help
489 Subscribers 
help > Average within / between network connectivity
Showing 1-25 of 31 posts
Apr 27, 2016 09:04 PM | Ruth Shaffer
Average within / between network connectivity
Hello,
I am looking into second level ROI-to-ROI analyses and am hoping to calculate average within- and between- network correlations for each of the networks of ROIs in two separate RSFC runs.
For example, if I had 3 networks, each with 5 ROIs, I would be trying to do two things:
1) to obtain an average within-network correlation during run1 and during run2 for each of the three networks (specifically I am looking for a single average correlation among the 5 ROIs in network 1 at run1 and then their average correlation at run 3--and then I would do the same calculation for the other two networks separately).
2) to obtain between network average correlations for each network (specifically I am looking for a single average correlation for 5 ROIs in network 1 with the 10 ROIs comprising networks 2 and 3, calculating this at run1 and then again at run 3--and tthen I would do the same calculation for the other two networks separately).
Is this possible to do in CONN, and, if so, how might I go about obtaining these measures?
Thank you so much for such a great program and for any help on this question you can give me!
Best,
Ruth
I am looking into second level ROI-to-ROI analyses and am hoping to calculate average within- and between- network correlations for each of the networks of ROIs in two separate RSFC runs.
For example, if I had 3 networks, each with 5 ROIs, I would be trying to do two things:
1) to obtain an average within-network correlation during run1 and during run2 for each of the three networks (specifically I am looking for a single average correlation among the 5 ROIs in network 1 at run1 and then their average correlation at run 3--and then I would do the same calculation for the other two networks separately).
2) to obtain between network average correlations for each network (specifically I am looking for a single average correlation for 5 ROIs in network 1 with the 10 ROIs comprising networks 2 and 3, calculating this at run1 and then again at run 3--and tthen I would do the same calculation for the other two networks separately).
Is this possible to do in CONN, and, if so, how might I go about obtaining these measures?
Thank you so much for such a great program and for any help on this question you can give me!
Best,
Ruth
May 4, 2016 01:05 AM | Alfonso Nieto-Castanon - Boston University
RE: Average within / between network connectivity
Hi Ruth,
Currently there is a separate script (part of the CONN package but not yet integrated into CONN's gui) that would allow you to perform these sort of within- and between- network analyses. To use it you should:
1) in CONN's gui second-level results tab, define there the specific model that you would like to test (i.e. select the subject-effects and associated between-subjects contrast, and the desired conditions and associated between-conditions contrast)
2) then in Matlab command line type
conn_withinbetweenROItest;
That will prompt you to select two networks (e.g. select the 5 ROIs that belong to each of your first two networks) and then it will output a file containing the within- and between- network connectivities (averaged across all the ROIs within each network) for each subject, as well as the statistics associated with your selected second-level model again for the within- and between- network connectivity values.
Let me know if this is what you had in mind.
Best
Alfonso
Originally posted by Ruth Shaffer:
Currently there is a separate script (part of the CONN package but not yet integrated into CONN's gui) that would allow you to perform these sort of within- and between- network analyses. To use it you should:
1) in CONN's gui second-level results tab, define there the specific model that you would like to test (i.e. select the subject-effects and associated between-subjects contrast, and the desired conditions and associated between-conditions contrast)
2) then in Matlab command line type
conn_withinbetweenROItest;
That will prompt you to select two networks (e.g. select the 5 ROIs that belong to each of your first two networks) and then it will output a file containing the within- and between- network connectivities (averaged across all the ROIs within each network) for each subject, as well as the statistics associated with your selected second-level model again for the within- and between- network connectivity values.
Let me know if this is what you had in mind.
Best
Alfonso
Originally posted by Ruth Shaffer:
Hello,
I am looking into second level ROI-to-ROI analyses and am hoping to calculate average within- and between- network correlations for each of the networks of ROIs in two separate RSFC runs.
For example, if I had 3 networks, each with 5 ROIs, I would be trying to do two things:
1) to obtain an average within-network correlation during run1 and during run2 for each of the three networks (specifically I am looking for a single average correlation among the 5 ROIs in network 1 at run1 and then their average correlation at run 3--and then I would do the same calculation for the other two networks separately).
