Dear all
I’ve tried to run fMRIPREP on multiband EPI data and have managed to run it through without producing any errors. However, the brain mask is clearly wrong, both viewing it from the HMTL output (link below) and when viewing the brainmask.nii.gz output. I’m still learning to use fMRIPREP and and probably making some newbie errors!
Here is the HTML output:
https://drive.google.com/file/d/18Xru0Xgcv0qUkl81s9giugeycCK8kBgh/view?usp=sharing
Here is the command I ran:
mriprep-docker
/home/cab79/Documents/CORE-MRI/
/home/cab79/Documents/CORE-MRI/ana
participant
-w /home/cab79/Documents/CORE-MRI/work
–participant_label 01
-t taskname
–output-space {T1w,template,fsaverage}
–template {MNI152NLin2009cAsym}
–template-resampling-grid native
–ignore slicetiming
–use-aroma
–aroma-melodic-dimensionality 200
–skull-strip-template OASIS
–fs-license-file /home/cab79/Documents/freesurfer-license.txt
–resource-monitor
–write-graph
Could it be an issue with choice of template?
I am using Linux Mint. I’m not sure which fMRIPREP version it is (I installed just one week ago) - how do I find this out?
Many thanks
Chris