Hi,
For example, if I get AtoB and BtoC transform matrix wih trilinear
interpolation, and concatenate the AtoC transform matrix, can I use
nearest neighbor interpolation when I apply AtoC tranform matrix to A
or should I also use trilinear interpolation?
In that case, if I use neighbor interpolation when I apply AtoC
tranform matrix to A, does the trilinear interpolation I used in
getting AtoB and BtoC tranform matrix count for the intensity of the
generated image?
Thank you.
Li
ÔÚ 08-2-8£¬Mark Jenkinson<[log in to unmask]> дµÀ£º
> Hi,
>
> If you are resampling your native space image into the MNI space, then
> you should concatenate your transforms (with ConcatXFM gui or convert_xfm)
> and then apply the concatenated transform directly to the native space
> image with ApplyXFM or flirt.
>
> Make sure you do not resample twice as that will certainly degrade your
> images more.
>
> It is only the interpolation method you select with ApplyXFM (or flirt)
> which
> will count for the intensities generated in your resampled image.
>
> All the best,
> Mark
>
>
>
> Li Jiang wrote:
> > Hi,
> >
> > Thank you very much. if the native space has lower resolution than
> > the standard space, for example, the native sapce is 3x3x3, first
> > transform to MPRAGE (1x1x1) within subject,then transform to MNI-space
> > (2x2x2), which interpolation methods is better? If I concact the
> > tranform matrix from the native space to MNI_space, do I only need to
> > use the Advanced Options tab in the ApplyXFM to select interpolation
> > method whenever which interpolation method I used in flirt steps?
> >
> > Thank you!
> >
> > Li
> >
> > 2008/2/5, Mark Jenkinson <[log in to unmask]>:
> >
> >> Hi,
> >>
> >> You are certainly correct that if you have a large intensity
> >> difference at the boundary of a region (like your 10000/1000/100
> >> simulations) and/or you have a higher resolution than in the
> >> reference image space (and your excel spreadsheet seems to
> >> indicate about 7 times more voxels for the same area in the
> >> native space) then you will certainly see a difference due to
> >> interpolation method.
> >>
> >> It is easy to select the interpolation method with flirt: either
> >> use "-interp nearestneighour" at the command line or use the
> >> Advanced Options tab in the ApplyXFM or FLIRT GUIs.
> >>
> >> However, if your native space has higher resolution than your
> >> standard space, then nearest neighbour will be effectively
> >> ignoring some voxels in your native space. The better solution
> >> would be to use nearest neighbour with the 1mm standard
> >> space in this case if you are very concerned about the change
> >> in average ROI intensity. You may find that with conservative
> >> thresholds (say 0.9) for the trilinear masks and using the
> >> 1mm space that there is little difference between the two methods.
> >>
> >> I hope this helps.
> >> All the best,
> >> Mark
> >>
> >>
> >> On 2 Feb 2008, at 21:06, Li Jiang wrote:
> >>
> >>
> >>> 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
> >>>>>>>>>> ---------------------------------------------------------------
> >>>>>>>>>> --
> >>>>>>>>>> --
> >>>>>>>>>> --
> >>>>>>>>>> ------
> >>>>>>>>>>
> >>>>>>>>>>
> >>>> <flirt_scale.xls>
> >>>>
>
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