Use the registration matrix found in $FREESURFER_HOME/average/mni152.register.dat
doug
Bruce Fischl wrote:
great, thanks Christian. I think Doug has some tools that can be used for this.
cheers Bruce On Tue, 7 Jul 2009, Christian F. Beckmann wrote:
Hi Bruce & Martina,
Yes, the easiest is to run melodic temporal concatenation on data pre- processed and warped into a common space by freesurfer. Melodic does not care about the space the data lives in - everything is reshaped into simple matrices anyways. Have a look at the melodic command line call (in the log file) to see how to call melodic with data pre-processed outside the FSL environment. Essentially you just need to create a single ASCII text file containing the N different input files (one per row) and then use
melodic -i <inputfilenames> -o <outputdir> -a concat [otheroptions]
Hope this helps cheers Christian
On 7 Jul 2009, at 12:59, Bruce Fischl wrote:
Hi Martina,
the freesurfer average subject lives in a spherical coordinate system created using nonlinear surface-based warps, so it's very far from any version of the mni. Maybe Steve or Christian can comment on integration, but certainly you would want to do the multi-subject ICA in the surface coordinate system.
cheers, Bruce
On Tue, 7 Jul 2009, Campanella Martina wrote:
Hi Freesurfer,
I've run a multi-subject analysis with MELODIC(FSL), resting-state data. Now I'd like to view the results on the Freesurfer average subject (made with make_average_subject)... But... FSL uses mni152 and Freesurfer mni305. Is it true? If so... any suggestion?
Thank you
Cheers,
Martina Campanella
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: c.beckmann@imperial.ac.uk 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: beckmann@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~beckmann
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