Hi Matt, Great, very helpful! That makes sense for the gradients. Will try as you suggest for the volume-based dense connectomes (good to know in terms of resource requirements, will request accordingly).
Many thanks! -Ely ________________________________ From: Glasser, Matthew [glass...@wustl.edu] Sent: Wednesday, August 17, 2016 1:16 PM To: Ely, Benjamin; HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] cifti-gradient vs. cifti-correlation-gradient, also volume-based dense connectomes Hi Ely, 1. The idea is to look for differences in connectivity patterns, rather than differences in timeseries. The second order correlation integrates information over the whole brain, instead of just the local neighborhood. The original connectivity gradients paper: http://www.sciencedirect.com/science/article/pii/S1053811908001171<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.sciencedirect.com_science_article_pii_S1053811908001171&d=AwMFAw&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=FUX5Pj9fH7xReJdwrOJyWkCrOYPCCM3Du1A3bMpl278&m=qeFRtBekmLL2SfIs-1S_J8EZr3wGsQM0eWsf3WLiK3Y&s=fisQxnYYHhW0dJieE2I-ec1ofTBPUQbP2z5oqf95gB8&e=> used eta^2 instead of correlation, however we found that eta^2 and correlation gave similar answers and at the time correlation was faster to compute. 2. It is possible, but be prepared to use a machine with a lot of CPU power, RAM, and storage. A 91282 X 91282 CIFTI grayordinate dense connectome is around 31GB, but a volume dense connectome at the same 2mm spacing and 228483 X 228483 would be around 195GB. You can import the NIFTI file using the subject’s brain mask (or a standard brain mask) using the wb_command -cifti-create-dense-timeseries function. Prior to that, you’ll want to set the brain mask to be a label volume and have the structure “OTHER." Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Ely, Benjamin" <benjamin....@mssm.edu<mailto:benjamin....@mssm.edu>> Date: Wednesday, August 17, 2016 at 11:58 AM To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] cifti-gradient vs. cifti-correlation-gradient, also volume-based dense connectomes Hi team HCP, I have two semi-related questions about generating resting-state gradients: 1) What is the theoretical motivation behind using cifti-correlation-gradient rather than cifti-gradient to generate a resting-state gradient .dscalar.nii from a .dconn.nii file, per this thread ( http://www.mail-archive.com/hcp-users%40humanconnectome.org/msg01431.html<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_hcp-2Dusers-2540humanconnectome.org_msg01431.html&d=AwMFAw&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=FUX5Pj9fH7xReJdwrOJyWkCrOYPCCM3Du1A3bMpl278&m=qeFRtBekmLL2SfIs-1S_J8EZr3wGsQM0eWsf3WLiK3Y&s=_s8F8I39h5ua5y8_HjdYE9oIzZfqkfoDqA5Ool4GMBs&e=> )? Based on the documentation, cifti-gradient takes the first spatial derivative of the input .dconn.nii (i.e. the correlation matrix of every voxel/vertex) and (optionally) averages them. Cifti-correlation-gradient, by contrast, first correlates the .dconn.nii correlation matrix, and then takes the spatial derivative of the resulting maps and averages them. What is the purpose of this second-order correlation? 2) Is it possible to generate volume-based dense connectomes and downstream resting-state gradients using the HCP tools? My goal is to examine resting-state gradients just beyond the edges of the subcortical volume as defined in grayordinate space. Thank you for any feedback! -Ely _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=AwMFAw&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=FUX5Pj9fH7xReJdwrOJyWkCrOYPCCM3Du1A3bMpl278&m=qeFRtBekmLL2SfIs-1S_J8EZr3wGsQM0eWsf3WLiK3Y&s=X8NGxyGCXomwBIbe9Gp35JMMC2-F4vv4RQZzVq9YFHk&e=> ________________________________ 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
