Hi Wolf,
Thanks for the response. It seems that regardless of what input parameters
I use, not a single voxel comes out active in any case, even when I set
the thresholds very very lightly. This is odd because the map has some
very robust activation. Have you experienced this before? Some strange
patterns near the edges suggest it may be a transformation issue.
I could try using cluster instead, but I wasn't able to figure out how to
output a thresholded image using that.
Thanks,
Sean
On 2013-03-21 5:02 PM, "wolf zinke" <[log in to unmask]> wrote:
>Hi,
>
>Have a look at the easythresh tool, that might simplify things for you a
>bit.
>
>cluster will also do. However, when you look into the easythresh script,
>you will notice, besides the relevant options for a cluster based
>thresholding, that it also produces an estimate for the smoothness of
>the data (smoothest).
>
>I hope this helps,
>wolf
>
>
>On 03/21/2013 05:17 PM, Sean wrote:
>> I'm looking for a way to perform FSL's cluster thresholding from the
>>command line. I'm hoping to do it the same way FEAT does it in
>>post-stats, but I'll be running it on a single NII file that wasn't
>>generated by FEAT. I've looked into the cluster command, but as far as I
>>can tell this only reports statistics about clusters. Is this possible
>>to do, and if so, how is it done? Are there any extra files (i.e.,
>>registration transformation matrix, etc) that I'll be needing? Thanks
>>for your help.
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