Hi All,
After running ICA Aroma and regressing out CSF and white matter, I applied a bandpass filter using the following command:
fslmaths $OUTPUT/denoise_residual_nocsfwm.nii.gz -bptf 25.0 -1 -add $ICADIR/timeMean.nii.gz $ICADIR/final_denoised_func_data.nii.gz
This worked for most of my 150+ runs; however, about 15 of them failed. When I viewed these output files in fslview they just showed an empty grey box. The denoise_residual_nocsfwm.nii.gz and timeMean.nii.gz files appear to be fine, so I'm not sure where this is going wrong. I also tried running this directly from the command line for one participant (rather than as a batch script), but that still did not work. Any suggestions would be appreciated!
Thanks,
Rachel
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