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FSL  February 2008

FSL February 2008

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Subject:

Re: mfast and FIRST

From:

Brian Patenaude <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 19 Feb 2008 13:37:41 +0000

Content-Type:

text/plain

Parts/Attachments:

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text/plain (105 lines)

Hi,

What area of the hippocampus is most problematic? Is there typically  
large atrophy? or are they relatively normal?

Cheers,

Brian



On 19 Feb 2008, at 13:42, Diana Tordesillas Gutiérrez wrote:

> Hi,
>
> I'm mainly interested in hippocampus. FIRST results are ok, but I  
> thought
> I could improve those results using the other contrasts I already  
> have,
> that's where FAST came in. I was wondering if mfast segmentation would
> perform better than FIRST's since you can add more channels.
>
> Thank you ,
>
> Diana
>
>
> Brian Patenaude dijo:
>> 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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