Hi Arun.
> I am running mcflirt from the shell for motion correction. I had been
> expecting an html report, but I do not see that in the options to the
> command. I guess I had been expecting a report similar to the one
> produced by doing the co-registration (such as between 2 MRIs) through
> the FEAT GUI. Are the html reports something available only through the
> GUIs?
You are nearly right. The web page report for the motion correction is
created by the main FEAT script. (This can get run without the GUI once
you have created a design.fsf file, but you wouldn't normally have a
reason to do this). The mcflirt binary does not produce the web page
report.
> I get the motion correction matrices in a subdirectory and a file
> outputfilename.mat which has the transformation parameters.
> How does not input this data into the stats analysis - as regressors of
> no interest ? In addition, does FEAT convert these matrices to total
> displacement distance ?
The best way to find out how FEAT gets the different outputs from mcflirt
is to do a FEAT run and then look in the report.com file to see the
mcflirt command-line call. For more information look in fsl/tcl/feat.tcl
and search for the mcflirt call.
If you want to take the motion parameters and put them into FEAT as EVs
(ie custom 1 format) then go to an existing FEAT directory and type
mccutup .
and you will find the parameter files as mc*.par inside the mc
subdirectory.
Regards, Steve.
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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