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