fslswapdim can switch the dimension. You'll have to figure out the
appropriate dimensions to swap/reverse. fslswapdim will give you a warning
if you've flipped the left/right orientation (which you should not do).
Cheers,
Brian
> 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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