Thank you very much.
Li
2008/2/10, Steve Smith <[log in to unmask]>:
> Hi,
>
> On 9 Feb 2008, at 14:03, Li Jiang wrote:
>
> > 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?
>
> Sure you can - the final application of the resampling, with any given
> choice of interpolation method, is independent of the interpolation
> method used originally to estimate the transform(s).
>
> > 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?
>
> No - the original estimated transform is just a spatial transform, a
> 4x4 matrix determining what co-ordinates go to what co-ordinates.
>
> Cheers.
>
>
> >
> >
> > 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>
> >>>>>>
> >>
>
>
> ---------------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------------
>
|