Hi Clark, I just made a modification to mri_binarize to make it take an FDR as input. It computes the threshold and binarizes the input based on the threshold. I've put a copy here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize.linux Run it with --help to get more info. doug On 08/29/2012 02:08 PM, Clark Fisher 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
