Sorry about the delay. The jacobian factor accounts for stretching or compression when transferring the data from the individual to the group. This makes sure that the total volume after conversion is the same as before (this is not needed for thickness but it is for surface area). If you are going to do a volume analysis, it is usually a good idea to scale the the estimated total intracranial volume (eTIV). We did a group interhemispheric volume analysis here:
Greve, Douglas N., Lise Van der Haegen, Qing Cai, Steven Stufflebeam, Mert R. Sabuncu, Bruce Fischl, and Marc Bysbaert. "A surface-based analysis of language lateralization and cortical asymmetry." (2013). Journal of Cognitive Neuroscience 25.9: 1477-1492. On 01/18/2017 02:30 PM, Ritobrato Datta wrote: > Dear All, > > The email below probably fell through the cracks so I am resending it. > Appreciate your thoughts and suggestions. > > Best > > Ri > > ----- Original Message ----- > From: Ritobrato Datta <rida...@mail.med.upenn.edu> > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Sent: Tue, 17 Jan 2017 14:05:10 -0500 (EST) > Subject: question about cortical volume group analyses > > Hi All, > > I have a analysed data from AD patients and healthy controls and want to do a > group analyses of cortical volume. > > I have run qcache on each subject. > > In the lh.volume.fsaverage.mris_preproc.log file, > > mri_surf2surf --srcsubject AD1 --srchemi lh --srcsurfreg sphere.reg > --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval > ./tmp.mris_preproc.76769/AD1.1.mgh --sval > /Applications/freesurfer5.1/subjects/AD1/surf/lh.volume --jac --sfmt curv > --noreshape --no-cortex > > what does -jac jacobian correction mean ? Is it accounting/correcting for > differences in hemispheric volume ? > > I want to do a group analyses between AD and controls for cortical volume, > can I just use the lh.volume.fwhm??.fsaverage.mgh at different smoothing > kernels ? Do I need to correct for whole brain volume or some scaling or is > it already taken care of ? > > Are there references that have used free surfer to report group analyses for > cortical volume ? Can someone point to a few ? > > Thanks > > Ri > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
