Hi Martin,
If you are using nifti images are either the qform or the sform are set
then it uses
this information to convert between voxel and mm coordinates. If you
are using
nifti without these being set, or Analyze without the origin set, then
you get
the simple scaled coordinates (voxels coord value times voxel dimension
in mm).
In general it is easier to work in voxel coordinates as there won't be any
inconsistencies between tools, since we still have a few which insist on
scaled
mm coords (the simple multiplication above) rather than the qform/sform type
of mm coordinate, even when the qform/sform is set. We hope to make things
completely consistent in the future, but for now you need to be aware
that some
tools (e.g. bet) need the scaled version in mm, and some will
need/provide the
qform/sform version.
All the best,
Mark
Christian Beckmann wrote:
> Hi Martin,
>
> I was referring to mm coordinates in voxel space for which you simply
> take the output of avwstats and then multiply by voxel dims. You can
> use any other coordinate convention you fancy by simply adding the
> relevant offsets to the previous results, e.g. if your roi is in MNI
> space and you want everything in mm coordinates from the AC then
> simply adjust the previous values by 90,-126,-72 mm for x,y,z .
> cheers
> Christian
>
>
>
>
>
> On 9 Feb 2007, at 01:44, Martin M Monti wrote:
>
>> Christian,
>>
>> thank you.
>>
>> Although for the conversion, wouldn't it be more like:
>>
>> Call Xo, Yo, Zo the three voxel coordinates of the middle voxel
>> (i.e. the voxel at mm 0,0,0)
>> call resX, resY, resZ the voxel resolution
>> call X,Y,Z the coordinates of a voxel you want to transform in mm
>> coords:
>>
>> X axis:
>> if(X<Xo) --> |X-Xo|*resX
>> if(X>=Xo) --> |X-Xo|*resX*-1
>>
>> Y axis:
>> if(Y<Yo) --> |Y-Yo|*resY*-1
>> if(Y>=Yo) --> |Y-Yo|*resY
>>
>> Y axis:
>> if(Z<Zo) --> |Z-Zo|*resZ*-1
>> if(Z>=Zo) --> |Z-Zo|*resZ
>>
>> Is there a more obvious way?
>>
>> martin
>>
>> Christian Beckmann wrote:
>>
>>> Hi Martin,
>>>
>>> 1) yep, absolutely correct, the first is the number of voxels, the
>>> second number is the same multiplied by the voxel volume (i.e. in
>>> mm^3)
>>> 2) avwstats(++) does not yet support outputting this in mm rather
>>> than voxels - but you only need to multiply by the appropriate
>>> x,y,z voxel dims to get this in mm
>>>
>>> hope this helps
>>> Christian
>>>
>>>
>>>
>>>
>>>
>>> On 8 Feb 2007, at 19:24, Martin M Monti wrote:
>>>
>>>> Dear FSL gurus,
>>>>
>>>> I have a couple small questions about avwstats(++)
>>>>
>>>> 1) avwstats -V: the frist number is the voxel count, the second,
>>>> volume, is that the same count but at the T1 resolution?
>>>> 2) avwstats -w: Is it possible to get a mm output rather than a
>>>> voxel output? (kind of like the -c vs -C option with avwstats++)
>>>> Alternatively, is there a tool to go from the former to the latter?
>>>>
>>>> cheers
>>>>
>>>> martin
>>>>
>>>>
>>>>
>>>>
>>>> --------------------------------------------
>>>> "Well! I've often seen a cat without a grin; but a grin without a
>>>> cat! It's the most curious thing I ever say in my life!" [Lewis
>>>> Carroll, Alice in Wonderland]
>>>>
>>>> - “Contrariwise,” continued Tweedledee, “if it was so, it might be;
>>>> - and if it were so, it would be;
>>>> - but as it isn’t, it ain’t.
>>>> - That’s logic.” [Lewis Carroll, Through the Looking-Glass]
>>>>
>>>> --------------------------------------------
>>>> Martin M. Monti, MA
>>>> Princeton University
>>>> Department of Psychology
>>>> Green Hall 3-S-8
>>>> (609) 258-5679
>>>> www.webmartin.net
>>>> --------------------------------------------
>>>
>>>
>>> --
>>> 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
>>
>>
>> --
>> --------------------------------------------
>> "Well! I've often seen a cat without a grin; but a grin without a
>> cat! It's the most curious thing I ever say in my life!" [Lewis
>> Carroll, Alice in Wonderland]
>>
>>
>> - Mais alors que dois-je devenir?
>> - Un curieux!
>> - Ce n’est pas un métier.
>> - Ce n’est pas encore un métier. Voyagez, écrivez, traduisez,
>> apprenez à vivre partout. Commencez tout de suite. L’avenir est aux
>> curieux de profession. [Truffaut - Jules et Jim]
>>
>>
>> I became insane, with long intervals of horrible sanity. [E.A. Poe]
>>
>>
>> - “Contrariwise,” continued Tweedledee, “if it was so, it might be;
>> - and if it were so, it would be;
>> - but as it isn’t, it ain’t.
>> - That’s logic.” [Lewis Carroll, Through the Looking-Glass]
>>
>>
>> - "Would you tell me, please, which way I ought to go from here?"
>> - "That depends a good deal on where you want to get to," said the Cat.
>> - "I don't much care where-" said Alice.
>> - "Then it doesn't matter which way you go," said the Cat.
>> - "As long as I get somewhere," Alice added as an explanation.
>> - "Oh, you're sure to do that," said the Cat, "if you only walk long
>> enough." [Lewis Carroll, Alice in Wonderland]
>>
>>
>> --------------------------------------------
>> Martin M. Monti
>> Princeton University
>> Department of Psychology
>> Green Hall 3-S-8
>> (609) 258-5679
>> www.webmartin.net
>> --------------------------------------------
>
>
> --
> 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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