2) to obtain between network average correlations for each network (specifically I am looking for a single average correlation for 5 ROIs in network 1 with the 10 ROIs comprising networks 2 and 3, calculating this at run1 and then again at run 3--and tthen I would do the same calculation for the other two networks separately).
Is this possible to do in CONN, and, if so, how might I go about obtaining these measures?
Thank you so much for such a great program and for any help on this question you can give me!
Best,
Ruth
I am looking into second level ROI-to-ROI analyses and am hoping to calculate average within- and between- network correlations for each of the networks of ROIs in two separate RSFC runs.
For example, if I had 3 networks, each with 5 ROIs, I would be trying to do two things:
1) to obtain an average within-network correlation during run1 and during run2 for each of the three networks (specifically I am looking for a single average correlation among the 5 ROIs in network 1 at run1 and then their average correlation at run 3--and then I would do the same calculation for the other two networks separately).
2) to obtain between network average correlations for each network (specifically I am looking for a single average correlation for 5 ROIs in network 1 with the 10 ROIs comprising networks 2 and 3, calculating this at run1 and then again at run 3--and tthen I would do the same calculation for the other two networks separately).
Is this possible to do in CONN, and, if so, how might I go about obtaining these measures?
Thank you so much for such a great program and for any help on this question you can give me!
Best,
Ruth
May 4, 2016 08:05 PM | Jon Dudley
RE: Average within / between network connectivity
Hi all,
Nice feature Alfonso, thanks! I'd like to double check though: the p-values of the output are for a one-tailed test right?
Jon
Nice feature Alfonso, thanks! I'd like to double check though: the p-values of the output are for a one-tailed test right?
Jon
May 5, 2016 05:05 PM | Alfonso Nieto-Castanon - Boston University
RE: Average within / between network connectivity
Hi Jon,
Yes, that is a good point, currently the p-values reported by this script for any T-stats are always one-tailed (to get two-tailed p-values simply compute 2*min(p,1-p))
Best
Alfonso
Originally posted by Jon Dudley:
Yes, that is a good point, currently the p-values reported by this script for any T-stats are always one-tailed (to get two-tailed p-values simply compute 2*min(p,1-p))
Best
Alfonso
Originally posted by Jon Dudley:
Hi all,
Nice feature Alfonso, thanks! I'd like to double check though: the p-values of the output are for a one-tailed test right?
Jon
Nice feature Alfonso, thanks! I'd like to double check though: the p-values of the output are for a one-tailed test right?
Jon
Feb 8, 2018 11:02 AM | Helene Veenstra
RE: Average within / between network connectivity
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?
Feb 8, 2018 09:02 PM | Stephen L. - Coma Science Group, GIGA-Consciousness, Hospital & University of Liege
RE: Average within / between network connectivity
Dear Helene,
I cannot answer for the second question, but for the first unfortunately p-uncorrected can never be assimilated to Bonferroni correction, as p-uncorrected does not perform any multiple comparison correction. Even for small volumes, it will always be more optimistic than Bonferroni. For more infos and a demonstration, you can read this excellent wiki page, where they advise to rather show unthresholded maps (but I don't know how well they are received by journal editors): http://imaging.mrc-cbu.cam.ac.uk/imaging/UncorrectedThreshold
An alternative can be to either use voxel-wise FDR, or even cluster-size FDR, as topological (cluster-wise) correction is more liberal than FWE.
Another alternative, particularly if you are doing a single case study, is to use non-parametric correction with a higher cluster-size or cluster-mass threshold than 0.05, using Alfonso's patch which fixes a few edge cases with non-parametric correction:
https://www.nitrc.org/forum/message.php?...
Indeed, it is usually recommended not to raise the cluster-size threshold above 0.05 nor the voxel-wise p-uncorrected threshold of 0.001 when doing parametric correction since Eklund et al's "Cluster failure" paper, because higher thresholds would lead to unquantified and exponentially higher nominal false positive rates, but with non-parametric correction you can use higher thresholds (both at voxel-wise and cluster-wise levels) as they reliably correct to the nominal rate as demonstrated in the same paper (and in others).
