Hello Douglas, What do you mean by not doing the adjustement for 1-tailed test ? Does this mean specify the sign as "abs" ?
I don't understand well how -log10(p) could be negative with 0<p<1 and so the subtility of the sign specified (pos, neg or abs) ? Since the negative or positive sign is already specified in the contrast sign, isn't it ? Sorry if my questions are kind of newbie. Thanks for helping and explaining this to me. Best regards, Matthieu Le 29 mai 2015 18:27, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> a écrit : > I think it should work with a t as input. When you set the threshold, put > in the t-value you want, not a -log10(p). Also, don't do the adjustment for > 1-tailed test because then it will interpret the input as -log10(p). > > On 5/29/15 10:46 AM, Matthieu Vanhoutte wrote: > > Dear experts, > > I would like to use the clusterwise correction specified in the group > analysis FreeSurfer wiki ( > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). In > this way, I would use mri_surfcluster with the known FWHM of my GLM > analysis and my input is an *uncorrected Tmap*. However, in the group > analysis wiki, the input for the mri_surfcluster command is : > > *sig.mgh -- significance, -log10(pvalue), uncorrected (surface overlay)* > > So, could I use my uncorrected Tmap instead of sig.mgh or should I apply a > transform to obtain kinf of -log10(pvalue) ? Is this is the case how to > convert Tmap ? > > Many thanks in advance for helping ! > > Best regards, > > Matthieu > > 2015-04-15 15:19 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > >> Sorry, I misread your previous email as "Indeed BPM does do Clusterwise >> correction." instead of "Indeed BPM doesn't do Clusterwise correction." The >> FWHM is the full-width-half-max and is a measure of the spatial smoothness. >> This is always needed for cluster-wise correction. This is usually obtained >> during the group analysis by examining the residuals, so it should come out >> of what ever you are using for group analysis. If it does not come out of >> BPM, then that is a problem that I cannot help you with (talk to whoever >> programmed BPM). >> >> doug >> >> >> On 4/15/15 3:30 AM, Matthieu Vanhoutte wrote: >> >> Hello Douglas, >> >> Sorry if I haven't been clear. I'm trying to explain my needs : >> >> 1) I use the BPM toolbox to compute the GLM analysis as mri_glmfit would >> do. However, outputs of this toolbox only give me beta maps and uncorrected >> Tmaps. >> 2) With only these uncorrected Tmaps outputs, I'd like to apply >> Clusterwise correction as mri_glmfit-sim would do with the same arguments >> if possible (--cache ; --cwp ; --2spaces ; ...). >> >> --> Is there a way to succeed in 2) with some manual scripting ? >> >> --> Is the mri_volcluster adapted as you proposed : in this case you said >> I need to know the FWHM of my BPM analysis, how could I obtain this ? >> >> --> Would I have access in this way to arguments --cache and --cwp as >> used in mri_glmfit-sim ? >> >> I hope I have been clearly. >> >> Thanks in advance for guiding me ! >> >> Best regards, >> >> Matthieu >> >> 2015-04-15 3:06 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: >> >>> I guess I don't understand what you are asking for. If BPM outputs a >>> cluster-corrected volume, then why can't you just map that to the surface >>> and be done with it? >>> >>> >>> On 4/14/15 6:48 PM, Matthieu Vanhoutte wrote: >>> >>> Hello Douglas, >>> >>> Indeed BPM doesn't do Clusterwise correction. >>> >>> What does the FWHM of the BPM analysis correspond to ? And how to find >>> it ? >>> >>> Manu thanks ! >>> >>> Best regards, >>> >>> Matthieu >>> Le 15 avr. 2015 00:23, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> a >>> écrit : >>> >>>> So BPM does not do clusterwise correction? You could use >>>> mri_volcluster, but you'll need to know the FWHM of your BPM analysis >>>> doug >>>> >>>> On 4/14/15 12:17 PM, Matthieu Vanhoutte wrote: >>>> >>>> Dear FreeSurfer's experts, >>>> >>>> For personnal need I use the BPM toolbox (Biological Parametric >>>> Mapping) to compute GLM analysis. The outputs of this Toolbox gave me beta >>>> maps and Tmaps. >>>> >>>> However, precedently I used the whole FreeSurfer group analysis >>>> tutorial on other datas, including the Clusterwise Correction for multiple >>>> comparisons. And now in order to compare results, I'd like to use this >>>> Clusterwise Correction consequently to my BPM Toolbox GLM analysis. >>>> >>>> Is it possible to manually adapt some scripts ? In this way, how could >>>> I upgrade my outputs to these of "mri_glmfit" in order to launch >>>> Clusterwise Correction after ? >>>> >>>> Many thanks in advance for helping ! >>>> >>>> Best regards, >>>> >>>> Matthieu >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing >>>> listfreesur...@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 mailing >>> listfreesur...@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 mailing >> listfreesur...@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 mailing > listfreesur...@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. > >
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