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
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>
> --
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