Hope this helps,
Stephen Larroque
I cannot answer for the second question, but for the first unfortunately p-uncorrected can never be assimilated to Bonferroni correction, as p-uncorrected does not perform any multiple comparison correction. Even for small volumes, it will always be more optimistic than Bonferroni. For more infos and a demonstration, you can read this excellent wiki page, where they advise to rather show unthresholded maps (but I don't know how well they are received by journal editors): http://imaging.mrc-cbu.cam.ac.uk/imaging/UncorrectedThreshold
An alternative can be to either use voxel-wise FDR, or even cluster-size FDR, as topological (cluster-wise) correction is more liberal than FWE.
Another alternative, particularly if you are doing a single case study, is to use non-parametric correction with a higher cluster-size or cluster-mass threshold than 0.05, using Alfonso's patch which fixes a few edge cases with non-parametric correction:
https://www.nitrc.org/forum/message.php?...
Indeed, it is usually recommended not to raise the cluster-size threshold above 0.05 nor the voxel-wise p-uncorrected threshold of 0.001 when doing parametric correction since Eklund et al's "Cluster failure" paper, because higher thresholds would lead to unquantified and exponentially higher nominal false positive rates, but with non-parametric correction you can use higher thresholds (both at voxel-wise and cluster-wise levels) as they reliably correct to the nominal rate as demonstrated in the same paper (and in others).
Hope this helps,
Stephen Larroque
Feb 12, 2018 10:02 AM | Helene Veenstra
RE: Average within / between network connectivity
Dear Stephen,
while I would prefer to use voxel-wise FDR, as I am very aware of the issues with using uncorrected or badly corrected p-values; for this specific CONN command line (conn_withinbetweenROItest) I am fairly sure uncorrected measures are used for the calculation between-network connectivity averaged over ROIs.
So I am where I am, doing a group study, having those values as output and in need to apply some sort of correction, or alternatively not use this command line for network investigation and comparison at all, and instead go for ROI-ROI connectivity values. However, since my hypothesis is in regard of whole networks and their between-network connectivity (DMN and Salience Networks), I would prefer to find a way to incorporate network analysis.
Helene
Originally posted by Stephen L.:
while I would prefer to use voxel-wise FDR, as I am very aware of the issues with using uncorrected or badly corrected p-values; for this specific CONN command line (conn_withinbetweenROItest) I am fairly sure uncorrected measures are used for the calculation between-network connectivity averaged over ROIs.
So I am where I am, doing a group study, having those values as output and in need to apply some sort of correction, or alternatively not use this command line for network investigation and comparison at all, and instead go for ROI-ROI connectivity values. However, since my hypothesis is in regard of whole networks and their between-network connectivity (DMN and Salience Networks), I would prefer to find a way to incorporate network analysis.
Helene
Originally posted by Stephen L.:
Dear Helene,
I cannot answer for the second question, but for the first unfortunately p-uncorrected can never be assimilated to Bonferroni correction, as p-uncorrected does not perform any multiple comparison correction. Even for small volumes, it will always be more optimistic than Bonferroni. For more infos and a demonstration, you can read this excellent wiki page, where they advise to rather show unthresholded maps (but I don't know how well they are received by journal editors): http://imaging.mrc-cbu.cam.ac.uk/imaging/UncorrectedThreshold
An alternative can be to either use voxel-wise FDR, or even cluster-size FDR, as topological (cluster-wise) correction is more liberal than FWE.
Another alternative, particularly if you are doing a single case study, is to use non-parametric correction with a higher cluster-size or cluster-mass threshold than 0.05, using Alfonso's patch which fixes a few edge cases with non-parametric correction:
https://www.nitrc.org/forum/message.php?...
Indeed, it is usually recommended not to raise the cluster-size threshold above 0.05 nor the voxel-wise p-uncorrected threshold of 0.001 when doing parametric correction since Eklund et al's "Cluster failure" paper, because higher thresholds would lead to unquantified and exponentially higher nominal false positive rates, but with non-parametric correction you can use higher thresholds (both at voxel-wise and cluster-wise levels) as they reliably correct to the nominal rate as demonstrated in the same paper (and in others).
