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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