We have unusually long EPI fMRI data files lasting just under 1 hour for a relatively rare condition in only 3 subjects. It is a block design the subjects each with 4x ~1hr EPI runs. As population inferences are underpowered with only 3 subjects, we are combining all runs into a single first level analysis with 12 sessions and not performing a second level analysis. Due to the large file sizes, we previously ran into difficulties with whole-brain contrasts specifying and estimating the SPM.mat files which was resolved by using the v7.3 switch and within multiple .m file scripts using SPM12b and matlab R2014a (https://www.jiscmail.ac.uk/cgi-bin/webad...). In case, the .mat files needed similarly changing to be saved in the 7.3 format in conn, I also did a search and replace for all .m files containing the string 'save(' and ammended these commands to save in the v7.3 format. Though this didn't appear to help so I reverted back and reinstalled conn.

When using conn 13 to import settings from our previously estimated spm.mat file, we got the error message below stating 'Index exceeds matrix dimensions' in matlab. When trying conn 14k, when importing the design data resulted in a message stating spm.mat file of 'unrecognised' format. After manually specifying the design, conn proceeded until the end of 'Denoising the functional data'. At this point the green progress bar appeared complete with ETA of 0 seconds but never progressed and 'hung'. No matlab error was produced and even after 16hrs there was no progress and needed cancelling. I note looking at systems performance stats that matlab was still requiring ++ ram throughout this time.
Given the long scans, I assume it may be a file size issue. It would be really appreciated if anyone had any advice on this?

Many thanks,

Tom