Hope this helps,
Stephen Larroque
I cannot answer for the second question, but for the first unfortunately p-uncorrected can never be assimilated to Bonferroni correction, as p-uncorrected does not perform any multiple comparison correction. Even for small volumes, it will always be more optimistic than Bonferroni. For more infos and a demonstration, you can read this excellent wiki page, where they advise to rather show unthresholded maps (but I don't know how well they are received by journal editors): http://imaging.mrc-cbu.cam.ac.uk/imaging/UncorrectedThreshold
An alternative can be to either use voxel-wise FDR, or even cluster-size FDR, as topological (cluster-wise) correction is more liberal than FWE.
Another alternative, particularly if you are doing a single case study, is to use non-parametric correction with a higher cluster-size or cluster-mass threshold than 0.05, using Alfonso's patch which fixes a few edge cases with non-parametric correction:
https://www.nitrc.org/forum/message.php?...
Indeed, it is usually recommended not to raise the cluster-size threshold above 0.05 nor the voxel-wise p-uncorrected threshold of 0.001 when doing parametric correction since Eklund et al's "Cluster failure" paper, because higher thresholds would lead to unquantified and exponentially higher nominal false positive rates, but with non-parametric correction you can use higher thresholds (both at voxel-wise and cluster-wise levels) as they reliably correct to the nominal rate as demonstrated in the same paper (and in others).
Hope this helps,
Stephen Larroque
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?
Feb 15, 2018 07:02 PM | Helene Veenstra
RE: Average within / between network connectivity
Dear Alfonso,
thank you, this is very helpful information and a welcome suggestion for the first question so that I can present my results a bit more reviewer-friendly. I enjoy the use of CONN and am grateful for the quick feedback on the forum.
Helene
Originally posted by Alfonso Nieto-Castanon:
thank you, this is very helpful information and a welcome suggestion for the first question so that I can present my results a bit more reviewer-friendly. I enjoy the use of CONN and am grateful for the quick feedback on the forum.
Helene
Originally posted by Alfonso Nieto-Castanon:
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?
Feb 16, 2018 06:02 AM | Himanshu Joshi - National Institute of Mental Health and Neurosciences
RE: Average within / between network connectivity
Hi Alfonso,
Thankyou for this wonderful script (conn_withinbeteenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
Thankyou for this wonderful script (conn_withinbeteenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
Feb 26, 2018 11:02 AM | Himanshu Joshi - National Institute of Mental Health and Neurosciences
RE: Average within / between network connectivity
Hi Alfonso et al,
May I request your valuable inputs on my earlier query made on on this thread dated Feb 16 2018 at 12:02 PM.
Thanks and Regards
Himanshu Joshi
May I request your valuable inputs on my earlier query made on on this thread dated Feb 16 2018 at 12:02 PM.
Thanks and Regards
Himanshu Joshi
Mar 13, 2018 11:03 AM | Himanshu Joshi - National Institute of Mental Health and Neurosciences
RE: Average within / between network connectivity
Hi Alfonso,
I am expecting your response on my query dated Feb 16, 2018 given below.
Kindly consider it as a gentle reminder to comment on it...
Thankyou for this wonderful script (conn_withinbetweenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
I am expecting your response on my query dated Feb 16, 2018 given below.
Kindly consider it as a gentle reminder to comment on it...
Thankyou for this wonderful script (conn_withinbetweenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
Apr 9, 2018 01:04 PM | Himanshu Joshi - National Institute of Mental Health and Neurosciences
RE: Average within / between network connectivity
Hi Alfonso,
Kindly answer my query provided below
Originally posted by Himanshu Joshi:
The two tailed value which came significant can be reported or we need to perform a post-hoc comparison in the above case.
Thanks and Regards
Himanshu Joshi
Kindly answer my query provided below
Originally posted by Himanshu Joshi:
Hi Alfonso,
Thankyou for this wonderful script (conn_withinbeteenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
Thankyou for this wonderful script (conn_withinbeteenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
The two tailed value which came significant can be reported or we need to perform a post-hoc comparison in the above case.
