You could use the structural image as source, but you'd need to re-run
the segmentation in order to do the spatial normalisation (because the
previous *_seg_sn.mat will no longer work for that image because it
has been moved by the coregistration).
Best regards,
-John
On 11 November 2010 09:46, Brian Murphy <[log in to unmask]> wrote:
> Thanks John, that worked perfectly. Just one further question - you suggest
> that after deskulling I coregister ...
>>
>> the functional data to the output of ImCalc.
>> This would be done by having the ImCalc result as "reference", one of
>> the fMRI scans as the "source", and all the others as "other".
>
> ... and use the resulting ***_seg_sn.mat for subsequent MNI normalisation.
>
> Isn't it usually more straightforward to use the structural image as source
> (in this case the ImCalc result as dependency), and a representative
> functional image as reference (here the mean realigned one)? Then I can put
> the original unskulled structural image as "other".
>
> best,
>
> Brian
>>
>> sJohn Ashburner wrote:
>> Sometimes there is a bit too much extra information in the anatomical
>> scans, which can confuse the (normalised) mutual information
>> coregistration. Here is a recycled response (
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0906&L=SPM&P=R49092
>> ), which may help.
>>
>> Probably the easiest fix for this would be to use the Segment button
>> (maybe the New Segment of SPM8) to generate native space tissue class
>> images of GM, WM and CSF, as well as a bias corrected version of your
>> anatomical scan. The c1, c2 and c3 images could be used to skull strip
>> the bias corrected anatomical scan, which should give you an image that
>> coregisters rather better.
>>
>> The skull stripping bit can be done using ImCalc, where you would select
>> the m***.img, c1***.img, c2***.img and c3***.img. The expression to
>> evaluate would then be i1.*((i2+i3+i4)>0.5) .
>>
>> If you plan to use the ***_seg_sn.mat file for spatially normalising,
>> then you should coregister the functional data to the output of ImCalc.
>> This would be done by having the ImCalc result as "reference", one of
>> the fMRI scans as the "source", and all the others as "other".
>>
>> Best regards,
>> -John
>>
>>
>> On 8 November 2010 09:48, Brian Murphy <[log in to unmask]> wrote:
>>
>>>
>>> Hi,
>>>
>>> I have one participant session that will not coregister for me correctly.
>>> I
>>> am using the same preprocessing procedure as worked well on two previous
>>> participants, so I don't think there is an error in the script.
>>>
>>> The result I am getting is that the structural image is rolled a little
>>> to
>>> the left (~0.05 rad), pitched forward (~.1-.2 rad) and displaced
>>> downwards.
>>> Functional realignment is working fine, and I am using the resulting mean
>>> image as the reference.
>>>
>>> The things I have tried so far are to make the tolerances smaller, to
>>> move
>>> the origin in the structural image on to the AC (using the Display
>>> function), to approximately align the functional and structural images by
>>> hand (with Check Reg), and combinations of these. But always when I
>>> re-run
>>> coregistration I get the same result.
>>>
>>> I guess it might have something to do with my functional scanning
>>> parameters
>>> - I'm scanning broad coverage of cortex (just missing a bit of motor and
>>> temporal) on a short TR (1s) and coarse resolution (3x3x5mm). Is it
>>> generally difficult to get such low resolution, low contrast images to
>>> coregister correctly?
>>>
>>> (BTW on this third participant, I'm using dummy scans. On the previous
>>> two
>>> that coregistered well, I did record the initial high-contrast scans.
>>> Since
>>> I am using the mean of ~400 functional images as reference, I guess those
>>> few initial scans shouldn't make a difference, but I thought I should
>>> mention it just in case).
>>>
>>> Of course I can simply coregister this participant by hand, but it would
>>> be
>>> more satisfying to understand why it is going awry. Any suggestions?
>>>
>>> thanks,
>>>
>>> Brian
>>>
>>>
>>> --
>>> Brian Murphy
>>> Post-Doctoral Researcher
>>> Language, Interaction and Computation Lab
>>> Centre for Mind/Brain Sciences
>>> University of Trento
>>> http://clic.cimec.unitn.it/brian/
>>>
>>>
>
>
> --
> Brian Murphy
> Post-Doctoral Researcher
> Language, Interaction and Computation Lab
> Centre for Mind/Brain Sciences
> University of Trento
> http://clic.cimec.unitn.it/brian/
>
>
|