I would recommend running the multi-run FIX pipeline for that on all the fMRI data together. That works on the volume data and then also cleans the CIFTI data at the same time.
Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi <lto...@stanford.edu<mailto:lto...@stanford.edu>> Date: Tuesday, January 8, 2019 at 11:35 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Identifying noise components in group MELODIC on ciftis Dear experts, I have preprocessed with the minimal preprocessing pipeline some data which includes resting state and 3 fMRI tasks. I have then ran MELODIC group ICA on the resulting dtseries.nii files (for each task separately). My question is this: I have only greyordinate data in the outputs, so how can I optimally identify the noise components since I have no data for example from the CSF or white matter? I am also wondering if running the ICA on the greyordinate data is already somehow excluding the noise components that are predominantly in the CSF and white matter. I was thinking one way I could proceed is to use the statistics produced from MELODIC of the comparison between the components and the “background noise” (although I am unsure about how this is defined) and/or enter the GLMs of my tasks in MELODIC and see if I find components that correlate with the design (but then I would not know what to do with resting state). Another possibility would be to use the FIX pipeline, but I am not sure if it’s implemented for tasks and if it can be used at the group level. In any case, I wanted to make sure that the processing is the same for resting state and task data. Also, I would probably need to retrain the classifier, since we are conducting our experiment at a different site and on a GE magnet, correct? I would appreciate any pointers on how to best proceed with this matter. Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 _______________________________________________ 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. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