Thanks and Regards
Himanshu Joshi
Apr 28, 2018 12:04 PM | Himanshu Joshi - National Institute of Mental Health and Neurosciences
RE: Average within / between network connectivity
Originally posted by Himanshu Joshi:
The two tailed value which came significant can be reported or we need to perform a post-hoc comparison in the above case.
Thanks and Regards
Himanshu Joshi
Hi Alfonso,
Kindly consider it as a gentle reminder to
answer my query given below
Thanks and Regards
Himanshu Joshi
Hi
Alfonso,
Kindly answer my query provided below
Originally posted by Himanshu Joshi:
Kindly answer my query provided below
Originally posted by Himanshu Joshi:
Hi Alfonso,
Thankyou for this wonderful script (conn_withinbeteenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
Thankyou for this wonderful script (conn_withinbeteenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
The two tailed value which came significant can be reported or we need to perform a post-hoc comparison in the above case.
Thanks and Regards
Himanshu Joshi
Apr 28, 2018 03:04 PM | Alfonso Nieto-Castanon - Boston University
RE: Average within / between network connectivity
Hi Himanshu,
Sorry for the late reply. Yes, that significant result can be directly reported and it means that there is a group effect in the between-networks connectivity (i.e. the average connectivity between the two networks is different among the groups). In addition, after getting a result like this, typically you would want to follow it up performing post-hoc analyses to better characterize those between-group differences (e.g. by performing a series of two-sample t-tests between pairs of groups; or you could plot the individual average between-network connectivity values for each group -e.g. by loading the "between-networks" column in the csv file as a new second-level covariate in conn so that you can use the tools.calculator gui there to plot those between-network connectivity values)
Hope this helps
Alfonso
Originally posted by Himanshu Joshi:
Sorry for the late reply. Yes, that significant result can be directly reported and it means that there is a group effect in the between-networks connectivity (i.e. the average connectivity between the two networks is different among the groups). In addition, after getting a result like this, typically you would want to follow it up performing post-hoc analyses to better characterize those between-group differences (e.g. by performing a series of two-sample t-tests between pairs of groups; or you could plot the individual average between-network connectivity values for each group -e.g. by loading the "between-networks" column in the csv file as a new second-level covariate in conn so that you can use the tools.calculator gui there to plot those between-network connectivity values)
Hope this helps
Alfonso
Originally posted by Himanshu Joshi:
Hi Alfonso,
Thankyou for this wonderful script (conn_withinbeteenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
Thankyou for this wonderful script (conn_withinbeteenROItest). I have also used this script for exploring within and between network connectivity for three resting state networks; two networks at a time. I had four groups in my study and as per suggestions, using CONN's gui second-level results tab, ANOVA was implemented for between subjects contrast. After specifying the ANOVA model [1 -1 0 0; 0 1 -1 0; 0 0 1 -1] and selecting three networks in second level results tab, I ran the script "conn_withinbetweeROItest". This promted me to select, two networks which further resulted in
Within matrix Set-1 (4 x 4 ROIs; 12 valid ROI pairs; 99 subjects);
Within matrix Set-2 (7 x 7 ROIs; 42 valid ROI pairs; 99 subjects);
Between matrix (4 x 7 ROIs; 28 valid ROI pairs; 99 subjects;
Set-1 Within-network test (average effect between Set-1 ROIs):F(3 90 )=0.79 (p=0.505040)
Set-2 Within-network test (average effect between Set-2 ROIs): F(3 90 )=1.77 (p=0.159140)
Between-networks test (average effect between Set-1 & Set-2 ROIs):F(3 90 )=4.33; (p=0.006720).
The p-value for between network test was then converted into two-tailed p value: 2*min(p,1-p)= 0.0134.
Since the model specified here is ANOVA model, I was wondering, if we need to perform post-hoc tests. Or two tailed p value of 0.0134, which is significant, can be reported.
