Hi,
It is still true that FSL will have some issues with neurologically
ordered
data (although less than before). These typically arise in coordinate
lookups between standard space and native voxel coordinates which
haven't been completely dealt with, particularly in fdt I'm afraid. So
we still recommend reordering your data into radiological order
initially
if you want to deal with FSL and have the coordinate correct.
As for DTI, I'm not sure exactly how all this effects the processing but
either Tim or Steve should be able to answer this.
All the best,
Mark
On 21 Apr 2006, at 21:29, jolinda wrote:
> One (actually two) more things. First: is the following statement
> in the FAQ
> still true?
>
> "With the current version of FSL we do not recommend storing in
> neurological
> convention as not all utilities will work in an intuitive or 'correct'
> manner with neurologically ordered data, especially when mixing it
> with
> radiologically ordered data."
>
> Second: for DTI analysis, should the bvecs file give gradient
> directions
> according to the order of the data on disk, or with x = R, y = A,
> and z = S?
>
> Jolinda
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Mark Jenkinson
> Sent: Friday, April 21, 2006 8:46 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Yet another orientation question
>
>
> Dear Jolinda,
>
> The latest version of FSL (3.3) should now support the qform
> fields. The
> previous version (3.2beta) did not. Could you let me know where you
> got the
> information about FSL not supporting the qform field - as we no
> doubt have
> some documentation that still needs to be properly updated. Thanks.
>
> All the best,
> Mark
>
>
> On 21 Apr 2006, at 16:40, Jolinda Smith wrote:
>
>> 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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