Thanks very much that's very helpful; I hadn't thought of the problem of
signal loss.
Best wishes
Tom
Hi Tom,
>
> I'm afraid I don't know the details of SPM well enough to comment on the
> first issue. Does anyone else?
>
> If you can see the filtered model time courses from SPM then you can
> compare these to the filtered time courses that are shown in the FEAT
> design matrix, which should give you some idea of whether there is a
> substantial difference or not.
>
> As for the registration problem, we recommend that people take fieldmaps
> and undistort their EPI data using prelude and fugue. However, if you do
> not have fieldmaps then I would still not advise 12 dof as it will tend to
> incorrectly stretch the brain to fill in the "gaps" in the EPI that
> occur due to
> signal loss. So in this case the best thing to do is to use cost function
> weighting and draw (or derive by some other means) a volume which has
> zero in the areas where there is bad signal loss or distortion (a large
> blob
> around the inferior frontal and temporal areas normally does the trick)
> and has one in all other areas (including the background). Then if you
> register using this volume as a cost function weight and stick with
> 6 dof (or 7 dof if you mistrust the precise volumetric calibration on the
> scanner - which is sensible if the structural was not acquired in the same
> session) the registration should be improved. If this is the case then
> you
> will need to do this registration manually and generate the appropriate
> matrices to be put in the "reg" subdirectory of the ".feat" directory
> in order for feat to work correctly for higher level analyses.
>
> Hope this at least answers your second question.
> All the best,
> Mark
>
>
> Tom Cullen wrote:
>
>>Hi there,
>>
>>I'd be grateful for your help on two points:
>>
>> The equivalence of high pass filters in FSL and SPM
>> I have analysed a block design experiment using FSL which has
>> also been
>>analysed by a colleague using SPM; we obtained quite different results.
>>One reason may be the length of the high pass-filter. In FSL we have set
>>this to 60 (twice the block length) and accepted the default given by SPM
>>which is 128. What would a high pass filter cutoff of 60 in FSL
>>correspond to in SPM? and vice versa what is the FSL equivalent of the
>>SPM setting of 128?
>>
>> The appropriate degrees of freedom when registering warped EPI
>> data to the
>> high-res.
>> We have registered each subjects functional EPIs to their high
>> res scan
>>using Flirt set to 7 degrees of freedom. However, the EPIs and the high
>>res from each subject are different shapes because there is quite a lot
>>of warping--we are scanning at 3T. Would it make sense to use a transform
>>with 12 degrees of freedom?
>>
>>Thanks very much,
>>
>>Best wishes,
>>
>>Tom
>>
>>
>>
>>
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>
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