Thanks and Regards
Himanshu Joshi
Sep 20, 2018 12:09 PM | Chabran Eléna
RE: Average within / between network connectivity
Dear Alfonso,
I would like to use this script (conn_withinbetweenROItest) for my analysis, and I followed the instructions you gave to Ruth earlier in this thread, but I get this error every time (whatever the networks I choose):
Subscripted assignment dimension mismatch.
Error in conn_withinbetweenROItest (line 42)
Y(:,:,:,n0)=permute(Z(iroi1,iroi2,:),[3,1,2]);
Do you know how I could fix the problem?
Thank you very much for your help, and for this toolbox which is great!
Best regards
Eléna
I would like to use this script (conn_withinbetweenROItest) for my analysis, and I followed the instructions you gave to Ruth earlier in this thread, but I get this error every time (whatever the networks I choose):
Subscripted assignment dimension mismatch.
Error in conn_withinbetweenROItest (line 42)
Y(:,:,:,n0)=permute(Z(iroi1,iroi2,:),[3,1,2]);
Do you know how I could fix the problem?
Thank you very much for your help, and for this toolbox which is great!
Best regards
Eléna
Apr 30, 2020 08:04 PM | Mariah DeSerisy - Fordham University
RE: Average within / between network connectivity
Hi,
I am attempting to use the conn_withinbetweenROItest script to run a dimensional regression analysis across a single group of participants. This analysis previously worked (as recently as about a month ago, using CONN v 18) according to recommendations provided on May 14, 2016. I recently updated my CONN version to v19.c (MatLab R2019b) and am now getting the error in the attached image. As a note, this script is no longer auto-generating a GUI that asks me to input the seeds in each network.
Can I still conduct within network/between network analyses using CONN v19.c? Is there a different way that this is done in the latest version?
Best,
Mariah
I am attempting to use the conn_withinbetweenROItest script to run a dimensional regression analysis across a single group of participants. This analysis previously worked (as recently as about a month ago, using CONN v 18) according to recommendations provided on May 14, 2016. I recently updated my CONN version to v19.c (MatLab R2019b) and am now getting the error in the attached image. As a note, this script is no longer auto-generating a GUI that asks me to input the seeds in each network.
Can I still conduct within network/between network analyses using CONN v19.c? Is there a different way that this is done in the latest version?
Best,
Mariah
May 16, 2020 02:05 PM | Elizabeth Olson
RE: Average within / between network connectivity
Originally posted by Mariah DeSerisy:
I'm getting the same error as Mariah when attempting to use conn_withinbetweenROItest in CONN 19.c. Any ideas?
Thanks,
Liz
Hi,
I am attempting to use the conn_withinbetweenROItest script to run a dimensional regression analysis across a single group of participants. This analysis previously worked (as recently as about a month ago, using CONN v 18) according to recommendations provided on May 14, 2016. I recently updated my CONN version to v19.c (MatLab R2019b) and am now getting the error in the attached image. As a note, this script is no longer auto-generating a GUI that asks me to input the seeds in each network.
Can I still conduct within network/between network analyses using CONN v19.c? Is there a different way that this is done in the latest version?
Best,
Mariah
I am attempting to use the conn_withinbetweenROItest script to run a dimensional regression analysis across a single group of participants. This analysis previously worked (as recently as about a month ago, using CONN v 18) according to recommendations provided on May 14, 2016. I recently updated my CONN version to v19.c (MatLab R2019b) and am now getting the error in the attached image. As a note, this script is no longer auto-generating a GUI that asks me to input the seeds in each network.
Can I still conduct within network/between network analyses using CONN v19.c? Is there a different way that this is done in the latest version?
Best,
Mariah
I'm getting the same error as Mariah when attempting to use conn_withinbetweenROItest in CONN 19.c. Any ideas?
