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Thank you for your email. When I type invwrap into my terminal, it is not recognized. Please can you tell me how I can use this command? With thanks, Shirin On Tue, Jul 3, 2018 at 12:12 PM, paul mccarthy <[log in to unmask]> wrote: > Hi Shirin, > > You need to transform your pre-threshold mask into the subject's native > fMRI space, so you would carry out this transformation after registration, > and before statistics. > > So you could do this: > > 1. Run preprocessing using FEAT (choose "Preprocessing" from the > upper-rigth drop down box) > 2. Invert the functional->standard warp, and transform your mask into > functional space > 3. Run your stats using FEAT (choose "Statistics" from the upper-right > drop down box) > > Cheers, > > Paul > > On 3 July 2018 at 08:56, Shirin Davies <[log in to unmask]> wrote: > >> Hi Paul, >> >> Thank you for your email. At what stage do I carry out the transformation >> you have mentioned. >> >> Using FEAT, Im setting everything up for a first level full analysis >> including the nifti binarized standard space mask before pressing Go to run >> it all. >> >> With thanks, >> Shirin >> >> On Mon, Jul 2, 2018 at 3:47 PM, paul mccarthy <[log in to unmask]> >> wrote: >> >>> 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/standard2 >>> example_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 >>> >> >> >> >> -- >> Shirin Davies, MSci, MSc MedPhys >> MRI Scientist, >> BRAIN Unit, >> >> Cardiff University Brain Research and Imaging Center & >> Cardiff and Vale University Health Board >> >> ------------------------------ >> >> 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 > -- Shirin Davies, MSci, MSc MedPhys MRI Scientist, BRAIN Unit, Cardiff University Brain Research and Imaging Center & Cardiff and Vale University Health Board ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1