Hello Mark,
I attached the image to this email, and can you help me to check it?
Thanks,
Hongyu
2010/11/12 Mark Jenkinson <[log in to unmask]>:
> Hi,
>
> Sometimes it can help to take an ROI, cutting down the image FOV
> rather than masking. Plus, it can be very difficult to get good bias
> correction working on an EPI. Also, if you make the structural data
> available then we can try a couple of other techniques here and
> see if they work.
>
> All the best,
> Mark
>
>
> On 12 Nov 2010, at 17:19, Marta Moraschi wrote:
>
>> Hi Wolf,
>> first of all thank for replying me.
>> Yes, I've first tried to register the functional data (from surface coil) to
>> the whole brain and it didn't work, but I've also tried to zero parts of the
>> brain that are not present in the functional data, but it didn't work too.
>> As you have suggested, running flirt, I've used masks selecting the part of
>> functional data that did not show an intensity loss (in both cases, thus
>> using the whole brain and the 'reduced whole brain').
>> The data are oriented the same so I've also tried to use small search
>> angles.
>> I've not mentioned in my first mail but I'm working on the mean image
>> obtained when correcting data for motion (spm).
>>
>> Thanks!!!!
>> Marta
>>
>>
>>
>>
>>
>> Dr. Marta Moraschi -MARBILab -"Enrico Fermi" Center @ Fondazione Santa Lucia
>> -
>> Via Ardeatina 306 - Rome, Italy - Tel +390651501527
>> -----Messaggio originale-----
>> Da: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Per conto di
>> wolf zinke
>> Inviato: venerdì 12 novembre 2010 16.34
>> A: [log in to unmask]
>> Oggetto: Re: [FSL] surface coil data registration
>>
>> Hi,
>>
>> Do you try to register the functional data to the whole brain? Maybe it
>> helps, if you zero parts of the brain that for sure are not present in
>> the functional data (fslmaths -roi option could help). Also, it might be
>> helpful, if you use masks selecting the part of your functional data
>> that does not show a strong intensity loss (flirt -inweight and
>> -refweight options). With a rigid body registration, this might work out
>> good enough. Make sure that the data is already oriented the same, so
>> you can use small search angles. Instead of using -nosearch, I set
>> -searchrx (/y and /z) to a small range.
>> Is the functional data already corrected for motion? If so, you might
>> try the average image (fslmaths -Tmean) instead of only the first
>> volume. corratio seems to give reasonable results for me.
>> This are just a few suggestions I can make based on my experience with
>> monkey surface coil data, so maybe this could help you. I guess zeroing
>> parts of the reference volume might help quiet a bit.
>>
>> Good luck,
>> wolf
>>
>>
>>
>>
>> Marta Moraschi wrote:
>>> Dear all,
>>>
>>> I’m trying to register epi images of human visual cortex acquired with a
>> surface coil ( ftp://lab-g1.phys.uniroma1.it/pub/surfcoil.nii.gz), thus
>> suffering from large intensity variation and partial brain coverage, to T2
>> weighted images acquired with a volume coil. I've run FLIRT, but it didn't
>> work very well.
>>> I’ve tried to use FAST before, in order to get the restored epi. I’ve
>> tried to register the restored epi, using its bias field (previously max
>> intensity normalised) as input weighting volume; I’ve mainly used 6 dof and
>> normalised mutual information as cost function, but in point of fact I’ve
>> tried every combination of DOF<6 and cost function. In any case the result
>> was very far away from being good.
>>> As advised in the forum, I’ve also tried to use the Nudge Gui, thus i’ve
>> found my initial alignment and then i’ve run FLIRT with the search set
>> "Already virtually aligned (no search)" and also use a cost-function
>> weighting volume (i've tried both the intensity normalised bias field and a
>> mask set to 1 everywhere except in the areas where distortion and signal
>> loss are evident, both were previously reported in the partial epi space
>> with nudge). In particular I’ve used the suggested command line:
>>>
>>> flirt -in partial_brain -ref anatomical -dof 6 -nosearch -init
>> nudge_matrix.mat -inweight partial_brain_weighting_volume -out partial2anat
>> -omat partial2anat.mat
>>>
>>> However, running flirt I’ve noticed a worsening of the alignment i've
>> reached before with the Nudge gui.
>>>
>>> I would appreciate any advice. Many thanks in advance.
>>>
>>> Marta
>>>
>>
>
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