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I run the field mapping scripts but the FSL routines bomb, whats wrong?

April 26, 2017bomb field FSL Mapping routines run scripts wrong

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I run the field mapping scripts but the FSL routines bomb, whats wrong?

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If you are using FSL 3.2 or higher, check to make sure that the default output type in fsl.sh is set to ANALYZE instead of NIFTI. (NOTE: For ppge2, which uses NIFTI, the output type should be NIFTI).For information on where the fsl.sh (or equivalent files such as fsl.csh), check with your system administrator or check out this FSL web page Once in a while when I run the field mapping correction for scans the results are all wacky, but most of the time it’s fine. Check to make sure that you are running the fm_TE1_NFS protocol prior to running fm_TE2_NFS protocol. This is because TE1 will run autoshim, while TE2 just uses the shim values from TE1.