hi there,
i’ve encountered an error somewhere after the topup procedure in dwifslpreproc
i ran this:
dwifslpreproc gdntensors.mif DWI_out.mif -rpe_pair -se_epi fmap.nii.gz -pe_dir ap -readout_time 0.12705 -align_seepi -fslgrad CHIF002_ADNI3_advanced_MB_DTI_.bvec CHIF002_ADNI3_advanced_MB_DTI_.bval -eddy_options "--slm=linear"
here are the details from the log.txt
mrconvert /scratch/junhong.yu/CHIF/dicom/CHIF002/DTI/gdntensors.mif /scratch/junhong.yu/CHIF/dicom/CHIF002/DTI/dwifslpreproc-tmp-WQ2SUJ/dwi.mif -fslgrad /scratch/junhong.yu/CHIF/dicom/CHIF002/DTI/CHIF002_ADNI3_advanced_MB_DTI_.bvec /scratch/junhong.yu/CHIF/dicom/CHIF002/DTI/CHIF002_ADNI3_advanced_MB_DTI_.bval -json_export /scratch/junhong.yu/CHIF/dicom/CHIF002/DTI/dwifslpreproc-tmp-WQ2SUJ/dwi.json
mrconvert /scratch/junhong.yu/CHIF/dicom/CHIF002/DTI/fmap.nii.gz /scratch/junhong.yu/CHIF/dicom/CHIF002/DTI/dwifslpreproc-tmp-WQ2SUJ/se_epi.mif
mrconvert dwi.mif dwi_first_bzero.mif -coord 3 0 -axes 0,1,2
mrconvert se_epi.mif - -coord 3 1 | mrcat dwi_first_bzero.mif - se_epi_firstdwibzero.mif -axis 3
mrinfo dwi.mif -export_grad_mrtrix grad.b
mrconvert se_epi_firstdwibzero.mif -coord 2 80 - | mrcat se_epi_firstdwibzero.mif - se_epi_firstdwibzero_pad2.mif -axis 2
mrconvert dwi.mif -coord 2 80 - | mrcat dwi.mif - dwi_pad2.mif -axis 2
mrconvert se_epi_firstdwibzero_pad2.mif topup_in.nii -import_pe_table se_epi_manual_pe_scheme.txt -strides -1,+2,+3,+4 -export_pe_table topup_datain.txt
topup --imain=topup_in.nii --datain=topup_datain.txt --out=field --fout=field_map.nii.gz --config=/usr/local/fsl-6.0.5/etc/flirtsch/b02b0.cnf --verbose
mrconvert dwi_pad2.mif -import_pe_table dwi_manual_pe_scheme.txt - | mrinfo - -export_pe_eddy applytopup_config.txt applytopup_indices.txt
mrconvert dwi_pad2.mif dwi_pad2_pe_0.nii -coord 3 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126 -strides -1,+2,+3,+4 -json_export dwi_pad2_pe_0.json
applytopup --imain=dwi_pad2_pe_0.nii --datain=applytopup_config.txt --inindex=1 --topup=field --out=dwi_pad2_pe_0_applytopup.nii --method=jac
mrconvert dwi_pad2_pe_0_applytopup.nii.gz dwi_pad2_pe_0_applytopup.mif -json_import dwi_pad2_pe_0.json
and from the error.txt
dwi2mask dwi_pad2_pe_0_applytopup.mif - | maskfilter - dilate - | mrconvert - eddy_mask.nii -datatype float32 -strides -1,+2,+3
dwi2mask: preloading data for "dwi_pad2_pe_0_applytopup.mif"... [==================================================]
dwi2mask: [ERROR] no valid diffusion gradient table found
dwi2mask: [ERROR] error importing diffusion gradient table for image "dwi_pad2_pe_0_applytopup.mif"
maskfilter: [ERROR] no filename supplied to standard input (broken pipe?)
maskfilter: [ERROR] error opening image "-"
mrconvert: [ERROR] no filename supplied to standard input (broken pipe?)
mrconvert: [ERROR] error opening image "-"