dougla
