Hi,
FIRST and mfast both give the segmentations in the native image
space. FIRST applies the inverse im1_to_std_sub.mat to the shape
models to transform the models into native space.
By "mask that to the mfast output", can you be a little more precise.
Also, what structures are you looking at ? Have you observed and area
where FIRST is not performing well, such that it may require the mask?
Cheers,
Brian
On 19 Feb 2008, at 11:55, Diana Tordesillas Gutiérrez wrote:
> Brian,
>
> Thank you for the fast reply.
>
> What do you think of the following pipeline:
>
> - $first_flirt on T1
> - $run_first on T1
> -Apply the inverse im1_to_std_sub.mat to the output_image and mask
> that to
> the mfast output. Then use fslmaths to extract volume
> values....would that
> give a better registration and segmentation or that's an incorrect
> pipeline?
>
> Diana
>
>
>
> -------------------------------------------------
>
> Brian Patenaude dijo:
>> Hi,
>>
>> There is no direct means of incorporating other modalities into
>> FIRST. The training data
>> for the model only had the T1-weighted images and thus first expects
>> T1 contrast. One simple use of another contrast, could be to use it
>> for the boundary correction (provided that it was less noisy and
>> better contrast).
>>
>> Cheers,
>>
>> Brian
>>
>>
>> On 18 Feb 2008, at 12:07, Diana Tordesillas wrote:
>>
>>> Dear FSL users,
>>>
>>> I’ve just learned successfully how to run FIRST on my subjects
>>> using the T1
>>> images, but since I also have T2 and PD images I wonder if I would
>>> have
>>> better results if I use all information I have.
>>>
>>> I would like to know if it’s possible to use the segmented image
>>> (mfast
>>> output) as im1 input in first_flirt and further analysis or there
>>> is a
>>> better way to introduce that information in FIRST.
>>>
>>> Thanks in advance,
>>>
>>> Diana
>>>
>>
>
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