Apologies - I am new to imaging analysis and all these software.
I am trying to go down the pipeline to generate tractography for a batch of 14 DTI images for patients.
While trying to run dwifslpreproc my code seems to get stuck at
Command: eddy --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --out=dwi_post_eddy --verbose
I know this preprocessing stage can take many hours and so I left it overnight but it still was stuck at the same time.
This is the code I am running (I do not have PA images, so only working with AP):
$ dwifslpreproc PT1_preop_DTIden.mif PT1_preop_DTIden_preproc.mif -rpe_none -pe_dir ap -readout_time 0.044856
Could anyone suggest a solution for this please?