I am trying to process some data from the aging human connectome project.
Before processing, I concatenate the 4 diffusion images they collected
mrcat dwi_98_AP.mif dwi_99_AP.mif dwi_98_PA.mif dwi_99_PA.mif dwi.mif
Then I run it through
dwidenoise & mrdegibbs
I then use eddy current correction using the -rpe_header verison
dwifslpreproc -force -eddyqc_text QC -rpe_header dwi_denoised_unringed.mif dwi_prep.mif
This seems to work, however, when trying to run dwimask or dwibiascorrect afterwards I get the following errors.
dwi2mask: [100%] preloading data for “dwi_prep.mif”
dwi2mask: [ERROR] number of studies in base image (199) does not match number of rows in diffusion gradient table (398)
dwi2mask: [ERROR] unable to get valid diffusion gradient table for image "dwi_prep.mif"
dwibiascorrect: [ERROR] Unhandled Python exception:
dwibiascorrect: [ERROR] TypeError: can only concatenate str (not “int”) to str
dwibiascorrect: [ERROR] Traceback:
dwibiascorrect: [ERROR] /Applications/MRtrix3Tissue/bin/dwibiascorrect:49 (in execute())
dwibiascorrect: [ERROR] raise MRtrixError(‘DW gradient scheme contains different number of entries (’ + str(len(dwi_header.keyval()[‘dw_scheme’])) + ’ to number of volumes in DWIs (’ + dwi_header.size() + ‘)’)
I am not sure what is causing this issue? Does it have something to do with the header information? This would be weird as eddy correction seemed to work and I imported all the information from the .json for all of the dwi_98_AP.mif files.
Let me know if you have any ideas on how to twouble shoot this issue.