Do they have any strange orientation to begin with?
Cheers,
Brian
> Yes the failure(s) have been at the first level. Sometimes the brain
> ends upside-down and flipped, sometimes it appears zoomed in and skewed.
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Brian Patenaude
> Sent: Wednesday, September 26, 2007 1:41 PM
> To: [log in to unmask]
> Subject: Re: [FSL] first_flirt
>
> Hi,
>
>
>> Is the outcome of run_first_all supposed to be in standard mni space,
>> or native subject space?
>
> All the segmentations should be in native space. The FIRST takes the
> transformation matrix inputed, inverts it, then applies it to the model
> prior to fitting.
>
>
>> Also, any suggestions as what to do when first_flirt fails to register
>> even after masking out the neck?
>
> Does the failure occur at the first stage (use -d option)?
>
> Cheers,
>
> Brian
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