Hello,
one more question to follow up on this thread...
I understand that rmsdiff calculates the rms values using a sphere as
an approximation for the brain volume. How is the radius of the sphere
determined?

Thanks
zrinka
On Friday, August 15, 2003, at 03:03 PM, Mark Jenkinson wrote:

> Hi,
>
> Yep, it is the same rmsdiff.
> The refvol determines the centre of the FOV (in mm) so you can use
> any image from the functional time series as they all have the same
> FOV.
>
> Cheers,
>        Mark
>
>
>
> On Friday, August 15, 2003, at 07:55  pm, Zrinka Bilusic wrote:
>
>> Thanks, that clarifies things...
>>
>> one more question - about rmsdif. Is rmsdiff the same algorithm that
>> is
>> behind rms values reported by mcflirt? In other words, if I have a
>> series of MAT* files from a mcflirt run, and if I execute:
>>        rmsdiff MAT_0000 MAT_0001 vol0000
>> that should give me the "estimated mean displacement" between vol0001
>> and vol0000 (where vol0000 and vol0001 anre 0th and 1st volume in a
>> functional run)? And that number should be the same as the first value
>> in rel rms, as reported by mcflirt for the same functional series?
>>
>> For rmsdiff: Usage: rmsdiff matrixfile1 matrixfile2 refvol, I am
>> assuming that refvol is the volume corresponding to transformation
>> matrix in matrixfile1?
>>
>>
>> thanks
>> zrinka
>> On Friday, August 15, 2003, at 02:35  AM, Mark Jenkinson wrote:
>>
>>> Hi Zrinka,
>>>
>>> There are two ways of dealing with transformations in mcflirt.
>>> One is dealing with the matrix files (the *.mat ascii files produced
>>> by
>>> flirt
>>> and mcflirt) and the other is dealing with mcflirt parameters in the
>>> *.par file.
>>> If you are dealing only with the matrix files, as generated with the
>>> -mats
>>> flag to mcflirt then the (0,0,0) mm coordinate is in the corner of
>>> the
>>> (0,0,0)
>>> voxel, exactly the same as for flirt and does not depend on the
>>> centre
>>> of
>>> mass.  I would definitely recommend working with these matrices when
>>> comparing methods as there is much less arbitrariness in how they are
>>> constructed.
>>>
>>> However, for the parameters - yes - the translations are with respect
>>> to
>>> the centre of mass.  Hence this is much more awkward to deal with and
>>> use.  The problem arises because the decomposition of the affine
>>> matrix
>>> into parameters is arbitrary.  There are lots of perfectly acceptable
>>> choices
>>> and we have picked one that works well internally, as it is close to
>>> decoupling
>>> rotations from translations.  It is also a little more intuitive to
>>> look at the plots
>>> when they are nearly decoupled.  However, to convert between the
>>> matrix transform and these parameters is much more difficult since
>>> you
>>> need
>>> to know the centre of mass, which we don't save anywhere.
>>>
>>> So can I suggest that you forget about the output of -plots and just
>>> use the
>>> -mats output, then the matrix is simple, the origin is always in the
>>> corner
>>> (the 0,0,0 voxel), as the "mm coordinate = voxel size * voxel
>>> coordinate"
>>> and the "new mm coordinate = matrix * old mm coordinate" for the
>>> transformation.
>>>
>>> All the best,
>>>        Mark
>>>
>>>
>>>
>>> On Thursday, August 14, 2003, at 10:53  pm, Zrinka Bilusic wrote:
>>>
>>>> Hello,
>>>> I am back to comparing transformation matrices from mcflirt and air
>>>> and I have a question...
>>>> oh, well...
>>>>
>>>> from some previous postings, I understand that fsl uses different
>>>> coordinate system for
>>>> "voxel" and for "mm". voxels are described with respect to image
>>>> storage and the origin, or
>>>> (0,0,0) voxel is the first (corner) voxel in the dataset. The mm
>>>> coordinates are voxel
>>>> coordinates multiplied by voxel dimensions. Also, transformation
>>>> matrices are always given
>>>> with respect to mm coordinates. But, the origin of mm coordinates
>>>> (at
>>>> least with regards to
>>>> transformation matrices output by mcflirt) is not set to (0,0,0)
>>>> voxel, but to the "center of
>>>> mass" of the image.
>>>>
>>>> So, in other words, if I wanted to find a position of a voxel after
>>>> transformation I would have
>>>> to do the following:
>>>> 1. transform old voxel coordinates into mm coordinates:
>>>> old_mm=T*old_vox;
>>>> 2. transform old mm coordinates into new mm coordinates:
>>>> new_mm=XFM*old_mm
>>>>
>>>> where XFM is  the transformation matrix from the .mat file. But what
>>>> is T? Is it possible to find
>>>> out what is the center of mass that mcflirt uses for each
>>>> transformation?
>>>>
>>>> I believe that is the piece that I am missing in order to compare
>>>> air
>>>> and fsl transformations,
>>>> because it seems that the only difference in the matrices is that
>>>> air
>>>> transformation matrices
>>>> are always with respect to the first voxel in the dataset.
>>>>
>>>> Thanks!
>>>> zrinka
>>>
>>>
>> Zrinka Bilusic-Vezmar
>> UCLA Brain Mapping
>> 660 Charles Young Drive South
>> Los Angeles, CA  90095
>>
>> 310-794-5060
>> [log in to unmask]
>> www.brainmapping.org
>
>
Zrinka Bilusic-Vezmar
UCLA Brain Mapping
660 Charles Young Drive South
Los Angeles, CA  90095

310-794-5060
[log in to unmask]
www.brainmapping.org