You just have to do two separate steps with FLIRT.
In the first you take two 3D images and determine the registration
that maps one onto another and save the transformation matrix.
In the second step to take the matrix from above and use the
-applyxfm flag to transform your 4D data (-in) to the space of
the reference (-ref), which will be the MNI152 image if you are
transforming to standard space.
In the first step you should extract a typical 3D image from your
4D image series to act as the input image. If you have done
motion correction (which is a good idea) then whatever image
was the reference for the motion correction should be used as
the input image in the first step (with the reference image for
the first step being the MNI152 image again).
All the best,
On 10 Aug 2009, at 15:33, Elisa Molinari wrote:
> I probably found the problem.
> In registration step I trasformed my 4D data in 3D...
> Therefore I change my question. How can I apply the FLIRT
> trasformation to my 4D data saving the correct size? I'm trying to
> use applyxfm4D... but I've some problem...
> Elisa wrote:
>> Hi all,
>> this is my first time in your mailing list.
>> I used FSL to register my fmri data (at rest) to MNI152 and now i'd
>> like to
>> make a group analysis with melodic by-passing all pre-processing and
>> registration steps.
>> I tried to follow your suggestions (I red in this mailing list) and
>> melodic without GUI specified the file list and concat as approach
>> decomposition but it doesn't work:
>> melodic -i restfiles.txt -v --report -o groupICA -a concat --tr=0.7
>> Melodic Version 3.09
>> Melodic results will be in groupICA
>> Create mask ... done
>> Reading data file ../FLIRT/
>> flirted_PREMOT_31_rest_mcf_to_MNI152 ... done
>> Estimating data smoothness ... done Removing mean image ... done
>> ERROR:: too many components selected
>> Do you have any suggestions?
>> Thanks a lot,
> Elisa Molinari, PhD Robotics Brain & Cognitive Science Dept.
> Italian Institute of Technology Via Morego, 30 - 16163 Genova, Italy
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> phone +39 010 71781479 fax +39 010 7170817