Thank you, Alfonso! It turned out that our masks and functional data were in different spaces. Aligning them resolved part of the issue, but we were still encountering the "Mean functional file not found" error. I was able to fix that by selecting "First functional volume as reference" during segmentation in preprocessing, as suggested in your reply from this post: https://www.nitrc.org/forum/message.php?msg_id=36463.

After applying these two fixes, the denoising process seems to be working, but the aCompCor variables still appear as "White Matter (1P)" and "CSF (1P)," as shown in the attached screenshots. Additionally, changing the confound dimensions from 5 to 10 doesn’t seem to have any effect. Could this be an issue if the data appears to be reasonably well denoised? If so, what would you recommend to address it?

I also had two additional questions:

1) Would it be advisbale to try to try to get the meanusub-XXX...nii file from FSL preprocessing rather than using the first functional volume as reference, since there may be a chance that the first image could be an outlier?

2) We are using a symmetric atlas for normalization in our analysis and in the CONN denoising preview, the whole brain doesn't seem to be covered. I changed the background reference atlas in the GUI to the same symmetric atlas we used for normalization and redid the steps, but the issue still persists. I also did another trial run where I updated both the background reference and the anatomical atlas in the gui and got the same reults. I also get the following error message as well. Is there any way to fix this?

"Array indices must be positive integers or logical values.

Error in conn_menu>conn_menubuttonmtnfcn (line 1343)
                            txt0=CONN_gui.refs.rois.labels{CONN_gui.refs.rois.labelsidx(v)};

Error in conn_menu>@(varargin)conn_menubuttonmtnfcn('volume',CONN_h.screen.hfig,h.h1,h.h2,h.h6a,h.h2c,varargin{:}) (line 351)
        conn_menumanager('onregion',h.h6a,1,position,h.h2,@(varargin)conn_menubuttonmtnfcn('volume',CONN_h.screen.hfig,h.h1,h.h2,h.h6a,h.h2c,varargin{:}));

Error in conn_menumanager>conn_menumanager_mousemove (line 745)
if nargin>0, feval(varargin{:}); end

Error in conn_menumanager (line 262)
                        if cond, anymtn=true; conn_menumanager_mousemove(CONN_MM.onregionmotioncallback{n0},handle); end
 
Error while evaluating Figure WindowButtonMotionFcn."

Thanks,

Nam