Hi Joelle - any chance you can make the T1 available for download? I
could take a look if you'd like.
On Mon, Aug 3, 2015 at 3:03 PM, Joelle Zimmermann
<[log in to unmask]> wrote:
> Hi,
>
> Thanks again for this suggestion. A follow-up question here - I tried using
> fslmaths to replace the NaN's by doing:
>
> fslmaths T1.nii -nan
>
> I'm not sure how to check if this actually did what I want it to do -
> replace the NaN's with 0's; and if I am using the command correctly.
>
> After trying to correct the NaN's in the T1 image in this way, I run bet ,
> followed by epi_reg, and still get that same: ERROR:set_bbr_seg: could not
> find any boundary points!
>
> Thanks,
> Joelle
>
>
> On Sat, Aug 1, 2015 at 1:52 PM, Mark Jenkinson
> <[log in to unmask]> wrote:
>>
>> Hi,
>>
>> This error is almost always due to the fact that the segmentation of the
>> structural image has failed. It might have just completely failed for some
>> reason (including the job dying for various IT reasons like lack of disk
>> space, or incorrect filename, as well as problems with the image such as
>> strong artefact) or it could be caused if the image initially contained NaN
>> values (Not a Number) due to it having been processed by some other package
>> (e.g. matlab often inserts these). So check the structural image, check its
>> segmentation, and check the structural image for NaN values (you can use the
>> -nan or -nanm flag in fslmaths to fix/identify these).
>>
>> FYI: BBR is Boundary-Based Registration, and is the cost function used
>> inside the registration method for EPI to structural registrations.
>>
>> All the best,
>> Mark
>>
>>
>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of
>> Joelle Zimmermann <[log in to unmask]>
>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>> Date: Saturday, 1 August 2015 00:38
>> To: "[log in to unmask]" <[log in to unmask]>
>> Subject: [FSL] set_bbr_seg ERROR
>>
>> Hi everyone,
>>
>> While registering one subject from functional>T1>standard space, I'm
>> getting the following error:
>>
>> ERROR:set_bbr_seg: could not find any boundary points!
>> WARNING: Found NaN in BBR cost(2)
>>
>> This is the case for only one of my 20 subjects. Does anybody have any
>> ideas of why this happens; or where exactly the NaN's are found? (Not sure
>> what a BBR cost is).
>>
>> Thanks for any suggestions,
>> Joelle
>
>
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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