MSMAll is a cerebral cortical surface alignment approach. The subcortical volume portions of CIFTI are aligned with FNIRT volume-based nonlinear registration. As to whether that is better or worse than the volume-based nonlinear registration used by SUIT it is hard to say. One would have to try both approaches and see which had better functional alignment (which is not always the approach with better fitting of folds—on the cerebral cortex tighter folding alignment leads to worse functional alignment). Unfortunately no one has yet developed a way of performing cerebellar surface segmentations of individual subjects reliably, however surface registration would be better than volume-based registration if it were possible. CIFTI is designed to allow a surface-based cerebellum if we ever get the ability to make cerebellar surfaces in individuals reliably and MSM would be able to do a functional alignment in that case as well.
Peace, Matt. From: Kajsa Igelström <kajsa.igelst...@gmail.com<mailto:kajsa.igelst...@gmail.com>> Date: Tuesday, March 7, 2017 at 1:10 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files Thanks a lot! I have a follow-up question: Do you know how cerebellar alignment in CIFTI/MSMAll data compares to that achieved with the SUIT Toolbox? Many thanks, Kajsa On Tue, Mar 7, 2017 at 2:05 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I think there is a bug in melodic, which I also encountered. I would report this to the FSL list, but it is likely the issue will be fixed in the next FSL release. Also, if you are running melodic in the volume and combining across subjects, this is not recommended because much of the brain is not well aligned in the volume. It is instead recommended that you use the CIFTI data that has been aligned with MSMAll. ICA gives very different results depending on whether the data are well aligned or not. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Kajsa Igelström <kajsa.igelst...@gmail.com<mailto:kajsa.igelst...@gmail.com>> Date: Tuesday, March 7, 2017 at 12:40 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ICA failure with volumetric ICA-FIX denoised files Hi Jenny and others! I'm also unable to run these files through Melodic. The most common problem is that it doesn't converge, and under some circumstances it seems like Melodic just stops in the middle of normalizing individual files, at points that are not logical to me, or reproducible. Best, Kajsa On Tue, Mar 7, 2017 at 12:24 PM, Jenny Gilbert <jennyrg...@gmail.com<mailto:jennyrg...@gmail.com>> wrote: Hello HCP! I am trying to complete ICA using the volumetric ICA-FIX de noised data (rfMRI_REST1_RL_hp2000_clean.nii.gz files), and melodic keeps failing. It looks like melodic gets hung up on some participants cannot progress while removing the mean image and normalizing by the voxel-wise variance. Has anyone come across this same problem? Any advice on how to fix? Thank you! Jenny _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
