Hi,
Thank you for all of your help. I think I am pretty clear now on how FSL reads Analyze and NiFTI files with or without qform data. I would prefer to leave the data in the original coordinates and include the transformation in the qform fields. However, FSL doesn't support the qform fields yet. So, until it does, I should write the transform into the sform fields, correct?
Jolinda
On Fri, 21 Apr 2006 07:34:42 +0100, Mark Jenkinson <[log in to unmask]> wrote:
> Hi,
>
> Glad that helps.
> Sorry - my mistake about swapping - we swap in FSLView (and
> slices) when it is neurological (i.e. *positive* determinant).
> The reason is that we always try to display radiologically, so
> this is why we swap neurologically ordered data.
>
> Note that the newest version of FSLView also labels the axes
> based on the sform/qform information, so that helps figure out
> what is what.
>
> All the best,
> Mark
>
>
> On 20 Apr 2006, at 22:38, jolinda wrote:
>
> > Hi Mark,
> >
> > Sorry - for some reason I was thinking that RAS = radiological. That
> > explains a lot of my confusion. Now almost everything is consistent.
> >
> > Are you sure FSLView only swaps left and right if the determinant is
> > negative? I see it swap L/R for positive qform determinants. I
> > haven't tried
> > feeding it a negative one yet.
> >
> > Jolinda
> >
> >
> > -----Original Message-----
> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> > Behalf
> > Of Mark Jenkinson
> > Sent: Thursday, April 20, 2006 1:43 PM
> > To: [log in to unmask]
> > Subject: Re: [FSL] Yet another orientation question
> >
> >
> > Dear Jolinda,
> >
> > Just to clarify:
> > We consider "neurological" to have positive determinant.
> > We consider "radiological" to have negative determinant.
> > We treat *all* Analyze files as being "radiological".
> > I believe that this is all consistent with the FAQ and what you see.
> >
> > If you convert Analyze to Nifti and it is originally RAS ordered,
> > then you
> > need to make sure that you set an sform/qform appropriately. The
> > default
> > one provided by avwchfiletype is based on our assumptions of LAS.
> > You can
> > easily change this by using avworient -swaporient.
> >
> > Currently in FSLView we simply swap left and right if the
> > determinant is
> > negative. This isn't ideal in many ways, but we don't yet have the
> > capability to do arbitrary transforms on the fly, so we've left it
> > at that
> > (although doing arbitrary transforms based on the sform/qform is on
> > our todo
> > list).
> >
> > We have this behaviour so that it is possible to see what happens
> > when the
> > sform/qform matrix information is changed. This is particularly
> > important
> > for Analyze files and for nifti files where no sform or qform is
> > set. In
> > this case we feel it is important to show how FSL will interpret the
> > left-right order (our default choices).
> >
> > So although this isn't the behaviour you'd most like from FSLView (and
> > slices) I think it is behaving correctly. Does this accord with
> > your view?
> >
> > I hope this is clear.
> > All the best,
> > Mark
> >
> >
> >
> >
> > On 20 Apr 2006, at 19:38, jolinda wrote:
> >
> >> Thanks Mark. I just want to make sure that my converted files are
> >> correctly
> >> interpreted by FSL. I haven't run them through all the tools yet,
> >> but I have
> >> found a few things.
> >>
> >> With older analyze files, running avwchfiletype NIFTI adds the
> >> following
> >> sform information:
> >>
> >> sform_name Aligned Anat
> >> sform_code 2
> >> sto_xyz:1 -3.125000 0.000000 0.000000 96.875000
> >> sto_xyz:2 0.000000 3.125000 0.000000 -96.875000
> >> sto_xyz:3 0.000000 0.000000 4.000002 -60.000031
> >> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> >> sform_xorient Right-to-Left
> >> sform_yorient Posterior-to-Anterior
> >> sform_zorient Inferior-to-Superior
> >>
> >> Because of this, if the data was originally RAS, it will now be
> >> left-right
> >> flipped in all of the analysis reports. Is this based on
> >> information in the
> >> analyze header, or an assumption about the order of the data? I
> >> understand
> >> that some assumptions must be made, but it appears to contradict the
> >> statement in the FSL faq that the latest version of FSL treats all
> >> Analyze
> >> images as radiological.
> >>
> >> FSLView appears to interpret the qform matrix in the same way that
> >> avworient
> >> -getorient does, and to flip LR accordingly. Thus, if you feed it:
> >>
> >> qform_name Scanner Anat
> >> qform_code 1
> >> qto_xyz:1 3.130000 0.000000 0.000000 0.000000
> >> qto_xyz:2 0.000000 3.130000 0.000000 0.000000
> >> qto_xyz:3 0.000000 0.000000 4.000000 0.000000
> >> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> >> qform_xorient Left-to-Right
> >> qform_yorient Posterior-to-Anterior
> >> qform_zorient Inferior-to-Superior
> >>
> >> or:
> >>
> >> qform_name Scanner Anat
> >> qform_code 1
> >> qto_xyz:1 -3.124945 -0.001332 -0.023744 101.946167
> >> qto_xyz:2 0.009799 -2.767111 -1.858704 103.824890
> >> qto_xyz:3 -0.015807 -1.452144 3.541846 2.113121
> >> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> >> qform_xorient Right-to-Left
> >> qform_yorient Anterior-to-Posterior
> >> qform_zorient Inferior-to-Superior
> >>
> >> using the same raw data, it will display the image with left and
> >> right
> >> flipped (when compared with the same data with qform_code = 0).
