Hi Sebastian, I think you are right, both about tksurfer thresholding and the correct interpretation of FDR. As you point out though, there is some value in having maps that show how relatively well different points on the surface fit your model.
At the very least, is there any way to automate the retrieving of the threshold that tksurfer provides? I'd still also be interested in some adjustment to the whole map, if there's a way to do that as well. I could probably find a way to do this in Matlab, but I trust the bug-squishing abilities of the freesurfer community more than I trust my own. -Clark On Aug 28, 2012, at 2:34 PM, Sebastian Moeller wrote: > Hi Clark, > > > On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote: > >> Hi Bruce, >> >> Thanks. I actually have used this function of tksurfer, but am looking for >> a way to save the corrected maps, so that they could be manipulated by other >> tools (for instance, viewed by PySurfer). > > Does it really correct the map? I thought all it does is figure out the > corrected threshold. By the way, if I understand correctly, FDR maps should > be considered to be binary, that is you really do not know which voxels might > be false positives, so you should not interpret all voxels to be equally > significant. Having said that, almost everybody I know still looks at the > p-value spatial distribution when looking at those FDR thresholded maps… > (then again, I do not know any statistician...) > > > best > Sebastian > >> I recognize that this may not be an officially supported functionality, but >> is there some way to save the adjusted overlays from tksurfer, or create >> them in some other way? >> >> Best, >> Clark >> >> >> On Aug 28, 2012, at 1:58 PM, Bruce Fischl wrote: >> >>> Hi Clark >>> >>> you shouldn't need either. Load your overlays then click the button to >>> compute the FDR threshold in the tksurfer configure overlay interface. >>> >>> cheers >>> Bruce >>> On Tue, 28 Aug 2012, Clark Fisher wrote: >>> >>>> Ok, maybe I'm making this question too intricate. Here's the short version: >>>> How can I FDR correct painted surface significance maps when I have no >>>> talraich .xfm file and no cortical segmentation? >>>> Thanks again, >>>> Clark >>>> Hi Freesurfers, >>>> I have another monkey-specific question. I'd like to output FDR-corrected >>>> signficance surface maps for my monkey data, or at least FDR-threshold the >>>> maps. It seems like mri_surfcluster might be one way to go about this >>>> however: >>>> 1) I don't have any .xfm files for my monkeys, as I'm working in >>>> native space, and >>>> 2) Without segmentation, I don't have a good mask to use for the >>>> cortex only. My first attempts at work-arounds would be: >>>> 1)Try to create an identity .xfm file >>>> 2)Use the cortical ribbons from mris_volmask as a cortex mask >>>> Should these work? If so, how should I make an identity .xfm file? If >>>> not, is there another way to FDR correct my surface data? >>>> Thanks, >>>> Clark >>>> _______________________________________________ >>>> 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 list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Sebastian Moeller > > telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 > fax: 626-395-8826 > German GSM: +49 - 15 77 - 1 90 31 41 > mobile: +1-626-325-8598 > +1-626-807-5242 > US CDMA: +1-626-807-5242 > moel...@caltech.edu > > Division of Biology > MC 114-96 > California Institute of Technology > 1200 East California Boulevard > CA 91125, Pasadena > USA > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
