Re: [Freesurfer] cluster threshold
Hi Doug, That sounds good! Thanks so much! Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/8/13 10:15 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Hi Daniel, there is no difference. Once you select the appropriate threshold, it does not matter whether it is a z-field, p-field, t-field, or -log10(p)-field because it gets binarized. doug On 9/8/13 9:33 PM, Yang, Daniel wrote: Hi Doug, Thanks! I didn't realize that the threshold is a negative exponent to a base of 10! Just wondering, is there a webpage that I can read to understand why FreeSurfer chooses this exponent approach instead of z-value? Also are 1.3, 2.3, 3.3, 4.3 two-sided, and 1, 2, 3, 4, one-sided? For example, when we specify configure overlay in Freeview? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/8/13 6:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: It is not a z-value. It is -log10(p), so -log10(.01) = 2 doug On 9/7/13 9:13 PM, Yang, Daniel wrote: Hi FreeSurfer Experts, On this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons), it says: In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common thresholds. I am wondering how these thresholds were computed. In my own computation, I found z-value to be the following, but neither one-sided nor two-sided matches the thresholds of 1.3, …, 4 as shown above? one-sided: p-value=0.0500, z-value=1.6 p-value=0.0100, z-value=2.3 p-value=0.0050, z-value=2.6 p-value=0.0010, z-value=3.1 p-value=0.0005, z-value=3.3 p-value=0.0001, z-value=3.7 two-sided: p-value=0.0500, z-value=2.0 p-value=0.0100, z-value=2.6 p-value=0.0050, z-value=2.8 p-value=0.0010, z-value=3.3 p-value=0.0005, z-value=3.5 p-value=0.0001, z-value=3.9 Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cluster threshold
It is not a z-value. It is -log10(p), so -log10(.01) = 2 doug On 9/7/13 9:13 PM, Yang, Daniel wrote: Hi FreeSurfer Experts, On this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons), it says: In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common thresholds. I am wondering how these thresholds were computed. In my own computation, I found z-value to be the following, but neither one-sided nor two-sided matches the thresholds of 1.3, ..., 4 as shown above? one-sided: p-value=0.0500, z-value=1.6 p-value=0.0100, z-value=2.3 p-value=0.0050, z-value=2.6 p-value=0.0010, z-value=3.1 p-value=0.0005, z-value=3.3 p-value=0.0001, z-value=3.7 two-sided: p-value=0.0500, z-value=2.0 p-value=0.0100, z-value=2.6 p-value=0.0050, z-value=2.8 p-value=0.0010, z-value=3.3 p-value=0.0005, z-value=3.5 p-value=0.0001, z-value=3.9 Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cluster threshold
Hi Doug, Thanks! I didn't realize that the threshold is a negative exponent to a base of 10! Just wondering, is there a webpage that I can read to understand why FreeSurfer chooses this exponent approach instead of z-value? Also are 1.3, 2.3, 3.3, 4.3 two-sided, and 1, 2, 3, 4, one-sided? For example, when we specify configure overlay in Freeview? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/8/13 6:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: It is not a z-value. It is -log10(p), so -log10(.01) = 2 doug On 9/7/13 9:13 PM, Yang, Daniel wrote: Hi FreeSurfer Experts, On this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons), it says: In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common thresholds. I am wondering how these thresholds were computed. In my own computation, I found z-value to be the following, but neither one-sided nor two-sided matches the thresholds of 1.3, …, 4 as shown above? one-sided: p-value=0.0500, z-value=1.6 p-value=0.0100, z-value=2.3 p-value=0.0050, z-value=2.6 p-value=0.0010, z-value=3.1 p-value=0.0005, z-value=3.3 p-value=0.0001, z-value=3.7 two-sided: p-value=0.0500, z-value=2.0 p-value=0.0100, z-value=2.6 p-value=0.0050, z-value=2.8 p-value=0.0010, z-value=3.3 p-value=0.0005, z-value=3.5 p-value=0.0001, z-value=3.9 Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] cluster threshold
Hi Daniel, there is no difference. Once you select the appropriate threshold, it does not matter whether it is a z-field, p-field, t-field, or -log10(p)-field because it gets binarized. doug On 9/8/13 9:33 PM, Yang, Daniel wrote: Hi Doug, Thanks! I didn't realize that the threshold is a negative exponent to a base of 10! Just wondering, is there a webpage that I can read to understand why FreeSurfer chooses this exponent approach instead of z-value? Also are 1.3, 2.3, 3.3, 4.3 two-sided, and 1, 2, 3, 4, one-sided? For example, when we specify configure overlay in Freeview? Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/8/13 6:03 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It is not a z-value. It is -log10(p), so -log10(.01) = 2 doug On 9/7/13 9:13 PM, Yang, Daniel wrote: Hi FreeSurfer Experts, On this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons), it says: In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common thresholds. I am wondering how these thresholds were computed. In my own computation, I found z-value to be the following, but neither one-sided nor two-sided matches the thresholds of 1.3, …, 4 as shown above? one-sided: p-value=0.0500, z-value=1.6 p-value=0.0100, z-value=2.3 p-value=0.0050, z-value=2.6 p-value=0.0010, z-value=3.1 p-value=0.0005, z-value=3.3 p-value=0.0001, z-value=3.7 two-sided: p-value=0.0500, z-value=2.0 p-value=0.0100, z-value=2.6 p-value=0.0050, z-value=2.8 p-value=0.0010, z-value=3.3 p-value=0.0005, z-value=3.5 p-value=0.0001, z-value=3.9 Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] cluster threshold
Hi FreeSurfer Experts, On this page (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons), it says: In particular, thresholds of 1.3, 2, 2.3, 3, 3.3 and 4, corresponding to p-values of 0.05, 0.01, 0.005, 0.001, 0.0005 and 0.0001, which are common thresholds. I am wondering how these thresholds were computed. In my own computation, I found z-value to be the following, but neither one-sided nor two-sided matches the thresholds of 1.3, …, 4 as shown above? one-sided: p-value=0.0500, z-value=1.6 p-value=0.0100, z-value=2.3 p-value=0.0050, z-value=2.6 p-value=0.0010, z-value=3.1 p-value=0.0005, z-value=3.3 p-value=0.0001, z-value=3.7 two-sided: p-value=0.0500, z-value=2.0 p-value=0.0100, z-value=2.6 p-value=0.0050, z-value=2.8 p-value=0.0010, z-value=3.3 p-value=0.0005, z-value=3.5 p-value=0.0001, z-value=3.9 Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