Thanks,
Liz
May 19, 2020 01:05 PM | Alfonso Nieto-Castanon - Boston University
RE: Average within / between network connectivity
Hi Mariah and Elizabeth,
Yes, you should be able to run conn_withinbetweenROItest in 19c just the same as before. As far as I can tell that error message indicates that may have not yet set up your second-level model in the main CONN GUI? (or, if you have done so, you may have not done that on an ROI-to-ROI second-level results tab). Please let me know if that does not seem to be the case here
Best
Alfonso
Originally posted by Elizabeth Olson:
Yes, you should be able to run conn_withinbetweenROItest in 19c just the same as before. As far as I can tell that error message indicates that may have not yet set up your second-level model in the main CONN GUI? (or, if you have done so, you may have not done that on an ROI-to-ROI second-level results tab). Please let me know if that does not seem to be the case here
Best
Alfonso
Originally posted by Elizabeth Olson:
Originally posted by Mariah DeSerisy:
I'm getting the same error as Mariah when attempting to use conn_withinbetweenROItest in CONN 19.c. Any ideas?
Thanks,
Liz
Hi,
I am attempting to use the conn_withinbetweenROItest script to run a dimensional regression analysis across a single group of participants. This analysis previously worked (as recently as about a month ago, using CONN v 18) according to recommendations provided on May 14, 2016. I recently updated my CONN version to v19.c (MatLab R2019b) and am now getting the error in the attached image. As a note, this script is no longer auto-generating a GUI that asks me to input the seeds in each network.
Can I still conduct within network/between network analyses using CONN v19.c? Is there a different way that this is done in the latest version?
Best,
Mariah
I am attempting to use the conn_withinbetweenROItest script to run a dimensional regression analysis across a single group of participants. This analysis previously worked (as recently as about a month ago, using CONN v 18) according to recommendations provided on May 14, 2016. I recently updated my CONN version to v19.c (MatLab R2019b) and am now getting the error in the attached image. As a note, this script is no longer auto-generating a GUI that asks me to input the seeds in each network.
Can I still conduct within network/between network analyses using CONN v19.c? Is there a different way that this is done in the latest version?
Best,
Mariah
I'm getting the same error as Mariah when attempting to use conn_withinbetweenROItest in CONN 19.c. Any ideas?
Thanks,
Liz
Feb 23, 2021 05:02 PM | Nadine Smith
RE: Average within / between network connectivity
Dear experts,
I am facing a similar issue with version 20b (I have run the script without any problems in version 18b before).
I get the following error when I try to run conn_withinbetweenROItest although I have properly set up the model in the main GUI on the ROI-to-ROI tab:
"Reference to non-existent field 'roiselected2'.
Error in conn_withinbetweenROItest (line 16)
ntargets=CONN_x.Results.xX.roiselected2; % selected target ROIs (indexes
to names below)"
Any help on this is greatly appreciated!
Best,
Nadine
I am facing a similar issue with version 20b (I have run the script without any problems in version 18b before).
I get the following error when I try to run conn_withinbetweenROItest although I have properly set up the model in the main GUI on the ROI-to-ROI tab:
"Reference to non-existent field 'roiselected2'.
Error in conn_withinbetweenROItest (line 16)
ntargets=CONN_x.Results.xX.roiselected2; % selected target ROIs (indexes
to names below)"
Any help on this is greatly appreciated!
Best,
Nadine
Apr 28, 2021 05:04 PM | Jose Maximo
RE: Average within / between network connectivity
Hi,
I had the same issue, but ended up using version 19c and it worked just fine.
Best,
Omar
Originally posted by Nadine Smith:
I had the same issue, but ended up using version 19c and it worked just fine.
Best,
Omar
Originally posted by Nadine Smith:
Dear experts,
I am facing a similar issue with version 20b (I have run the script without any problems in version 18b before).
I get the following error when I try to run conn_withinbetweenROItest although I have properly set up the model in the main GUI on the ROI-to-ROI tab:
"Reference to non-existent field 'roiselected2'.
Error in conn_withinbetweenROItest (line 16)
ntargets=CONN_x.Results.xX.roiselected2; % selected target ROIs (indexes
to names below)"
Any help on this is greatly appreciated!
Best,
Nadine
I am facing a similar issue with version 20b (I have run the script without any problems in version 18b before).
I get the following error when I try to run conn_withinbetweenROItest although I have properly set up the model in the main GUI on the ROI-to-ROI tab:
"Reference to non-existent field 'roiselected2'.
