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What is "FA" data? ----- Original Message ----- From: "Erik-Jan Vlieger" <[log in to unmask]> To: <[log in to unmask]> Sent: Friday, November 01, 2002 1:00 AM Subject: Re: FEAToutput, ANALYZE hdr and HRF parameters. > > > Hi - yes, you can easily turn the grand-mean scaling off by editing > > > fsl/tcl/feat.tcl and commenting-out/deleting the line > > > set thecommand "$thecommand -I $global_mean" > > > I'm not sure why you would want to turn this off though? > > We are analyzing DTI images with Feat (I know what to do with the design > > matrix and the issues on pre-whitening to make it valid), and I would like > > to see the original FA values. > I would be interested in doing the same. Could you send me a set of > instructions on how to analyze FA data? Certainly. I would love to get some comments on this design! In the following design, you look for areas for which patients have higher gray-values than controls. If you want to look for areas with lower gray-values, in step (2), put the controls at the front, the patients at the end, and correct for this when specifying the model. 1) Perform spatial normalizing on all the FA scans of alle the subjects (I use flirt for this, with the MNI templates. First I BET a 3D T1W scan, then register the B0 image to the betted 3D scan. The betted 3D scan is registered to the template. After that the combined transformation is applied to the FA image). 2) Merge these normalized scans into a 4D data-set (avwmerge), e.g. 30 controls and 32 patients. Put the controls at the beginning. 3) Use Feat for the analysis: Data: Set the TR to 1.0 Pre-Stats: No slice time correction No motion correction No BET Quite some smoothing (I would not know an optimum) No intensity normalization (FA are absolute values!) No temporal filtering Stats: No film prewhitening Full Model setup: Skip : 0 Off: 30 (controls) On: 32 (patients) Convolution: none NO temporal filtering NO temporal derivative Post-stats: whatever you want Registration: turn it all off (you already did this). GO! Erik-Jan