Hello!

I'm using 3dTProject and I have some questions after looking at the output from this command:

3dTproject -input bold_orig.nii.gz -polort 1 -prefix bold_project.nii.gz

1. the time-series plots look identical between bold_orig and bold_project but the two images look very different. bold_orig looks like a standard bold image whereas bold_project is more like a homogeneous image of gray voxels. I cannot really identify brain structures in bold_project anymore but maybe that's how the output is supposed to look like? I know 3dTProject appears to center the data around zero, so maybe that explains it. Are there any example output images from 3dTProject I can compare mine with?

2. What do you recommend the mask to be? At the moment I'm using a whole-brain mask, but I'm wondering if it's better to include only gray matter, would that be more sensible?

3. I'm not sure if I should use the option blur option, especially if a whole-brain mask is given, because white matter voxels will be blurred with gray matter voxels, right? What about the norm option? Is that recommended?

Thank you!
Sam