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Subject:

Re: Two quick questions

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 19 Jul 2004 16:22:26 +0100

Content-Type:

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text/plain (76 lines)

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
>
>
>
>
>Any information, including protected health information (PHI), transmitted
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>

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