I already checked the forum for same error messages but could not find any solution.
So when I run 5ttgen I got following error message:
FSL FIRST has failed; not all structures were segmented successfully
When I check the log file it says the following:
Cannot open volume first-L_Accu_corr for reading! Image Exception : #22 :: ERROR: Could not open image first_all_none_firstseg
Strangely the 5ttgen command works fine with some of my data.
All my data has been on the same way preprocessed and created in a directory of same structure.
I also started running just the fsl
run_first_all command and it works fine. I also could run
It seemed to be a problem with the coregistered T1 images. The T1 is for all measurements the same, I just did a coregistration (6 rigid transform FLIRT) between the T1 and each DWI as recommended before running 5ttgen. Last I took the unregistered T1 and repeated 5ttgen. It worked!
I really dont know why because when I checked via mrinfo/mrview both T1 seemed to be ok.
Thank you for any kind of help