Hi Masaki,

Regarding error 1, Conn reads the WM and CSF masks and erodes it so that only voxels belonging to that tissue class are retained. The error message indicates that the CSF mask after erosion did not have any voxels which survived the erosion process. It also mentions that the original file only had 234 voxels which is quite strange. Does the CSF mask cover whole brain or is it restricted to ventricles or something like that?

The CSF and WM masks are important for the implementation of aCompCor approach which Conn uses so you might want to look at this step carefully to ensure that everything looks okay. Maybe you want to upload a snapshot of your structural data and the same slice containing WM and CSF masks?

For the second point that you raised: the snapshot shows that there are way too many scans detected as outliers.Specifically, 238 scans out of the 240 that you have are being detected as outliers. That does not seem okay.

Let us say that for a given subject you have 240 volumes. Now, you want to "scrub" 4 volumes out of these: say volume #6, #7, #8, and #9. The .mat file will consist of a variable named "R". This dimensions of this variable will be 240x4 where 240 is the number of volumes and 4 is the number of volumes that you want to scrub. This matrix will be all zeros except the following entries:

row 6, col 1 = 1 (corresponding to volume 6 that needs to be scrubbed)
row 7, col 2 = 1 (corresponding to volume 7 that needs to be scrubbed)
row 8, col 3 = 1 (corresponding to volume 8 that needs to be scrubbed)
row 9, col 4 = 1 (corresponding to volume 9 that needs to be scrubbed)

Is your matrix designed in a similar way?


Hope this helps


Best
Pravesh