Hi,
Thank you very much.My friend told me that if using nearest neighbour
interpolation, the intensity decrease less than using trilinear
interpolation. I don't know the principle of these two methods. If so,
When doing flirt, how to choose the interpolation method?
I attach the email here. Could you help me how to explain it£¿ Thank you!¡¢
Dear All,
I've looked at this transformation/scaling issue in a more robust way.
The drop in mean intensity value is *not* due to scaling the voxel
intensity values.
The drop in mean intensity value is due to trilinear interpolation.
I am attaching two files:
(1) PDF outlining what I did to isolate and assess the problem;
(2) Excel spreadsheet of statistics I calculated to assess the problem.
If the PDF does not explain what I did clearly, please let me know and
I'll try to explain again.
The ordering of the data in the plot, from left to right, is:
Truth = mprage in subject space; mask in subject space
Tri Vol = mprage in MNI-space with trilinear interpolation; mask in
MNI-space with trilinear interpolation and thresholded in such a way
as to approximate the same *volume* in subject-space
Tri 50% = mprage in MNI-space with trilinear interpolation; mask in
MNI-space with trilinear interpolation and thresholded at 0.50
Tri NN = mprage in MNI-space with trilinear interpolation; mask in
MNI-space with nearest neighbor (NN) interpolation
NN Vol = mprage in MNI-space with NNinterpolation; mask in MNI-space
with trilinear interpolation and thresholded in such a way as to
approximate the same *volume* in subject-space
NN 50% = mprage in MNI-space with NN interpolation; mask in MNI-space
with trilinear interpolation and thresholded at 0.50
NN NN = mprage in MNI-space with NNinterpolation; mask in MNI-space
with NN interpolation
Li
2008/1/30, Mark Jenkinson <[log in to unmask]>:
> Hi,
>
> If it is an average then the way you rethreshold your mask
> after transforming it can be very important. For small binary
> masks there can be a large difference between rethresholding
> at low levels (near zero) or high values (near one) as this will
> include/exclude contributions of voxels just outside the
> original ROI. For large masks this should be less important.
>
> Try rethresholding near 1 (if you are not already) and see if
> the values are more consistent.
>
> All the best,
> Mark
>
>
> On 29 Jan 2008, at 08:04, Li Jiang wrote:
>
> > 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
> >>>>>> -----------------------------------------------------------------
> >>>>>> --
> >>>>>> --
> >>>>>> ------
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> >
>
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