Dear Jean-Sebastien,
If the brain extraction is proving very difficult then you can try and
run the registration without brain extraction. We normally recommend
it for healthy brains as it makes things a bit more robust, but there is
no reason you have to use it for the registration. Therefore I would
try without brain extraction and see if this helps.
All the best,
Mark
On 3 Apr 2012, at 16:26, JSP wrote:
> Dear Dr. Jenkinson,
>
> Thank you very much for your input.
> I think I have a greater issue with the brain extraction process than the
> registration itself at this stage. When I launch BET, I put FA=0.25 to make
> sure that I get the most brain possible. However, BET doesn't seem to
> consider the extensive lesion as part of the brain, so there is a big chunk
> of the brain missing (like a shark bite) corresponding to the area of the
> lesion. I was told to put a mask on my lesion, but I am afraid that I need
> some guidance regarding the next step.
>
> Again, thank you very much for your help,
>
> Jean-Sebastien
>
> Le 4/3/12 8:20 AM, « Mark Jenkinson » <[log in to unmask]> a écrit :
>
>> Dear Jean-Sebastien,
>>
>> It is difficult to know might be going wrong without knowing more.
>> A complete failure, with very wrong orientation, is not uncommon when things
>> go wrong. However, something with the right "orientation" but poor
>> registration
>> is really no better and you should not use either.
>>
>> It is probably best to use the brain extracted version if you have this and
>> the
>> brain extraction is good. In that case I would try the following options with
>> FLIRT
>> (in various combinations):
>> -usesqform
>> -nosearch (you may already by using this)
>> -cost mutualinfo
>>
>> If none of these (or combinations of these) help then let us know.
>>
>> All the best,
>> Mark
>>
>>
>>
>>
>> On 2 Apr 2012, at 17:38, Jean-Sebastien Provost wrote:
>>
>>> Dear FSL experts,
>>>
>>> Like many, I'm trying to register into the standard space scans with
>>> extensive lesions. So far, I have followed the instructions that was
>>> previous given in another email, and they have been working well. Basically,
>>> I have created a mask by manually drawing a ROI over the stroke area,
>>> inverted the mask with the following command "fslmaths originalmask -mul -1
>>> -add 1 -thr 0.5 -bin invertedmask", and registered using FLIRT and putting my
>>> inverted mask into the weighting option as an input.
>>>
>>> Like I said, it has been working well for 2 subjects, but didn't for 2
>>> others. In the latter case, when I look at the data in FSLview, the image is
>>> no longer aligned: it has suffered a severe rotation making the axial view
>>> now the coronal view with a 90 degree rotation, and so on for the other
>>> views.
>>> Now, I also tried to do the registration with a betted anatomical scan. Here
>>> the orientation is fine, but the registration itself doesn't look good.
>>>
>>> Any suggestions would be useful.
>>>
>>> Thank you in advance,
>>> Kindest regards,
>>>
>>> Jean-Sebastien
>>>
>
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