 |
 |
Thanks for all of these replies, this was all very helpful. The formulas Tom suggested seem to have done the trick (effect sizes needed for simple one-way and two-way t-tests only). Thanks again, very grateful for your expertise. On Thu, Feb 14, 2019 at 2:50 PM Glasser, Matthew <[log in to unmask]> wrote: > Maybe you can use %BOLD instead as a measure of effect size. > > Matt. > > From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of > Thomas Nichols <[log in to unmask]> > Reply-To: FSL - FMRIB's Software Library <[log in to unmask]> > Date: Thursday, February 14, 2019 at 5:04 AM > To: "[log in to unmask]" <[log in to unmask]> > Subject: Re: [FSL] Converting t-statistics to Cohen's d? > > Hi Nicole, > > Getting a Cohen's d for an arbitrary contrast out of a GLM is basically > impossible. That's because Cohen's d is only precisely defined for > one-sample and two-sample comparisons. > > I can offer three options: > > 1. One-sample t-test. If your design is nothing more than a one-sample > t-test, then you can use this relationship to compute Cohen's d from the t > statistic image *_tstat* > > d = t / sqrt(N) > > > 2. Two-sample t-test. If your design is just a two-sample t-test of > groups of size N1 and N2, and your contrast tests for the difference, then > you can use > > d = t * sqrt( 1/N1 + 1/N2 ) > > > 3. For any other contrast, you need to work with R^2 or Cohen's f^2. > These relationships will get you there. Make an F test if you don't > already have it, as F = t^2, and then > > f2 = F * v1/v2 > R2 = f2 / ( f2 + 1 ) > > where v1 is the numerator DF and v2 is the denominator DF of your F-test; > for a squared t-test, this is v1=1, v2=N-p, where p is the total number of > regressors in your model. > > f2 is the noncentrality parameter used for power analyses, while R2 has > the more natural "variance explained" interpretation. > > -Tom > > On Thu, Feb 14, 2019 at 7:31 AM Steve Smith <[log in to unmask]> wrote: > >> Hi - Cohen's D is the effect divided by the standard deviation of the >> errors, whereas varcope is similar but is the stddev is divided by the >> degrees of freedom, so that it reflects the uncertainty of the cope. To get >> back to D you would need to divide cope/varcope by the temporal degrees of >> freedom. The *exact* calculations here are slightly complicated by >> adjustmet for temporal smoothness in the prewhitening step. >> >> Cheers. >> >> >> >> >> On 13 Feb 2019, at 21:09, Nicole Petersen <[log in to unmask]> wrote: >> >> Hi Matthew (and others), >> >> Thanks for this recommendation. I have done this (finally) and then >> divided the cope images by sqrt(varcope) to produce what I believe are >> effect size maps in Cohen's D. However, some of the Cohen's D values seem >> improbably high -- higher than 4. (These maps are being used to visualize >> differences that were NOT statistically significant, so I was expecting >> small Cohen's D values.) Questions: >> >> 1. Is my math wrong, and there is another way to get Cohen's D from these >> images? >> 2. If my math is right, does this also seem improbably high to you? >> >> Thanks in advance for any advice. >> >> >> Best, >> Nicole >> >> >> On Tue, Nov 27, 2018 at 8:40 AM Matthew Webster < >> [log in to unmask]> wrote: >> >>> Hello, >>> You can use the --glm_output option to output this glm info >>> directly from randomise. >>> >>> Kind Regards >>> Matthew >>> -------------------------------- >>> Dr Matthew Webster >>> FMRIB Centre >>> John Radcliffe Hospital >>> University of Oxford >>> >>> > On 26 Nov 2018, at 20:38, Nicole Petersen <[log in to unmask]> wrote: >>> > >>> > Hi FSL experts! >>> > >>> > I have been tasked with creating effect size maps in Cohen's d out of >>> randomise outputs. I understand that this could be done by using film_gls >>> --noest to produce PE and COPE images, which can then be converted to >>> Cohen's d through fslmaths. I'd like to try converting the t-statistic >>> images produced by randomise directly (since those are the analyses we're >>> reporting on). Do you all have recommendations as to how to compute these >>> maps? >>> > >>> > >>> > Thanks for any help, >>> > Nicole Petersen >>> > >>> > >>> ######################################################################## >>> > >>> > To unsubscribe from the FSL list, click the following link: >>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>> >>> ######################################################################## >>> >>> To unsubscribe from the FSL list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >>> >> >> >> -- >> Nicole Petersen, Ph.D >> Postdoctoral Fellow >> London Lab >> Semel Institute for Neuroscience and Human Behavior >> Department of Psychiatry and Biobehavioral Sciences >> University of California, Los Angeles >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> >> >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Head of Analysis, WIN (FMRIB) Oxford >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 610470 >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >> >> --------------------------------------------------------------------------- >> >> Stop the cultural destruction of Tibet <http://smithinks.net> >> >> >> >> >> >> >> >> >> >> ------------------------------ >> >> To unsubscribe from the FSL list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 >> > > > -- > __________________________________________________________ > Thomas Nichols, PhD > Professor of Neuroimaging Statistics > Nuffield Department of Population Health | University of Oxford > Big Data Institute | Li Ka Shing Centre for Health Information and > Discovery > Old Road Campus | Headington | Oxford | OX3 7LF | United Kingdom > T: +44 1865 743590 | E: [log in to unmask] > W: http://nisox.org | http://www.bdi.ox.ac.uk > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > ------------------------------ > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > -- Nicole Petersen, Ph.D Postdoctoral Fellow London Lab Semel Institute for Neuroscience and Human Behavior Department of Psychiatry and Biobehavioral Sciences University of California, Los Angeles ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1