I am new to Conn and have used the default preprocessing pipeline for a set of subjects.  I am using spm12 with conn18b.  I have two problems.  Problem 1: One of the subjects had a large brain but all slices appeared on the original Bold images and looked similar to the other subjects.  That is they did not appear to be cropped prior to the normalization.  After normalization the bottom part of the brain is cropped in this one subject but not the others.  I thought the problem might be related to the large brain which fills the vertical image space of the Bold image.  The structural image (which did not fill the image matrix but had some blank space surrounding the image) did not have this problem and the normalization looked fine. 

Problem 2:  My subjects had 2 scans several weeks apart - one pre and one post intervention.  I wanted to enter them as two sessions with two conditions similar to what was recommended in another post for a paired t-test analysis.  The problem with one of the subjects is that the pre functional scan had 200 time series but the post scan had 300 and I got the error message that the dimensions must agree.  If I enter all the scans as being separate subjects the pipeline runs fine.

Conn seems like a great tool.  I would greatly appreciate any help with these problems.

Thanks very much
jean