Hi,
It normally doesn't make a lot of difference if you brain extract the
functional or not (as there is normally fat suppression turned on
which means that not much non-brain signal is there anyway).
If your brain extraction results on the functional are good then go
with it, otherwise don't do it. Out of interest, all of this is handled
by the FEAT GUI, so you could just use that and not worry too much
about all of these details that we've already gone through.
All the best,
Mark
On 24 Aug 2011, at 01:14, Benjamin Kay wrote:
> On Tuesday, August 23, 2011 20:08:48 you wrote:
>> On 23 Aug 2011, at 20:55, Benjamin Kay wrote:
>>> I'd been considering doing something like this:
>>>
>>> mkdir func func-brain
>>> fsl4.1-fslsplit func.nii.gz run/func- -t
>>> for FILE in func/*; do fsl4.1-bet "${FILE}" "run-brain/${FILE##*/}"; done
>>> fsl4.1-fslmerge -t func-brain.nii.gz func-brain/*
>>> fsl4.1-mcflirt -in func-brain.nii.gz -out func-brain-mcf.nii.gz
>>>
>>> However it's been mentioned twice before on this mailing list (by Steve
>>> Smith) that one should not perform brain extraction before invoking
>>> mcflirt.
>>>
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;1f232570.05
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;9b7f3193.0906
>>>
>>> On the other hand, the FAQ recommends doing brain extraction on both
>>> volumes before running flirt.
>>>
>>> http://www.fmrib.ox.ac.uk/fslfaq/#title_flirt
>>>
>>> Given that flirt and mcflirt are ostensibly both doing linear
>>> registration, why is brain extraction helpful to one but harmful to the
>>> other?
>>
>> Dear Benjamin,
>>
>> As the resolution and contrast are worse in functional images
>> by comparison with structural images then two things happen:
>> (a) the brain extraction is less accurate; and (b) the registration
>> is more influenced by any errors in the brain extraction. As a
>> consequence mcflirt, as run on functional images, works much
>> better without brain extraction. By comparison, normal T1-weighted
>> high-resolution images benefit from brain extraction as it often
>> removes large portions of neck (also rarely imaged in functionals)
>> that improve the robustness of anatomical registration (with flirt)
>> without sacrificing accuracy, since the features within the brain
>> are strong enough to make the registration insensitive to small
>> errors in the brain extraction.
>>
>> So please don't run brain extraction on your functionals prior to
>> using mcflirt.
>>
>> All the best,
>> Mark
> Dear Mark,
>
> Thank you for clarifying this! I take it that although I should not run bet on
> my functional data before using mcflirt, it wouldn't hurt to run bet on a
> reference or meaned functional volume before using flirt to register it to a
> high-resolution T1 anatomical (also brain-extracted).
>
> Benjamin
>
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