Hi,
For example, with the methods I mentioned above, for one subject,the
intensity of the subjects data is 52.4554, but that of the subjects
data in MNI-space is only 36.1254. For another subject, the intensity
is 46.7794 and 43.8556, which is similar. I don't know how to explain
the different.I know that interpolation will affect a little. Compare
trilinear and nearest neighbour, which is better?
Thank you!
Li
2008/1/26, Mark Jenkinson <[log in to unmask]>:
> Hi,
>
> Those commands are fine for flirt.
> But how are you judging that the intensity is decreased?
>
> Could it be due to including slightly different voxels on the
> edge of your ROI mask? When you transform a binary
> mask you need to rethreshold it afterwards to decide
> whether to be inclusive of small partial volume overlap
> (of the mask and the new voxels) or exclusive.
> This could be the source of changes in average intensity
> over the ROI. In addition, trilinear interpolation will do
> some smoothing of the image a little - which affects sharp
> peaks particularly.
>
> All the best,
> Mark
>
>
> On 25 Jan 2008, at 17:24, Li Jiang wrote:
>
> > Hi,
> >
> > That's what I have done.
> >
> > * get the transformation matrix file (*.mat) that transforms
> > subject-space CBF
> > volume to MNI-space
> > * get ROI volume in subject-space
> > * transform ROI volume into MNI-space using the same *.mat file
> > * use flirt:
> >
> > flirt -in <ROIVol> -ref <MNIVol> -out <ROIinMNIVol> -applyxfm
> > -init <matFile>
> >
> > Thanks.
> >
> > Li
> >
> > 2008/1/25, Steve Smith <[log in to unmask]>:
> >> Hi,
> >>
> >> I'm still not sure you have a problem. How are you judging that the
> >> intensity is decreased?
> >>
> >> Cheers.
> >>
> >>
> >> On 22 Jan 2008, at 06:28, Li Jiang wrote:
> >>
> >>> Hi,
> >>>
> >>> Thank you very much. I still have a question. The original subject
> >>> image is epi sequence.After I transform this image to highres T1
> >>> image
> >>> and then to MNI-space, the intensity of the transformed sub2mni
> >>> image
> >>> decreased compare to the original epi image. When transform, I use
> >>> trilinear interpolation and cost function is correlation ratio.
> >>> How
> >>> can I improve this problem? Which interpolation method and cost
> >>> function should I apply?
> >>>
> >>> Li
> >>>
> >>> 2008/1/21, Steve Smith <[log in to unmask]>:
> >>>> Hi,
> >>>>
> >>>> avscale gives you a whole set of different pieces of information
> >>>> about
> >>>> the spatial affine transform, including the average scaling (size)
> >>>> change. It does not tell you anything about intensities. On
> >>>> average,
> >>>> in general, intensities don't change upon resampling, though of
> >>>> course
> >>>> any given voxel will change!
> >>>>
> >>>> Cheers.
> >>>>
> >>>>
> >>>> On 19 Jan 2008, at 15:12, Li Jiang wrote:
> >>>>
> >>>>> Dear Steve Smith,
> >>>>>
> >>>>> I use fsl to process the functional MR data. It is a great
> >>>>> software.
> >>>>> To process the data, I first transform the EPI (subject image)
> >>>>> data
> >>>>> to T1 volume then to MNI_space with affine transformation. And
> >>>>> I'll
> >>>>> measure the absolute value from the images have been
> >>>>> coregistered to
> >>>>> MNI-space . I learned from the lectures and noticed the avscale
> >>>>> for
> >>>>> Inter-subject Registration. I wonder what's the scale mean. If the
> >>>>> signal intensity of the subject image will change after affine
> >>>>> transformation or global intra-subject transformation.
> >>>>>
> >>>>>
> >>>>>
> >>>>> Best regards.
> >>>>>
> >>>>> Li Jiang
> >>>>>
> >>>>
> >>>>
> >>>> -------------------------------------------------------------------
> >>>> --------
> >>>> Stephen M. Smith, Professor of Biomedical Engineering
> >>>> Associate Director, Oxford University FMRIB Centre
> >>>>
> >>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> >>>> +44 (0) 1865 222726 (fax 222717)
> >>>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >>>> -------------------------------------------------------------------
> >>>> --------
> >>>>
> >>>
> >>
> >>
> >> ---------------------------------------------------------------------
> >> ------
> >> Stephen M. Smith, Professor of Biomedical Engineering
> >> Associate Director, Oxford University FMRIB Centre
> >>
> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> >> +44 (0) 1865 222726 (fax 222717)
> >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> >> ---------------------------------------------------------------------
> >> ------
> >>
> >
>
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