Hi Eugene, Thank you for your response and your time. I added –f to my command: featregapply 003A_PP.feat -f -s ../003A_fullPPICA.ica/3_denoised_data.nii.gz -r 3 –e Which gave me this in my terminal window: /bin/rm -rf reg_standard /usr/local/fsl/bin/applywarp --ref=reg/standard --in=example_func --out=frgrot_0HzLAq --warp=reg/highres2standard_warp --premat=reg/example_func2highres.mat --interp=spline /usr/local/fsl/bin/applywarp --ref=reg/standard --in=mean_func --out=frgrot_3pMDm1 --warp=reg/highres2standard_warp --premat=reg/example_func2highres.mat --interp=spline /usr/local/fsl/bin/applywarp --ref=reg/standard --in=mask --out=frgrot_j2DUJF --warp=reg/highres2standard_warp --premat=reg/example_func2highres.mat --interp=nn And now I have a modified regstandard folder and a report log.html in my feat directory. Any tips? My rsfmri data seems to be unchanged. Noelle Dalin From: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Eugene Duff <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Date: Wednesday, August 31, 2016 at 2:56 PM To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: Re: [FSL] Voxel and Dimension Change after using Featregapply on Functional Connectivity data Hi Noelle - I'm not sure, but did you try -f option to force featregapply to rerun? Eugene On 31 August 2016 at 22:10, Noelle Dalin <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hello All, After I am done with my preprocessing (including Motion scrubbing and manual denoising) and single session ICA, I am trying to put my functional connectivity data into standard space before proceeding to command line Group Level ICA (melodic). After this, however, I am still having an issue with convergence when running group level ICA. I have noticed that my voxels and dimensions change when I put my functional connectivity data into standard space using this command: featregapply 003A_PP.feat -s ../003A_fullPPICA.ica/3_denoised_data -r 3 –e My input functional connectivity data has 96 x 96 x 54 voxels and dimensions of 3 x 3 x 3.00003 mm where as my output has 91 x 109 x 91 and dimensions of 2 x 2 x 2 mm. I have tried using both 2 and 3 for resolution(-r) with the same outcome. The output also looks streaky around the edges. Any tips or suggestions? Thank you for your time. Noelle Dalin