Hi Mark,
Recently, I had an experience with flirt where a LPI->LPI registration
did not compute properly. The data (brainA.nii) was in Freesurfer form
and came from an outside lab, so I am not at liberty to provide it. I
used the Wash U 711-2B template, which I flipped to LPI using AFNI's
3daxialize. I similarly flipped brainA.nii to LPI. (The talairach_avi
xfm was bad in this case, owing to the brain being rotated off AC-PC.
Source and template were initially not in the same orientation, and the
associated surfaces were in LPI orientation, so to save a bit of sanity,
I flipped all to LPI.)
Flirt did a very fine job of rotating the volume to AC-PC and keeping
the brain within the template bounding box / cerebral hull. The origin
was 8mm anterior to the AC, but this brain did have some issues
(tumor/lesion in the frontal lobe).
The reason I'm posting is that the transform was somehow confused so
that what started as a very pronounced occipital petalia (left torquing
into right) ended up flipped -- right torquing into left. It wasn't
just a translation or x-flip; the affine transform itself was implicated.
Anyway, flipped both source and target to RPI, and then flirt gave me a
very sensible result (although the origin was still translated a bit
anterior).
I think if you take any source and target on your end; flip them to LPI;
try flirt on them; and don't see any misbehavior, then I wouldn't
worry. My brainA.nii did have extenuating circumstances, which is why I
didn't post before seeing Regina's post.
Donna
On 03/10/2009 08:20 AM, Mark Jenkinson wrote:
> Hi,
>
> FSL should currently handle radiological and neurological
> data fine, even if it is mixed - although I'd still probably
> avoid mixing them if possible.
>
> All the best,
> Mark
>
>
> On 10 Mar 2009, at 13:06, Regina Lapate wrote:
>
>> I have a pretty straightforward question that I haven't been able to
>> find a
>> definite answer to by searching in the documentation of fsl: how well
>> does
>> fslview and flirt currently handle NIFTI images with a LPI
>> (RAS/neurological) orientation?
>>
>> I found that for the fsl version 3.3, images in neurological orientation
>> were not recommended (cf.
>> http://www.fmrib.ox.ac.uk/fslfaq/#general_lr), but
>> is that still the case? I currently have a preprocessed dataset in the
>> neurological orientation I would like to run first and second level
>> analyzes
>> with using fsl. Before converting everything to radiological
>> orientation, I
>> would like to make sure that this step is actually necessary- or still
>> highly recommended.
>>
>> Thank you very much for any input.
>>
>> Regina
>>
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