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. > >
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