Hi,
It is an average over an ROI.
First I genarate a ROI mask on the subject image. Then apply the
subject to MNI transformation matrix (.mat) to the ROI-to-MNI
volume.Then measure the intensity of ROI on the subject image and that
of ROI-to-MNI on the subject-to-MNI image with Matlab.
Thanks.
Li
2008/1/28, Mark Jenkinson <[log in to unmask]>:
> Hi,
>
> This still doesn't answer the important question:
>
> *HOW* are you measuring these intensities?
>
> Is it an average over an ROI?
> Is it from a single voxel?
>
> If it is a single voxel, is it a peak value surrounded by
> much smaller (even negative) values?
>
> If it is an ROI, how are you generating the ROIs and
> creating the average?
>
> All the best,
> Mark
>
>
> On 27 Jan 2008, at 05:11, Li Jiang wrote:
>
> > 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
> >>>> -------------------------------------------------------------------
> >>>> --
> >>>> ------
> >>>>
> >>>
> >>
> >
>
|