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
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>
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> Sebastian Moeller
>
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