Re: [HCP-Users] Time series data
If you are looking for a network assignment of the parcels in the Glasser parcellation, see: https://github.com/ColeLab/ColeAnticevicNetPartition cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of "Glasser, Matthew" Date: Wednesday, December 19, 2018 at 6:30 PM To: "Rakib Al-Fahad (ralfahad)" , "HCP-Users@humanconnectome.org" Subject: Re: [HCP-Users] Time series data See my recommendation below. Matt. From: "Rakib Al-Fahad (ralfahad)" mailto:ralfa...@memphis.edu>> Date: Wednesday, December 19, 2018 at 5:46 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] Time series data Matt, I agree with your pint. My specialization is in signal processing and machine learning. I am not sure about ICA based time series. If we consider 100 ICA components, how can we define each node name for graph theoretical measures? For example, the paper ‘Chronnectomic patterns and neural flexibility underlie executive function” [Jason et al. NeuroImage 147 (2017): 861-871] talked about 100 components. They define DNN, subcortical, frontal, etc. networks. Can you give me any reference that can guide which component belongs to which network or how to name them? If somehow, I discover connectivity between Component_1 and Component_3 is significantly related to some behavior, how can I express it in neuroscience term? I believe my question is clear now. Thanks Rakib From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Wednesday, December 19, 2018 at 5:28 PM To: "Rakib Al-Fahad (ralfahad)" mailto:ralfa...@memphis.edu>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] Time series data What neuroscience questions are ICA timeseries unable to answer? Particularly that gyral/sulcal folding-based parcellation would be able to answer? If you want a neuroanatomical parcellation into cortical areas, this is available here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Rakib Al-Fahad (ralfahad)" mailto:ralfa...@memphis.edu>> Date: Wednesday, December 19, 2018 at 4:40 PM To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] Time series data Hello All, I want to analyze time series data and dynamic brain connectivity from rfMRI data. I don’t want to use ICA based time series because they cannot answer lot of neuroscience question. I prefer ROI based analysis. A 45+ ROI template would be useful (e.g. FreeSurfer template). Is it possible to use workbench on processed data to extract ROI based time series, or I have to run FreeSurfer on data? Please help me with some guidance and reference. [M logo] Rakib Al-Fahad Ph.D. Candidate Electrical and Computer Engineering The University of Memphis 901.279.4128 ___ 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 The materials in this message are private and may contain Protected Healthcare Information or other information
Re: [HCP-Users] Time series data
See my recommendation below. Matt. From: "Rakib Al-Fahad (ralfahad)" mailto:ralfa...@memphis.edu>> Date: Wednesday, December 19, 2018 at 5:46 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] Time series data Matt, I agree with your pint. My specialization is in signal processing and machine learning. I am not sure about ICA based time series. If we consider 100 ICA components, how can we define each node name for graph theoretical measures? For example, the paper ‘Chronnectomic patterns and neural flexibility underlie executive function” [Jason et al. NeuroImage 147 (2017): 861-871] talked about 100 components. They define DNN, subcortical, frontal, etc. networks. Can you give me any reference that can guide which component belongs to which network or how to name them? If somehow, I discover connectivity between Component_1 and Component_3 is significantly related to some behavior, how can I express it in neuroscience term? I believe my question is clear now. Thanks Rakib From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Wednesday, December 19, 2018 at 5:28 PM To: "Rakib Al-Fahad (ralfahad)" mailto:ralfa...@memphis.edu>>, "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: Re: [HCP-Users] Time series data What neuroscience questions are ICA timeseries unable to answer? Particularly that gyral/sulcal folding-based parcellation would be able to answer? If you want a neuroanatomical parcellation into cortical areas, this is available here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Rakib Al-Fahad (ralfahad)" mailto:ralfa...@memphis.edu>> Date: Wednesday, December 19, 2018 at 4:40 PM To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] Time series data Hello All, I want to analyze time series data and dynamic brain connectivity from rfMRI data. I don’t want to use ICA based time series because they cannot answer lot of neuroscience question. I prefer ROI based analysis. A 45+ ROI template would be useful (e.g. FreeSurfer template). Is it possible to use workbench on processed data to extract ROI based time series, or I have to run FreeSurfer on data? Please help me with some guidance and reference. [M logo] Rakib Al-Fahad Ph.D. Candidate Electrical and Computer Engineering The University of Memphis 901.279.4128 ___ 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
Re: [HCP-Users] Time series data
