Hi Rebecca, this is intentional. The whole brain is divided up into left cortical hemi, right hemi, and subcortical structures. the MNI305 is only supposed to handle the subcortical structures. If you want a brain volume with cortical and subcortical, you can use vlrmerge to merge the volume, lh, and rh into one volume. Alternatvely, you can run preproc-sess with the -no-subcort-mask and it will not mask the mni305 results
doug
On 7/10/13 10:26 PM, Lijia Wang wrote:
Hi experts,
When I'm pre-processing the 4D whole brain BOLD images using "preproc-sess -sf -mni305 -fwhm 5 -fsd bold -per-run" , the results of registration from BOLD images to the MNI305 template are always only a small part of the original images. I tried to use another T1_152 template instead(higher resolution) of the original MNI305 template, then"recon-all", "preproc-sess", but the results still remain the small part. How can I solve this problem?
Thanks!
Best Regards!
Rebecca
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