Re: [Freesurfer] FDR Correction of NHP Surface Data

Per Bruce's suggestion, I'm reposting this now. A synopsis: I'm looking for a way to correct painted statistical maps for multiple comparisons using Freesurfer's tools, without having segmentation or any .xfm files. Thanks, Clark On Aug 23, 2012, at 10:09 AM, Clark Fisher wrote: > Hi Freesurf

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

Re: [Freesurfer] FDR Correction of NHP Surface Data

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:

Re: [Freesurfer] FDR Correction of NHP Surface Data

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 k

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

Re: [Freesurfer] FDR Correction of NHP Surface Data

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 automat

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

Re: [Freesurfer] FDR Correction of NHP Surface Data

I'll leave that for Doug. Bruce On Tue, 28 Aug 2012, 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). I recog

Re: [Freesurfer] FDR Correction of NHP Surface Data

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). I recognize that this may not be an officially supported functionality, but is there some

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

[Freesurfer] FDR Correction of NHP Surface Data

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 monk