Hi,

The subcortical mask is at
${FSLDIR}/data/standard/MNI152lin_T1_1mm_subbr_mask . Though the FLIRT GUI
shouldn't solve the problem. If the first stage is fixed then the second
should have no problem.
The first_flirt script allows for you to either specify a mask for the
input image or to input a betted image, if neither of these work then you
may have to edit the first_flirt script (or pre-process the image).

Cheers,

Brian

>
>  Hi Brain,
>
> It seems like that I can run the two stage registrations if where the
> subcortical mask, which is being used during the second registration,
> is.
>
> Would you let me know where it is?
>
> Thank you,
>
> Buyean
>
>
>
>
>
>
>
> -----Original Message-----
> From: Brian Patenaude <[log in to unmask]>
> To: [log in to unmask]
> Sent: Mon, 10 Sep 2007 11:56 am
> Subject: Re: [FSL] Correction: [FSL] FIRST failed to segment a T1 MRI
>
>
>
>
>
>
>
>
>
>
> Hi,
>
> Is there a much neck in the image? If so, this is probably the reason
> for the failure at the first stage. If this is the case you have 2
> options:
>
> 1) Crop the image. If you use this option you must input the cropped
> image into run_first.
>
> 2) To create a mask omitting the lower portion of the image containing
> neck (i.e. zero for neck region and 1 elsewhere ). Then use the
> -inweight option in first_flirt, this will apply weighting mask to the
> input image such that the region where the mask is 0 will not contribute
> to the cost function. In this case run_first still takes in the
> uncropped image.
>
> Hope this helps,
>
> Cheers,
>
> Brian
>
>
>>
>>  Hi,
>>
>> The registered MRI image after first stage registration is not
>> correctly registered to the standard. After second stage registration,
>> the MRI is distorted, cut, and zoomed. Since the MRI is not registered
>> at all, all structures fail; all structures are located in wrong
>> place.
>>
>> I am wondering if I can run these two step registrations (only the
>> 'first_flirt') step by step using the GUI FLIRT. It looks like the
>> advanced option in FLIRT helps register this specific T1 MRI to the
>> standard (the first stage registration).
>>
>> Thank you,
>>
>> Buyean
>>
>>
>>
>>
>>
>>
>>
>>
>> -----Original Message-----
>> From: Brian Patenaude <[log in to unmask]>
>> To: [log in to unmask]
>> Sent: Mon, 10 Sep 2007 7:33 am
>> Subject: Re: [FSL] Correction: [FSL] FIRST failed to segment a T1 MRI
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi,
>>
>> The registered image, how well do the subcortical structures align? Is
>> it visible where the registration does not match up? Also, do all the
>> structures fail? When it fails are segementations was off or do they
>> mostly overlap except the boundaries are clearly not well aligned?
>>
>> Cheers,
>>
>> Brian
>>
>> P.S. The is no GUI version for the first_flirt script.
>>
>>
>>>
>>>
>>>
>>>
>>>
>>> Dear FSL users,
>>>
>>>
>>>
>>> I have very limited experience in FSL and have been trying out FIRST
>>> to generate the ROIs for my PET image analysis.
>>> FIRST did good job in segmenting the subcortical regions (20 T1 MRIs
>>> out of 21 T1 MRIs).
>>> But, it failed to segment the regions in one T1 MRI.
>>>
>>> When I ran 'first_flirst' with -d option, the image after the first
>>> stage looks OK, but it is not right; the image was not registered to
>>> the standard. The image after the second stage is not a mess.
>>>
>>> I will appreciate any suggestions to run 'first_flirt' successfully
>>> with this T1 image.
>>>
>>> Is there any way to run 'first_flirt' using GUI version FLIRT?
>>>
>>>
>>> Thank you,
>>>
>>> Buyean
>>>
>>>
>>>
>>>
>>>
>>>
>>> ________________________________________________________________________
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>>
>>
>>
>>
>>
>>
>> ________________________________________________________________________
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>
>
>
>
>
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