Hi,
To clarify, "The average 1.8 scaling factor is not explained by the
transformation parameters.". Are you saying that the transformation matrix
calculated from first_flirt differs in the scale component to that applied
to get the standardized image by a factor of 1.8.
If so, did you look at the output of first_flirt? Did it clearly fail?
If so, the failure may be due to the neck or possibly bias field? If the
neck is the problem, it may be corrected by masking the neck out. Did you
try and apply first_flirt to the standardized image?
Cheers,
Brian
> Hi Brian,
>
> Yes, I mean the amount of noise in the original data prior to
> any noise reduction.
>
> The other question is:
> result of FIRST on standardized data > result of FIRST on
> native.
>
> The average 1.8 scaling factor is not explained by the
> transformation parameters.
>
> Any ideas?
>
> Naj
>
>
>
>
> On Mon, 24 Sep 2007, Brian Patenaude wrote:
>
>> Hi,
>>
>> The only disadvantage is that you've interpolated the data during the
>> transofrmation to MNI152 space. By senstive to the noise in the raw
>> image, are you meaning prior to non-uniformity correction?
>>
>> When applying FIRST to the pre-processed data, you should still use
>> first_flirt to re-align the image since it uses the sub-cortical mask
>> (the segmentation will be in the original MNI152 space).
>>
>> The volumes are do take into account the boundary correction for the
>> set threshold.
>>
>> Cheers,
>>
>> Brian
>>
>>
>> > Hi,
>> >
>> > I am interested in comparing the results of FIRST with manual
>> > segmentation.
>> >
>> > Is there an impediment to doing FIRST on data that has
>> > undergone: non-uniformity correction, neck cropping and 12
>> > param-affine registeration to MNI152 space? (The reason: 1)
>> > FISRT is sensitive to noise in the raw image; 2) our manual
>> > segmentation is done in standard space.)
>> >
>> > Also, would you be considering the boundary in calculation of
>> > the structure's volume?
>> >
>> > Many thanks
>> > Naj
>>
>
> =========================================================
> http://www.bic.mni.mcgill.ca/~najma
|