Hi Pravesh,

Thanks to you I was able to register realignment parameters and I was able to move on to the next step. And now I am facing the following two problems.

1. ROI mask error
I could not use ROI mask of CSF created with FreeSurfer (MNI converted by AFNI) and I do not know what the meaning of the error message.
By executing without including ROI mask of CSF, we can move on to the Denoising step. Moreover, ROI mask of gray matter and white matter seems to be able to process without problems, so I think that there is a problem with the CSF ROI mask.
I'd like to use mask created with FreeSurfer as much as possible, could you tell your advice about this problem for me?
These are error messages bellow.
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ERROR DESCRIPTION:

エラー: conn_process (line 660)
No suprathreshold voxels in ROI file /Users/mrimac/Documents/MRIshell/data/compute_IFC/IFC0820QKZDb2/FT.11.bandpass.results/data4conn/roi_fsvent.nii after erosion (original file contained 234 suprathreshold voxels)
エラー: conn_process (line 16)
case 'setup', disp(['CONN: RUNNING SETUP STEP']); conn_process([0:4,4.5,5]);
エラー: conn (line 4439)
else conn_process('setup'); ispending=false;
エラー: conn_menumanager (line 120)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});
CONN v.17.f
SPM12 + DEM FieldMap MEEGtools
Matlab v.2018a
storage: 675.2Gb available
spm @ /Users/mrimac/Documents/MATLAB/spm12
conn @ /Users/mrimac/Documents/MATLAB/conn
# "roi_fsvent.nii" is CSF ROI mask.
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2. (probably) the result of incorrect functional Outlier detection

Thank you for telling me about scrubbing. However strange result was obtained from CONN, so I would like to consult with you. I will attach a file of screenshot. Scrubbing result looks like a correlation matrix, and it is different from usuall CONN's result. This result seems to be incorrect, but is there a way to fix it?

Thank you for your help in advance.

Masaki