Hi - 

I am trying to create a model for my dataset using fMRIPrep outputs. The model that I would like to create will consist of structural and functional resting state data. 

The majority of my subjects only have "Pre" MRI data in the study. Some subjects have both pre- and post-MRI data. In fMRIPrep, the pre-processing outputs for the anatomical and functional pipelines for subject who have only had a single MRI session are as follows:

fmriprep/sub-{subject}/ses-01/anat/sub-{subject}_ses-01_space-MNIxxxx

fmriprep/sub-{subject}/ses-01/func/sub-{subject}_ses-01_task-rest-xxxxx

However, for multiple sessions, when you run a subject through anatomical pre-processing, the anatomicals are averaged, so we only get 1 anatomical folder where the MNI image lives, like so:

fmriprep/sub-{subject}/anat/sub-{subject}_space-MNIxxxx

I am having the problem where CONN cannot seem to find the structural image it needs when I use the Tools -> Import from fMRIPrep. I believe it is either because 1) the folder structures are different when there are multiple session or 2) the naming of the MNI file is different (there is no session label when there are multiple sessions since it is averaged). 

When the import tool encounters this problem, it fails to import that subject, and my remaining subjects.

Is there a way to fix this in CONN? I have attached my log file and my .mat file from when this error occurred.

Thank you.
Hannah