Hi Pravesh,

Thank you for your advice. I understood error massages about error 1.
The CSF mask does not cover whole brain, but only ventricles. Is there a difference between the shape of the segmentation mask in FreeSurfer and CONN in the first place? FreeSurfer's mask has only ventricles data.

And now I noticed I had a big misunderstanding, that my original purpose is learning how to analyze the data preprocessed from other software with CONN. I already have data of preprocessed T1 and fMRI, So I need only ROI analyses without preprocessing and denoising steps. In denoising session, I can remove MASK auto-created by CONN from Confounds, but can I skip all denoising session such as bandpass filtering?

I have used Freesurfer and AFNI so far, but I would like to use CONN's interface and 2nd-analysis in the future. Also I would like to compare results from CONN or FreeSurfer and AFNI, from the view of preprocessing. Therefore I have these question. Thank you for your advice.


Regarding error 2, due to the above misunderstanding, I thought that a large amount of abnormal value was detected by scrubbing the data after preprocessing. I understood "R" in mat file, thank you for your lecture.

Thank you for your help in advance.

Best regards,
Masaki