We generally do use timeseries for single-subject analysis. The only involvement of ICA there is in cleaning up things like artifacts - think of it as using ICA to identify nuisance regressors. The end result is still a timeseries, but with greatly reduced artifacts. You can use wb_command -cifti-parcellate to take a dtseries file and take the within-ROI average timeseries of every area in a dlabel file. The main thing I know of where we actually use ICA/PCA components as the data to be analyzed is in MIGP, mainly as a way to do things that would normally require concatenating the timeseries of all subjects, which would take too much memory. Tim On Wed, Dec 19, 2018 at 5:46 PM Rakib Al-Fahad (ralfahad) < ralfa...@memphis.edu> wrote: > Matt, > > > > I agree with your pint. > > > > My specialization is in signal processing and machine learning. I am not > sure about ICA based time series. If we consider 100 ICA components, how > can we define each node name for graph theoretical measures? For example, > the paper ‘Chronnectomic patterns and neural flexibility underlie executive > function” [Jason et al. NeuroImage 147 (2017): 861-871] talked about 100 > components. They define DNN, subcortical, frontal, etc. networks. Can you > give me any reference that can guide which component belongs to which > network or how to name them? > > > > If somehow, I discover connectivity between Component_1 and Component_3 is > significantly related to some behavior, how can I express it in > neuroscience term? I believe my question is clear now. > > > > > > Thanks > > Rakib > > > > *From: *"Glasser, Matthew" > *Date: *Wednesday, December 19, 2018 at 5:28 PM > *To: *"Rakib Al-Fahad (ralfahad)" , " > HCP-Users@humanconnectome.org" > *Subject: *Re: [HCP-Users] Time series data > > > > What neuroscience questions are ICA timeseries unable to answer? > Particularly that gyral/sulcal folding-based parcellation would be able to > answer? If you want a neuroanatomical parcellation into cortical areas, > this is available here: > > > > https://balsa.wustl.edu/file/show/3VLx > > > > Matt. > > > > *From: * on behalf of "Rakib > Al-Fahad (ralfahad)" > *Date: *Wednesday, December 19, 2018 at 4:40 PM > *To: *"HCP-Users@humanconnectome.org" > *Subject: *[HCP-Users] Time series data > > > > Hello All, > > > > I want to analyze time series data and dynamic brain connectivity from > rfMRI data. I don’t want to use ICA based time series because they cannot > answer lot of neuroscience question. I prefer ROI based analysis. A 45+ ROI > template would be useful (e.g. FreeSurfer template). Is it possible to use > workbench on processed data to extract ROI based time series, or I have to > run FreeSurfer on data? Please help me with some guidance and reference. > > > > > [image: M logo] > > Rakib Al-Fahad > Ph.D. Candidate > Electrical and Computer Engineering > The University of Memphis > 901.279.4128 > > > > > > ___ > HCP-Users mailing list > 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 > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Time series data
Matt, I agree with your pint. My specialization is in signal processing and machine learning. I am not sure about ICA based time series. If we consider 100 ICA components, how can we define each node name for graph theoretical measures? For example, the paper ‘Chronnectomic patterns and neural flexibility underlie executive function” [Jason et al. NeuroImage 147 (2017): 861-871] talked about 100 components. They define DNN, subcortical, frontal, etc. networks. Can you give me any reference that can guide which component belongs to which network or how to name them? If somehow, I discover connectivity between Component_1 and Component_3 is significantly related to some behavior, how can I express it in neuroscience term? I believe my question is clear now. Thanks Rakib From: "Glasser, Matthew" Date: Wednesday, December 19, 2018 at 5:28 PM To: "Rakib Al-Fahad (ralfahad)" , "HCP-Users@humanconnectome.org" Subject: Re: [HCP-Users] Time series data What neuroscience questions are ICA timeseries unable to answer? Particularly that gyral/sulcal folding-based parcellation would be able to answer? If you want a neuroanatomical parcellation into cortical areas, this is available here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Rakib Al-Fahad (ralfahad)" mailto:ralfa...@memphis.edu>> Date: Wednesday, December 19, 2018 at 4:40 PM To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] Time series data Hello All, I want to analyze time series data and dynamic brain connectivity from rfMRI data. I don’t want to use ICA based time series because they cannot answer lot of neuroscience question. I prefer ROI based analysis. A 45+ ROI template would be useful (e.g. FreeSurfer template). Is it possible to use workbench on processed data to extract ROI based time series, or I have to run FreeSurfer on data? Please help me with some guidance and reference. [M logo] Rakib Al-Fahad Ph.D. Candidate Electrical and Computer Engineering The University of Memphis 901.279.4128 ___ 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
Re: [HCP-Users] Time series data
What neuroscience questions are ICA timeseries unable to answer? Particularly that gyral/sulcal folding-based parcellation would be able to answer? If you want a neuroanatomical parcellation into cortical areas, this is available here: https://balsa.wustl.edu/file/show/3VLx Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Rakib Al-Fahad (ralfahad)" mailto:ralfa...@memphis.edu>> Date: Wednesday, December 19, 2018 at 4:40 PM To: "HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>" mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] Time series data Hello All, I want to analyze time series data and dynamic brain connectivity from rfMRI data. I don’t want to use ICA based time series because they cannot answer lot of neuroscience question. I prefer ROI based analysis. A 45+ ROI template would be useful (e.g. FreeSurfer template). Is it possible to use workbench on processed data to extract ROI based time series, or I have to run FreeSurfer on data? Please help me with some guidance and reference. [fM logo] Rakib Al-Fahad Ph.D. Candidate Electrical and Computer Engineering The University of Memphis 901.279.4128 ___ 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
[HCP-Users] Time series data
Hello All, I want to analyze time series data and dynamic brain connectivity from rfMRI data. I don’t want to use ICA based time series because they cannot answer lot of neuroscience question. I prefer ROI based analysis. A 45+ ROI template would be useful (e.g. FreeSurfer template). Is it possible to use workbench on processed data to extract ROI based time series, or I have to run FreeSurfer on data? Please help me with some guidance and reference. [fM logo] Rakib Al-Fahad Ph.D. Candidate Electrical and Computer Engineering The University of Memphis 901.279.4128 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
