Hi Andreas
before feeding these subject-specific maps into melodic you would need
to register them into a common space. The output of the 2nd level
melodic is in that very space. If you have not co-registered all maps
prior to the higher-level maps then I would assume that results are
virtually uninterpretable. The easiest is to use the first-level
registration information (in example_func2standard.mat) and use this
to move your individual maps into standard space
flirt -in mapX -out mapX_hr -ref ${FSLDIR}/data/standard/MNI152T1_2mm -
applyxfm -init example_func2standard.mat
These files should be different for every subject, i.e. this needs to
be done separately for each subject and each map you intend to feed
into the higher-level run
After all the maps have been transformed simply proceed like before,
by concatenating these maps and running melodic. The output maps will
then already be in standard space, so no additional transformation is
required. In case your machine can;t handle the higher-level melodic
run on maps at 2mm isotropic resolution, you can downsample by
replacing the last two options with
-applyisoxfm 4 -init example_func2standard.mat
This will then move the maps into MNI space but at 4mm isotropic
resolution. In order to overlap the final outputs you either need to
resample into 2mm again or downsample the MNI152 to 4mm.
Hope this helps
Christian
On 16 Mar 2009, at 12:28, Andreas Pedroni wrote:
> Dear List
>
> We performed single subject ICA analysis on 23 subjects, then sorted
> IC maps of each subject acording to "task-relatedness" of the
> timecourse. In a second step "task related" IC maps went into another
> ICA using command line melodic (variance normalization = off) ,
> resulting in a new set of task related ICs. So far so good.
> But now, we are not able to overlay the "2ndlevel" IC-maps on a
> structural image (e.g. mni-template) to identify anatomical
> structures. We also tried to co-register these images in various
> ways, but never ended with a reasonable result.
>
> Does anyone have an idea how to co-register IC-maps to a structural
> image without having "filtered_func_data"- file as input?
>
> Cheers
>
> Andreas
_______________________________________________
Christian F. Beckmann, DPhil
Senior Lecturer, Clinical Neuroscience Department
Division of Neuroscience and Mental Health
Imperial College London, Hammersmith Campus
Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK
Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548
Email: [log in to unmask]
http://www.imperial.ac.uk/medicine/people/c.beckmann/
Senior Research Fellow, FMRIB Centre
University of Oxford
JR Hospital - Oxford OX3 9DU
Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717
Email: [log in to unmask]
http://www.fmrib.ox.ac.uk/~beckmann
