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
---------------------------------------------------------------------------
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