> >>
> >> I do not think this is good behavior. I think it should either
> >> ignore the
> >> qform matrix altogether, or use it to transform the image into RAS
> >> space.
> >> Right now it seems to simply look at the determinant of the matrix
> >> and
> >> decide whether to flip left and right -- and decide wrongly.
> >>
> >>
> >> Jolinda
> >>
> >> -----Original Message-----
> >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> >> Behalf
> >> Of Mark Jenkinson
> >> Sent: Thursday, April 20, 2006 9:50 AM
> >> To: [log in to unmask]
> >> Subject: Re: [FSL] Yet another orientation question
> >>
> >>
> >> Dear Jolinda,
> >>
> >> This issue is confusing and our documentation on this tries to walk
> >> the line
> >> between being comprehensive and comprehendable by the majority of
> >> users. I
> >> think that the issue of left-handed and right-handed coordinate
> >> systems is
> >> somewhere between incomplete, confusing and wrong. I think I will
> >> remove
> >> these statements as they are not helpful to most people, and the
> >> people who
> >> do appreciate thinking in these terms want more information than we
> >> provide.
> >>
> >> You are right about the nifti xyz coordinate system being RAS and
> >> therefore
> >> right-handed. It is also true that LPS is right-handed.
> >>
> >> What is the crucial part of our "radiological/neurological"
> >> definition
> >> is the
> >> mapping between two coordinate systems: the voxel coordinates (not
> >> in real
> >> space) and the mm (real space) coordinates. This *mapping* is
> >> what is
> >> important for us. Therefore we define radiological/neurological
> >> (terms
> >> which aren't very good here, but are used for familiarity and lack
> >> of better
> >> terms) on the basis of the sign of the determinant of the matrix
> >> that maps
> >> between these two coordinate systems. So I always think in these
> >> terms and
> >> not in terms of the handedness of the coordinate system (as there
> >> are too
> >> many potential coordinate systems).
> >>
> >> Sorry that this has been a source of confusion for you.
> >> I hope that this clears things up.
> >> I will edit the FAQ to remove the handedness text shortly.
> >>
> >> All the best,
> >> Mark
> >>
> >>
> >>
> >>
> >>
> >> jolinda wrote:
> >>
> >>> Okay...but I'm afraid I just don't see why a positive determinant
> >>> indicates a left-handed coordinate system. The qform matrix
> >>> relates the
> >>> voxel coordinates to the NiFTI standard right-handed RAS space ---
> >>> so,
> >>> if the image was already in the same space, the qform would be
> >>>
> >>> 1 0 0 0
> >>> 0 1 0 0
> >>> 0 0 1 0
> >>>
> >>> which certainly has a positive determinant. If you are using a qform
> >>> code = 1, the you are most likely relating the standard DICOM space
> >>> (LPS) to NiFTI space (RAS), both of which are right-handed, and your
> >>> qform matrix will indicate a 180 degree rotation and still have a
> >>> positive determinant.
> >>>
> >>> Can you explain this to me? What am I missing?
> >>>
> >>> Jolinda
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> >>> Behalf Of Christian Beckmann
> >>> Sent: Wednesday, April 19, 2006 1:05 PM
> >>> To: [log in to unmask]
> >>> Subject: Re: [FSL] Yet another orientation question
> >>>
> >>>
> >>> Hi,
> >>>
> >>> it's the qform matrix which counts, see http://www.fmrib.ox.ac.uk/
> >>> fslfaq/#general_radiologicaldef
> >>>
> >>> "Our technical definition of neurological convention for image
> >>> storage is that the coordinate system is left-handed, or
> >>> alternatively, that the determinant of the sform or qform matrix
> >>> that
> >>> relates real world coordinates to voxel coordinates, has a positive
> >>> determinant."
> >>>
> >>> In your case, the qform matrix has a positive determinant and the
> >>> volume is therefore understood to be in neurological convention.
> >>> cheers
> >>> christian
> >>>
> >>>
> >>> --
> >>> Christian F. Beckmann
> >>> Oxford University Centre for Functional
> >>> Magnetic Resonance Imaging of the Brain,
> >>> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> >>> Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/
> >>> ~beckmann/
> >>> Phone: +44(0)1865 222551 Fax: +44(0)1865 222717
> >>>
> >>>
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