Re: [Freesurfer] two questions: asymmetry and controlling for global thickness abnormality
Thank you Michael. I have more questions on this: 1. Is there a method to calculate if I have global difference in thickness between groups? 2. How can I control for global thickness difference vertex-wise using freesurfer? Best wishes, Tanja. On Mon, Sep 5, 2011 at 7:42 PM, Michael Harms wrote: > > Regarding #2: Yes, if you a have global difference in thickness between > groups, then it is appropriate to control for that in the same manner that > one frequently controls for total brain volume in volumetric analyses. > > cheers, > -MH > >> Dear list, >> >> I have two question: >> >> 1. Is it possible to do the asymmetry analysis in FS, I mean to >> compare left and right hemispheres within one group? >> >> 2. Is it necessary to somehow control for global abnormality of >> thickness while looking at regional abnormality, e.g. if one group has >> thinner brain overall, but also thinner brain in some regions? >> (Similar to dividing by total brain volume in volumetric analysis) >> >> Thank you and best wishes, >> Tanja. >> ___ >> 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. >> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] two questions: asymmetry and controlling for global thickness abnormality
for #1 you are probably best waiting for Doug and Mert's new laterality processing stream. Maybe one of them can give you an idea of when it would be ready Bruce On Mon, 5 Sep 2011, Michael Harms wrote: > > Regarding #2: Yes, if you a have global difference in thickness between > groups, then it is appropriate to control for that in the same manner that > one frequently controls for total brain volume in volumetric analyses. > > cheers, > -MH > >> Dear list, >> >> I have two question: >> >> 1. Is it possible to do the asymmetry analysis in FS, I mean to >> compare left and right hemispheres within one group? >> >> 2. Is it necessary to somehow control for global abnormality of >> thickness while looking at regional abnormality, e.g. if one group has >> thinner brain overall, but also thinner brain in some regions? >> (Similar to dividing by total brain volume in volumetric analysis) >> >> Thank you and best wishes, >> Tanja. >> ___ >> 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. >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] two questions: asymmetry and controlling for global thickness abnormality
Regarding #2: Yes, if you a have global difference in thickness between groups, then it is appropriate to control for that in the same manner that one frequently controls for total brain volume in volumetric analyses. cheers, -MH > Dear list, > > I have two question: > > 1. Is it possible to do the asymmetry analysis in FS, I mean to > compare left and right hemispheres within one group? > > 2. Is it necessary to somehow control for global abnormality of > thickness while looking at regional abnormality, e.g. if one group has > thinner brain overall, but also thinner brain in some regions? > (Similar to dividing by total brain volume in volumetric analysis) > > Thank you and best wishes, > Tanja. > ___ > 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] questions about mapping volume data to brain surface and extracting cortical thickness
Hi FS experts: I have two questions about FS. (1) Is there a way that can map volume data(.hdr and .img file) to brain surface in FS? (2) I find a way that can extract cortical thickness automatically,first,the statistical significant areas derived from group analysis on qdec are converted to annotation file using mri_surfcluster,then i use mri_annotation2label to convert the annotation file to label file,finally, mri_label2label and mri_anatomical_stats are used to map the label file to each subject and obtain cortical thickness. I want to know if the process is correct. any help appreciated___ 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.
[Freesurfer] two questions: asymmetry and controlling for global thickness abnormality
Dear list, I have two question: 1. Is it possible to do the asymmetry analysis in FS, I mean to compare left and right hemispheres within one group? 2. Is it necessary to somehow control for global abnormality of thickness while looking at regional abnormality, e.g. if one group has thinner brain overall, but also thinner brain in some regions? (Similar to dividing by total brain volume in volumetric analysis) Thank you and best wishes, Tanja. ___ 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.
[Freesurfer] Using different versions of FS for the same dataset (5.0 and 5.1)
Dear Freesurfer users and developers, I apologize if this question sounds rhetorically or maybe it has been asked previously (I didn't find the answers in the archives). But here it is... I have a big dataset of images and several workstations. I started the analysis on the first one and afterwards I installed Freesurfer on the others. But just right now I have noticed that their versions are different (I have v5.0 on the first computer, whereas other ones have 5.1). Could you please tell me if I should redo all the analyses from the first workstation or if it is ok and I can upgrade my version and keep it going? Thank you very much beforehand! --- Best Regards, Alex ___ 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.