Error in conn_withinbetweenROItest (line 16)
ntargets=CONN_x.Results.xX.roiselected2; % selected target ROIs (indexes
to names below)"
Any help on this is greatly appreciated!
Best,
Nadine
Oct 15, 2021 04:10 PM | Olivier Roy
RE: Average within / between network connectivity
Hi,
Is there any patch on the way for this function in Conn 20.b?
Thanks,
Olivier
Is there any patch on the way for this function in Conn 20.b?
Thanks,
Olivier
Nov 9, 2021 03:11 PM | Karli Carston - University of Colorado at Boulder
RE: Average within / between network connectivity
Hi Olivier,
I got the same message and then realized that I'd set up my second level as a Seed-to-Voxel analysis. Once I switched to ROI-to-ROI, it ran fine. I hope this helps!
Karli
I got the same message and then realized that I'd set up my second level as a Seed-to-Voxel analysis. Once I switched to ROI-to-ROI, it ran fine. I hope this helps!
Karli
Dec 16, 2021 09:12 PM | ryanw412
RE: Average within / between network connectivity
Dear experts,
I am also having this same error message using version 20b. I'm sure I have ROI-to-ROI selected on the first-level tab, although I'm not sure what has to be set up on the second-level tab in order for this to work.
Thanks,
Ryan
Originally posted by Nadine Smith:
I am also having this same error message using version 20b. I'm sure I have ROI-to-ROI selected on the first-level tab, although I'm not sure what has to be set up on the second-level tab in order for this to work.
Thanks,
Ryan
Originally posted by Nadine Smith:
Dear experts,
I am facing a similar issue with version 20b (I have run the script without any problems in version 18b before).
I get the following error when I try to run conn_withinbetweenROItest although I have properly set up the model in the main GUI on the ROI-to-ROI tab:
"Reference to non-existent field 'roiselected2'.
Error in conn_withinbetweenROItest (line 16)
ntargets=CONN_x.Results.xX.roiselected2; % selected target ROIs (indexes
to names below)"
Any help on this is greatly appreciated!
Best,
Nadine
I am facing a similar issue with version 20b (I have run the script without any problems in version 18b before).
I get the following error when I try to run conn_withinbetweenROItest although I have properly set up the model in the main GUI on the ROI-to-ROI tab:
"Reference to non-existent field 'roiselected2'.
Error in conn_withinbetweenROItest (line 16)
ntargets=CONN_x.Results.xX.roiselected2; % selected target ROIs (indexes
to names below)"
Any help on this is greatly appreciated!
Best,
Nadine
Feb 1, 2022 12:02 PM | max345
RE: Average within / between network connectivity
Hi Alfonso,
I'm very new to CONN (only did some exploratory seed-based connectivity analyses between 2 groups), but now I want to use the script conn_withinbetweenROItest (with ROIs of the Default Mode network) in CONN (version 20.b).
For this, I defined my between-subjects contrast etc. in the results (second-level) tab and typed conn_withinbetweenROItest in the MATLAB command line. But after that, the following error was displayed:
Reference to non-existent field 'roiselected2'.
Error in conn_withinbetweenROItest (line 16)
ntargets=CONN_x.Results.xX.roiselected2; %selected target ROIs
(indexes to names below)
I need to select my ROIs again or to name my selected ROIs, but how can I name or select my ROIs?
Thank you for your help!
I'm very new to CONN (only did some exploratory seed-based connectivity analyses between 2 groups), but now I want to use the script conn_withinbetweenROItest (with ROIs of the Default Mode network) in CONN (version 20.b).
For this, I defined my between-subjects contrast etc. in the results (second-level) tab and typed conn_withinbetweenROItest in the MATLAB command line. But after that, the following error was displayed:
Reference to non-existent field 'roiselected2'.
Error in conn_withinbetweenROItest (line 16)
ntargets=CONN_x.Results.xX.roiselected2; %selected target ROIs
(indexes to names below)
I need to select my ROIs again or to name my selected ROIs, but how can I name or select my ROIs?
Thank you for your help!