I am trying to run FSL top-up to create a field map as per the website below (method 2). I collected two EPI sequences. One with 4 volumes in P>>A direction (dist map) and the other is my task EP sequence with 637 volumes in A >> P.
I merged the dist and task EPI sequences and created a datain file.
In the terminal window I am typing…
topup -v --imain=merged_scan.nii.gz --datain=datain_file --config=b02b0.cnf --fout=my_fieldmap --iout=se_epi_unwarped
This does not error and seems to be running but is taking a very long time (over 5 hours) and the process isn’t finalizing before I am logged out.
Is this typical? If so, is there some way to restart the processing based on where I was when I was kicked off the computer (rather than having to restart every time). Is there some way to speed up processing?
Or does anyone know of any alternative processes to create a field map that might be faster? it would probably be best to create the fieldmap without fMRI prep (I think this is possible), but wanted to check the output before running.