Hi Clark, If you're loading the data into Python anyway to use with PySurfer, Nipy seems to have some utilities to do an FDR correction (docs<http://nipy.sourceforge.net/nipy/stable/api/generated/nipy.algorithms.statistics.empirical_pvalue.html> /source<https://github.com/nipy/nipy/blob/master/nipy/algorithms/statistics/empirical_pvalue.py>). I've never used these, but they look pretty straightforward.
Also it looks like FDR is built into mri_surfcluster. Best, Michael On Wed, Aug 29, 2012 at 2:08 PM, Clark Fisher <cfis...@mail.rockefeller.edu>wrote: > 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 >
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