Hi, Paul-

Thanks for the reply. That was a long post by me, I agree. Sorry about that :)

Q2: I had noticed the ~mm thing but I love these little tidbits about AFNI :) I think I agree with you that enorm does the job that it's supposed to be doing.

Q3: Partial volume effect was a concern for me as well, especially with this resolution. So, I am eroding the WM mask by -2 (3dmask_tool). I have attached a picture of this eroded WM mask with this message. There is not too much left, and perhaps it's an overkill with -2. Please let me know what you think. With this in mind, what do you think should be a reasonable radius for ANATICOR?

Q1: I am sorry I didn't explain it very well. There is a lot going on in those two figures. I will try to explain it a bit more. In the first figure with the matrices, column labeled ANATICOR represents the functional connectome (FC) when the data is processed with "just" ANATICOR. First, row is the FC while the second row is just the distribution of the correlation values in that FC. Now, the third column labeled wmpca3 for instance, corresponds to the pipeline where after ANATICOR, first 3 principal components of the WM signal are regressed out of the BOLD time-series before computing the connectome.

As for the second figure with the scatter plots, let's take the scatter plot in the 3rd column in the first row. It shows a scatter plot between correlation values of the FCs corresponding to the "just ANATICOR" pipeline vs the pipeline where after ANATICOR, first 5 principal components of the WM signal were also regressed out of the BOLD time-series.

DoF is definitely a concern. I am doing bandpass filtering using 3dTproject at the same time when I do all regressing out. The QC script does not detect the degrees related to bandpassing in this fashion. So, I have 320 time-points total (TR = 2.2 sec) and the QC script mostly shows that I am left with DoFs anywhere between 200-270 (approximately), after censoring and everything else. But, since I am also doing bandpass (0.01-0.1), I am actually loosing a lot more DoFs.

The main reason why I am doing bandpass filtering is to take care of the physiological noise (I don't have any physiological recordings) and so the reviewers won't hackle me :) Can you please give me a solid defense against this line of potential criticism against a reviewer? If yes, I would be happy to drop the bandpass filtering because I don't like this step much either, due to the fact that it costs so much DoF loss.

Thanks again for all your help!

Kausar