Good to hear you are ready for publication!
On 07/02/2014 03:26 PM, Peggy Skelly wrote:
Hi,
In our analysis of stroke patients, I've followed the recommendation http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg34040.html to process images, then flip the final surfaces with xhemi for only the subjects with RH lesions to group all healthy hemispheres together for statistical analysis (instead of flipping the initial/raw images prior to processing.)
1 - In documenting the process (and preparing for publication), can you expand upon the reasoning (and possibly point to a reference) for processing prior to flipping? (possibly L-R asymmetries in templates/atlases used in talairach registration, skull stripping, segmentation, parcellation?)
If you flip the images then run recon-all, then there could be mismatches between the images and the atlases (as your suggest) causing inconsistencies between the flipped and unflipped results (which would be very bad).
2 - The xhemi reference, Greve et al 2013, explains the symmetric template creation very well. Is fsaverage_sym the template from the ref? (N=42, mostly women)
fsaverage_sym is not the atlas that was created for that paper. fsaverage_sym is built from the same subjects used to create fsaverage :
39 Subjects 14 Male, 25 Female Ages 18-87 Young (18-22): 10 Mid (40-60): 10 Old Healthy (69+): 8 Old Alzheimer's (68+): 11 Siemens 1.5T Vision (Wash U)
First described in Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain, Fischl et al. (2002). Neuron, 33:341-355.
Thanks, Peggy
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