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From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Stephen Smith [[log in to unmask]]
Sent: Wednesday, March 20, 2013 11:51 AM
To: [log in to unmask]
Subject: Re: [FSL] how to input motion parameters in glm

Hi - the motion confounds should be expanded from the 6 affine parameters to the extended set of regressors, and highpass filtered to match what you did to the data - see the attached matlab snippet for help on that.

Then you can use fsl_glm and get the residuals from that to get the motion-cleaned data.

Cheers.




On 19 Mar 2013, at 13:51, Helen Sawaya wrote:

Dear experts,
 
Although I found many posts discussing motion regressors, I still don't understand how to input them in a design matrix. I ran mcflirt on a participant and therefore have a .par file with the rotation and translation parameters in 6 columns. How do I enter this file (with 400 volumes) in a GLM? I have a resting state fMRI design so I don't have any EVs/conditions to include? I tried running fsl_glm with the .par file as the design matrix but I'm obviously doing something wrong.
Please do advise
Thank you!!
Helen


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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR 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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