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Hi Shirin, Assuming that you have used FEAT for your preprocessing (and used conventional options for registration), you should be able to do this: 1. Invert the functional->standard warp file, so it can be used to transform images from standard space to fMRI space: invwarp -w my_analysis.feat/reg/example_func2standard_warp -r my_analysis.feat/reg/example_func -o my_analysis.feat/reg/standard2example_func_warp 2. Apply that warp file to your mask image: applywarp -i my_mask -r my_analysis.feat/reg/example_func -w my_analysis.feat/reg/standard2example_func_warp -o my_mask_fmri Cheers, Paul On 2 July 2018 at 15:04, Shirin Davies <[log in to unmask]> wrote: > Hi, > > Can anyone tell me how to reorient my standard space binary mask to that > of my 4D fMRI data space so that I can use the mask in pre-thresholding > step? > > Many thanks, > > Shirin Davies > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1