Hi Lena,
to second Marko,
On Fri, 16 Feb 2007, Marko Wilke wrote:
>> I am trying to analyse sructural MRI - VBM. When checking registration
>> (SPM5) if images are grossly not fitting with template, pitch,yaw and
>> roll needs to be corrected - according to SPM VBM wiki guide. Why cant we
>> use template and do a coreg;realign/estimate so the images will match the
>> template? or is this allowed only for within subject series ?
>
> Coregistration is meant to deal with images of different modalities from one
> subject, i.e. coregister a subject's EPI to its GM segment. It is a
> rigid-body procedure so not ideal for matching a source image to a template
> (this is what we use spatial normalization for :)
if your images are in correct overall orientation (i.e. left-right,
up-down, A-P are similar to SPMs templates), but with a rather large
distance to the template, coregistration may improve starting estimates
for segmentation.
>
>> The analyze files i have (structural scans) are not in
>> coronal/sagittal/axial order as the template - anyway of working this out?
>
> This is indeed a problem which you will need to correct. If you display the
> image, at the bottom left there are fields called pitch, roll and yaw.
> Specifiying rotations there (with values derived from pi, say, e.g. -3.14, 0,
> 1.57) will alter the "order of appearance". Once you worked out which values
> you need you can apply them to all images you need to reorient, but BE
> CAREFUL (sorry for shouting :) that you do not mess up handedness. BTW, this
> you can also use to correct slight tilts to one side which will improve spm's
> starting estimates for normalization.
Alternatively, you may use CheckReg to display both template and subject
image. On the subject image, choose "Reorient image" from the context menu
and proceed with moving the image around as Marko described. This way, you
will be able to move your image quite close to the template.
Volkmar
--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg http://fbi.uniklinik-freiburg.de/
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