Hi Bruce, Will do. Thanks again.
-Clark On Sep 3, 2012, at 2:33 PM, Bruce Fischl wrote: > Hi Clark > > sorry, the end of the summer has been a period when things slip through the > cracks. I think what you want is possible without a talairach or aseg, but it > will need to wait for Doug to get back. Can you repost at the end of next > week? > Bruce > > > On Thu, 30 Aug 2012, Clark Fisher wrote: > >> Thanks Michael, I'll look into Nipy's FDR tools. I actually started this >> thread asking for help getting mri_surfcluster running for my situation (I >> have no talraich .xfm and no segmentation for my monkeys). The silence on >> that topic suggest that it might not be possible, or it's at least not known >> to possible. >> Thanks again everyone. >> -Clark >> On Aug 29, 2012, at 6:55 PM, Michael Waskom wrote: >> >> 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/source). 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
