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help > RE: Average within / between network connectivity
Feb 14, 2018 12:02 PM | Alfonso Nieto-Castanon - Boston University
RE: Average within / between network connectivity
Dear Helene,
Regarding (1) yes, you are exactly right that a Bonferroni correction of 6 (3 within-/between- network comparisons and 2-tailed) would suffice for these analyses (that is the number of multiple tests that are being evaluated by that script). If you prefer, you could also (perhaps a bit more standard) first convert the three uncorrected p-values output by the script into two-sided p-values (using a p2 = 2*min(p,1-p) formula), and then apply FDR across those multiple tests (using a P = conn_fdr(p2) command). That should be similarly valid and a bit less conservative than Bonferroni.
Regarding (2), the former computation is used (i.e. the script averages the ROI-to-ROI connectivity values between all ROI pairs with ROI1 in set1 and ROI2 in set2)
Hope this helps, and my apologies that this conn_withinbetween* script/functionality is still undocumented, I will eventually get around to making this part of the standard set of ROI/network analyses in CONN
Alfonso
Originally posted by Helene Veenstra:
Regarding (1) yes, you are exactly right that a Bonferroni correction of 6 (3 within-/between- network comparisons and 2-tailed) would suffice for these analyses (that is the number of multiple tests that are being evaluated by that script). If you prefer, you could also (perhaps a bit more standard) first convert the three uncorrected p-values output by the script into two-sided p-values (using a p2 = 2*min(p,1-p) formula), and then apply FDR across those multiple tests (using a P = conn_fdr(p2) command). That should be similarly valid and a bit less conservative than Bonferroni.
Regarding (2), the former computation is used (i.e. the script averages the ROI-to-ROI connectivity values between all ROI pairs with ROI1 in set1 and ROI2 in set2)
Hope this helps, and my apologies that this conn_withinbetween* script/functionality is still undocumented, I will eventually get around to making this part of the standard set of ROI/network analyses in CONN
Alfonso
Originally posted by Helene Veenstra:
Dear Alfonso,
Reviving an older thread as I am using this code line for my analyses, as I was interested in network connectivity changes related to covariates and groups. I have a couple of questions.
1) since this analysis uses (uncorrected) two-tailed p-values; however draws from a small pool of regions to test, would it be appropriate to consider the results being adequately corrected with a Bonferroni correction for number of tests, and appropriate choice of number of tails?
Example: I investigate several hypotheses (different covariates/group comparisons) for the connectivity within two networks (SN, DMN) and the connectivity between those two. To obtain a p-value <0.05 per hypothesis, I use a corrected p-value with a Bonferroni correction of 6 (p<0.0083) based on 3 network (SN, DMN, SN-DMN) tests * 2 for two-tailed.
2) as you explained this gives an average over all ROI connections within each chosen network. But how exactly is the between-network value calculated? As an average of every possible ROI (group1) to ROI (group2) connection? Or a calculated connectivity of the averaged connectivity over all ROIs within each group?
Reviving an older thread as I am using this code line for my analyses, as I was interested in network connectivity changes related to covariates and groups. I have a couple of questions.
1) since this analysis uses (uncorrected) two-tailed p-values; however draws from a small pool of regions to test, would it be appropriate to consider the results being adequately corrected with a Bonferroni correction for number of tests, and appropriate choice of number of tails?
Example: I investigate several hypotheses (different covariates/group comparisons) for the connectivity within two networks (SN, DMN) and the connectivity between those two. To obtain a p-value <0.05 per hypothesis, I use a corrected p-value with a Bonferroni correction of 6 (p<0.0083) based on 3 network (SN, DMN, SN-DMN) tests * 2 for two-tailed.
2) as you explained this gives an average over all ROI connections within each chosen network. But how exactly is the between-network value calculated? As an average of every possible ROI (group1) to ROI (group2) connection? Or a calculated connectivity of the averaged connectivity over all ROIs within each group?
Threaded View
Title | Author | Date |
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Ruth Shaffer | Apr 27, 2016 | |
Alfonso Nieto-Castanon | May 4, 2016 | |
Chabran Eléna | Sep 20, 2018 | |
Maria Beser | Feb 11, 2022 | |
max345 | Feb 1, 2022 | |
Alfonso Nieto-Castanon | Feb 3, 2022 | |
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Alfonso Nieto-Castanon | Apr 28, 2018 | |
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Himanshu Joshi | Mar 13, 2018 | |
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Jon Dudley | May 4, 2016 | |
Alfonso Nieto-Castanon | May 5, 2016 | |
Helene Veenstra | Feb 8, 2018 | |
Alfonso Nieto-Castanon | Feb 14, 2018 | |
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