Problem with second-level analysis main CONN GUI & result explorer display , when using different template and atlas files.

Hello Alfonso and CONN users,

I pre-processed and analyzed my data set in CONN, and I have used a different template and atlas (used proper TPM file with the correct corresponding atlas, I have also used corresponding brain mask for analysis in Setup>options>analysis mask).

I am now looking at my second level results and have changed the GUI background structural to my template T1 and changed the labels to the corresponding atlas file.

Now I see clear miss-labeling to some areas when I hover my mouse over the display.

Also, the results explorer is improperly labeling the clusters, and when I export the mask from the results explorer window, I get a clusters mask that has different dimensions than the T1 image. (results mask : 89,113,92) Vs (T1: 121,145,121 / same as corresponding atlas).

First, is the analysis affected by this problem and are the results and clusters still valid?

Second, can I use the voxel coordinates (x,y,z in mm) from the GUI and result explorer reliably to create seeds?

Third, How can I fix this or at least generate a proper results mast that I can overlay onto my atlas and calculate the number of cluster voxels in the corresponding ROI's.

Any Help is much appreciated,
Mohammad Kawas