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Hi John,

You can use the FEAT gui to configure and run your preprocssing requirements (temporal filtering, spatial smoothing, registration, etc). When FEAT completes, the preprocessed 4D FMRI data, in the subject's native space, can be found in your .feat directory, and is calld 'filtered_func_data.nii.gz'.

You can transform this file to MNI152 space with the applywarp command (assuming that you have used non-linear registration):

applywarp -i filtered_func_data.nii.gz -r $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz -o ffds.nii.gz -w reg/example_func2standard_warp.nii.gz

Cheers,

Paul

On 3 May 2015 at 15:03, John Sheppard <[log in to unmask]> wrote:
Hi all,

I have a question about working with the original EPI functional time series in FSL. I am hoping to extract the raw BOLD signal from some ROIs, but rather than working with the original functional data, I'd like to extract the filtered functional data that has been temporally filtered (high pass filter with 90 s cutoff?) and spatially smoothed (Gaussian FWHM = 5 or 6 mm) in FEAT. Also, I'd like to extract functional data that has been transformed/registered into standard (ICBM142) space, rather than the original subject space.

Is it possible to do this in FSL? I'm not sure if FEAT generates a version of the filtered functional data transformed into standard space by default, but perhaps there are commands that can do this.

Thank you!

John Sheppard