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help > RE: Within-network connectivity after ICA
Jul 23, 2021 04:07 AM | Pravesh Parekh - University of Oslo
RE: Within-network connectivity after ICA
Dear Dr. Alfonso,
Thank you for your reply and the workflow for within-network connectivity. I will try this approach!
Would it be meaningful to take the BETA_Subject*_Condition*_Measure001_Component* files for all the subjects (pre-selected component) and then pass them to second-level analysis in SPM and provide an ICA ROI as an explicit mask? The reviewer seems to be a little unhappy with ROI-ROI connectivity (we had actually used the networks atlas and performed ROI-ROI connectivity within network) and seems to be in favour of voxel-wise analyses.
Thank you for your time and continued help!
Warm Regards
Pravesh
Originally posted by Alfonso Nieto-Castanon:
Thank you for your reply and the workflow for within-network connectivity. I will try this approach!
Would it be meaningful to take the BETA_Subject*_Condition*_Measure001_Component* files for all the subjects (pre-selected component) and then pass them to second-level analysis in SPM and provide an ICA ROI as an explicit mask? The reviewer seems to be a little unhappy with ROI-ROI connectivity (we had actually used the networks atlas and performed ROI-ROI connectivity within network) and seems to be in favour of voxel-wise analyses.
Thank you for your time and continued help!
Warm Regards
Pravesh
Originally posted by Alfonso Nieto-Castanon:
Dear
Pravesh,
For within-network connectivity I typically find more convenient to first create meaningful subcomponents of your network and then perform standard ROI-to-ROI analyses on those subcomponents. One simple way to do that is:
step 1) in the Summary tab of the second-level ICA results, select your network(s) of interest, switch the display from "spatial components" to "ICA parcellation" and modify the threshold value there to divide this network into meaningful sub-components, and then select in the ICA tools menu the option "Create ICA parcellation file" to create an ROI file defining those sub-components
step 2) in the Setup.ROIs tab import those new ROI-files as new ROIs for your project
step 3) in the Setup and Denoising tabs click 'Done' and select the 'do not overwrite' option to process only those new ROIs
step 4) in the first-level analysis tab define a new first-level RRC analysis entering only these new ROIs to evaluate the within-network connectivity (e.g bivariate correlations)
Hope this helps
Alfonso
Originally posted by Pravesh Parekh:
For within-network connectivity I typically find more convenient to first create meaningful subcomponents of your network and then perform standard ROI-to-ROI analyses on those subcomponents. One simple way to do that is:
step 1) in the Summary tab of the second-level ICA results, select your network(s) of interest, switch the display from "spatial components" to "ICA parcellation" and modify the threshold value there to divide this network into meaningful sub-components, and then select in the ICA tools menu the option "Create ICA parcellation file" to create an ROI file defining those sub-components
step 2) in the Setup.ROIs tab import those new ROI-files as new ROIs for your project
step 3) in the Setup and Denoising tabs click 'Done' and select the 'do not overwrite' option to process only those new ROIs
step 4) in the first-level analysis tab define a new first-level RRC analysis entering only these new ROIs to evaluate the within-network connectivity (e.g bivariate correlations)
Hope this helps
Alfonso
Originally posted by Pravesh Parekh:
Dear Dr. Alfonso/ Conn Experts,
I know that this topic has come up before but perhaps I am missing the relevant posts where the answer is.
I have performed an ICA analysis (20 components) on my sample and have identified a few networks of interest (DMN, FPN, DAN, etc.). Now, I am interested in performing a (voxel-level) within-network analysis for each of the selected network. What would be the best way forward? I see an option of including all the ICA components as masks in the ROI tab (Setup). How should I proceed after that?
P.S: I am using Conn 18b (this is some old analysis; the paper is in revision stage and the reviewer wants us to do some ICA analysis and comment on within-network connectivity of identified components).
Thank you for your time and help
Regards
Pravesh
I know that this topic has come up before but perhaps I am missing the relevant posts where the answer is.
I have performed an ICA analysis (20 components) on my sample and have identified a few networks of interest (DMN, FPN, DAN, etc.). Now, I am interested in performing a (voxel-level) within-network analysis for each of the selected network. What would be the best way forward? I see an option of including all the ICA components as masks in the ROI tab (Setup). How should I proceed after that?
P.S: I am using Conn 18b (this is some old analysis; the paper is in revision stage and the reviewer wants us to do some ICA analysis and comment on within-network connectivity of identified components).
Thank you for your time and help
Regards
Pravesh
Threaded View
| Title | Author | Date |
|---|---|---|
| Pravesh Parekh | Jul 20, 2021 | |
| Alfonso Nieto-Castanon | Jul 22, 2021 | |
| Pravesh Parekh | Jul 23, 2021 | |