Topup problem about EPI correction

When I type:
dwifslpreproc dwi_raw.mif dwi_raw_preproc.mif -nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options " --slm=linear --data_is_shelled"

I get:
dwifslpreproc:
dwifslpreproc: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwifslpreproc:
dwifslpreproc: Generated scratch directory: /media/sf_Host/BATMAN/DWI/dwifslpreproc-tmp-Y4MDM1/
Command: mrconvert /media/sf_Host/BATMAN/DWI/dwi_raw.mif /media/sf_Host/BATMAN/DWI/dwifslpreproc-tmp-Y4MDM1/dwi.mif -json_export /media/sf_Host/BATMAN/DWI/dwifslpreproc-tmp-Y4MDM1/dwi.json
Command: mrconvert /media/sf_Host/BATMAN/DWI/b0_pair.mif /media/sf_Host/BATMAN/DWI/dwifslpreproc-tmp-Y4MDM1/se_epi.mif
dwifslpreproc: Changing to scratch directory (/media/sf_Host/BATMAN/DWI/dwifslpreproc-tmp-Y4MDM1/)
Command: mrinfo dwi.mif -export_grad_mrtrix grad.b
Command: mrconvert se_epi.mif topup_in.nii -import_pe_table se_epi_manual_pe_scheme.txt -strides -1,+2,+3,+4 -export_pe_table topup_datain.txt
Command: topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/share/fsl/5.0/etc/flirtsch/b02b0.cnf --verbose

dwifslpreproc: [ERROR] topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/share/fsl/5.0/etc/flirtsch/b02b0.cnf --verbose (dwifslpreproc:805)
dwifslpreproc: [ERROR] Failed command did not provide any output information
dwifslpreproc: [ERROR] For debugging, inspect contents of scratch directory: /media/sf_Host/BATMAN/DWI/dwifslpreproc-tmp-Y4MDM1/
dwifslpreproc: Scratch directory retained; location: /media/sf_Host/BATMAN/DWI/dwifslpreproc-tmp-Y4MDM1/

I don’t know where the problem occurred. BATMAN is used for data.

1 Like

Welcome @MING_NI ,

The command is failing when calling topup, but why it is failing is not communicated back to dwifslpreproc. The best thing to do in this case, is to run the topup command manually in the scratch folder, and see what happens :slight_smile:

cd /media/sf_Host/BATMAN/DWI/dwifslpreproc-tmp-Y4MDM1/
topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/share/fsl/5.0/etc/flirtsch/b02b0.cnf --verbose