Yes those were from FSLview, and no they didn't start in the same
orientation as the standard. Actually that's true for all of our images.
Is there a utility in the fsl toolbox to easily flip the orientation of the
images, that would be helpful? Its easy enough in matlab, but I don't want
to mess up the header information.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Brian Patenaude
Sent: Thursday, September 27, 2007 3:16 PM
To: [log in to unmask]
Subject: Re: [FSL] first_flirt
Out of curiosity, were those images generated using FSLview? If so, it
doesn't look like it starts off in the same orientation as the MNI template.
Generally, I've never had to crop quite so high with the neck mask, but I'm
glad it works.
Cheers,
Brian
>
> The brains are our typical "LPS" axial. The neck goes to the bottom
> of the brain stem. I made a new mask, which masked out more of the
> neck/brain stem and it ran after that.
>
> I've attached a screenshot of a scan, with the successful mask. Is
> this the level I should be aiming for, or any other suggestions?
>
> Thanks,
>
> Chris
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Brian Patenaude
> Sent: Wednesday, September 26, 2007 4:57 PM
> To: [log in to unmask]
> Subject: Re: [FSL] first_flirt
>
> Does the brain within the image have an odd orientation? I'm just
> trying to figure out why flirt would fail. Is there any strong bias
> field effects? The ones that failed, did they have a significant
> amount of neck? If so, for the mask used, does it extend far below the
> cerebellum (preferably not)?
>
> Cheers,
>
> Brian
>
>
>> No, just 256x256x166 1x1x1mm axial.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> Behalf Of Brian Patenaude
>> Sent: Wednesday, September 26, 2007 4:35 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] first_flirt
>>
>> 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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