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 ridatta@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