Hi Donna,
I'm quite perturbed by this.
We did extensive testing in-house prior to the last release (4.1) to
make sure that registrations and FEAT runs (as well as other things)
were fine with different combinations of left/right (or radio/neuro-logical)
orderings. Everything tested fine here.
What can be confusing is whether the sform or qform are set or not,
as if they are not then there can be real problems in that the "flip"
operation may not do anything - depending on what you ran. Also,
displaying images with different software can be a problem. I'm
not sure if these relate to you or not. I would really like to be able
to track this problem down though. Would you be able to run some
tests for me if you cannot send the data?
To start with, it would be very helpful to see the fslhd output for
the pre and post registration image, and the reference image.
Hopefully we can sort out whether there is a problem to be fixed
in FSL or not.
All the best,
Mark
Donna Dierker wrote:
> 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
>>>
>
