Dear Freesurfer Mailing list,
While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 & .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold.
Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant.
Do you mean cluster-wise threshold or cluster-forming threshold?
On 11/06/2014 01:12 AM, Bronwyn Overs wrote:
Dear Freesurfer Mailing list,
While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 & .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold.
Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. --
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 7/11/2014 4:03 am, Douglas N Greve wrote:
Do you mean cluster-wise threshold or cluster-forming threshold?
On 11/06/2014 01:12 AM, Bronwyn Overs wrote:
Dear Freesurfer Mailing list,
While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 & .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold.
Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. --
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Can you upload the gtlmdir and I'll take a look?
On 11/06/2014 08:19 PM, Bronwyn Overs wrote:
I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 7/11/2014 4:03 am, Douglas N Greve wrote:
Do you mean cluster-wise threshold or cluster-forming threshold?
On 11/06/2014 01:12 AM, Bronwyn Overs wrote:
Dear Freesurfer Mailing list,
While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 & .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold.
Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. --
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Douglas,
How exactly should I upload the glmdir?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 11/11/2014 4:19 am, Douglas N Greve wrote:
Can you upload the gtlmdir and I'll take a look?
On 11/06/2014 08:19 PM, Bronwyn Overs wrote:
I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 7/11/2014 4:03 am, Douglas N Greve wrote:
Do you mean cluster-wise threshold or cluster-forming threshold?
On 11/06/2014 01:12 AM, Bronwyn Overs wrote:
Dear Freesurfer Mailing list,
While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 & .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold.
Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. --
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Through the file drop at the end of this email. But you might want to wait until next week as I will be out of the office until Dec 4. doug
On 11/26/14 12:50 AM, Bronwyn Overs wrote:
Hi Douglas,
How exactly should I upload the glmdir?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 11/11/2014 4:19 am, Douglas N Greve wrote:
Can you upload the gtlmdir and I'll take a look?
On 11/06/2014 08:19 PM, Bronwyn Overs wrote:
I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
On 7/11/2014 4:03 am, Douglas N Greve wrote:
Do you mean cluster-wise threshold or cluster-forming threshold?
On 11/06/2014 01:12 AM, Bronwyn Overs wrote:
Dear Freesurfer Mailing list,
While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 & .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold.
Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. --
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Douglas, I will upload it then.
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 27/11/2014 1:30 pm, Douglas Greve wrote:
Through the file drop at the end of this email. But you might want to wait until next week as I will be out of the office until Dec 4. doug
On 11/26/14 12:50 AM, Bronwyn Overs wrote:
Hi Douglas,
How exactly should I upload the glmdir?
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 11/11/2014 4:19 am, Douglas N Greve wrote:
Can you upload the gtlmdir and I'll take a look?
On 11/06/2014 08:19 PM, Bronwyn Overs wrote:
I believe it is the cluster-forming threshold. I was running the following: mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 1.3 abs --cwpvalthresh 0.05 --2spaces mri_glmfit-sim --glmdir site-gender-group-prothaplotype.glmdir --cache 2 abs --cwpvalthresh 0.05 --2spaces
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
On 7/11/2014 4:03 am, Douglas N Greve wrote:
Do you mean cluster-wise threshold or cluster-forming threshold?
On 11/06/2014 01:12 AM, Bronwyn Overs wrote:
Dear Freesurfer Mailing list,
While running a glm anlaysis with monte carlo correction (using cluster wise thresholds of .05 & .01), I encountered the following issue: When examining the clusters formed for each of the different cluster wise thresholds, the .05 threshold resulted in a superior temporal cluster, while the .01 threshold resulted in a two lateral occipital clusters that did not overlap with the cluster from the .05 threshold.
Do you know why there would be no overlap between significant regions at different cluster wise thresholds? I was aware that a cluster which is significant at .05 may split or be smaller at .01, but I do not know why entirely different regions would be significant. --
Kind regards,
Bronwyn Overs Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.auhttp://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazinehttp://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Douglas N Greve