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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