Dear Dr. McLaren,

I am using your toolbox to look at connectivity in a factorial design with many conditions (2x3x3) and everything seems to be working fine. However, the contrast images seem to get different names quite randomly. This is not necessarily disastrous, I could manually change names of the images that go into my 2nd level analysis, but having 18 participants and 18 conditions, it would be great if I don't have to go through that.

The problem is as follows:
I wrote a wrapper to loop over subjects and different seed regions. Something happens while looping over regions. For some subjects, all contrast images for all regions get a name that is specified as: ['con_PPI_' mycontrastname '_' subjectno]. For others, all images get the output I normally get from SPM, which is ['con_' contrastno]. And for most, the contrast images for the 1st seed region get the first version (with the contrast name in it), and the contrast images for the 2nd seed region get the second version (with only a number).

As I don't change anything inside the loop, the only thing I could think of that may be causing this is that some file gets overwritten. Indeed, there is 1 file that seems to have a generic name and gets overwritten with every next seed region ([subjectno '_PPIstructure.mat']). This file contains the P structure and is saved in whatever directory I start the analysis in. There is another file containing the P structure, which gets appended with the name of the seed region and the date and is saved in the SPM directory. The P structures in these files are identical, except for the last one gets an extra field "correct" added to it (value 1).

Somehow it is hard to understand how to fix this problem. I do not understand how overwriting the P file with the generic name could cause this, as the contrasts in all files are identical. Also, this does not really explain why it randomly changes for different participants. Maybe there's some other file that interferes?

Any ideas what could be the problem?

Thanks for your time!

Fleur