Hello MRtrix3 community,
I encountered an error when using the dwifslpreproc command, and I couldn’t solve it, so I came here for help. Thank you very much.
The phase encoding direction of the original image is AP, and the bvals are 0, 250, 1000, 2250, 4000. Each bval has 60 directions, and there is only one b0. At the same time, the b0 of a single PA direction is also collected. The instrument sets the deviation of the collected b value to 60 for b250, 110 for b1000, 155 for b2250, and 205 for b4000.
After dwidenoise and mrdegibbs, I extracted b0 from dwi, paired it with b0 in the PA direction, and then used the following command to calibrate degibbs.mif, but it always reports an error.
command:
dwifslpreproc degibbs.mif geomcorr.mif -nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options " --data_is_shelled --slm=linear --niter=8 "
Error:
dwifslpreproc: Changing to scratch directory (/media/fmost/image_group_data/luzk_upan/invivo614/20250612_145249_lzk20250616_879/NIFTI/singelb0/dwifslpreproc-tmp-WKKJP0/)
mrinfo: [WARNING] The following image volumes were not successfully assigned to a b-value shell:
mrinfo: [WARNING] 0 (15)
mrinfo: [WARNING] The following image volumes were not successfully assigned to a b-value shell:
mrinfo: [WARNING] 0 (15)
dwifslpreproc: [ERROR] Unhandled Python exception:
dwifslpreproc: [ERROR] AssertionError:
dwifslpreproc: [ERROR] Traceback:
dwifslpreproc: [ERROR] /home/l/mrtrix3/bin/dwifslpreproc:343 (in execute())
dwifslpreproc: [ERROR] assert all(index >= 0 for index in vol2shell)
I think the error is caused by not clustering the shells successfully, so I tried to use -config BValueEpsilon 220 and -config BZeroThreshold 20 to re-use the command, but no matter how I try, the same error is reported. I don’t know what to do now?
The b values is as follows:
15 305 315 305 335 300 315 325 310 300 330 335 305 305 340 325 305 300 340 320 310 335 295 335 285 310 335 330 305 310 325 305 335 330 300 320 305 340 305 330 300 340 300 295 340 340 305 330 280 315 300 300 325 295 335 285 330 300 315 290 335 1085 1100 1085 1140 1075 1100 1120 1095 1080 1130 1135 1085 1090 1145 1115 1090 1080 1150 1110 1095 1145 1065 1135 1045 1095 1135 1130 1090 1095 1120 1085 1140 1130 1075 1110 1090 1145 1095 1130 1075 1145 1075 1070 1150 1145 1090 1130 1040 1095 1080 1080 1120 1065 1135 1045 1135 1075 1100 1060 1140 2355 2375 2355 2435 2345 2380 2405 2375 2345 2420 2430 2355 2365 2445 2400 2365 2350 2450 2390 2370 2440 2325 2430 2300 2370 2430 2415 2360 2370 2405 2360 2435 2420 2340 2395 2360 2440 2370 2415 2340 2445 2340 2330 2450 2445 2365 2420 2295 2370 2350 2345 2400 2330 2430 2295 2425 2340 2375 2320 2435 4115 4140 4115 4220 4105 4145 4180 4140 4105 4200 4215 4120 4130 4230 4170 4130 4110 4240 4160 4140 4230 4075 4210 4045 4140 4210 4195 4125 4140 4185 4120 4220 4205 4100 4165 4125 4230 4135 4195 4095 4235 4100 4085 4235 4235 4130 4205 4035 4130 4110 4105 4175 4080 4215 4040 4205 4100 4145 4070 4220
bvecs is as follows:
| 0 | 0 | 0 |
|---|---|---|
| -0.951008 | -0.081357 | -0.298269 |
| 0.951008 | 0.081357 | -0.298269 |
| -0.763081 | -0.573361 | 0.29827 |
| 0.763081 | 0.573361 | 0.29827 |
| -0.970739 | -0.184669 | 0.153499 |
| 0.970739 | 0.184669 | 0.153499 |
| -0.618304 | 0.184671 | 0.763935 |
| 0.618304 | -0.184671 | 0.763935 |
| -0.846662 | -0.509511 | -0.1535 |
| 0.846662 | 0.509511 | -0.1535 |
| -0.2904 | 0.50951 | 0.80998 |
| 0.2904 | -0.50951 | 0.80998 |
| -0.492719 | -0.549849 | 0.674459 |
| 0.492719 | 0.549849 | 0.674459 |
| -0.896235 | 0.205431 | 0.393143 |
| 0.896235 | -0.205431 | 0.393143 |
| -0.53106 | -0.75061 | -0.393141 |
| 0.53106 | 0.75061 | -0.393141 |
| -0.733817 | 0.081357 | -0.674458 |
| 0.733817 | -0.081357 | -0.674458 |
| -0.490489 | 0.853928 | 0.173859 |
| 0.490489 | -0.853928 | 0.173859 |
| -0.2037 | 0.963472 | -0.17386 |
| 0.2037 | -0.963472 | -0.17386 |
| -0.724734 | -0.372602 | -0.579593 |
| 0.724734 | 0.372602 | -0.579593 |
| -0.864311 | 0.372601 | -0.33784 |
| 0.864311 | -0.372601 | -0.33784 |
| -0.78859 | -0.20543 | 0.57959 |
| 0.78859 | 0.20543 | 0.57959 |
| -0.337742 | -0.549852 | -0.763933 |
| 0.337742 | 0.549852 | -0.763933 |
| -0.123231 | 0.573362 | -0.809982 |
| 0.123231 | -0.573362 | -0.809982 |
| -0.352432 | 0.184671 | -0.917436 |
| 0.352432 | -0.184671 | -0.917436 |
| -0.556269 | 0.509509 | -0.656479 |
| 0.556269 | -0.509509 | -0.656479 |
| -0.830458 | 0.549849 | 0.089475 |
| 0.830458 | -0.549849 | 0.089475 |
| -0.606 | 0.75061 | -0.26334 |
| 0.606 | -0.75061 | -0.26334 |
| -0.395811 | -0.853931 | 0.33784 |
| 0.395811 | 0.853931 | 0.33784 |
| -0.639851 | 0.573361 | 0.511711 |
| 0.639851 | -0.573361 | 0.511711 |
| -0.048722 | 0.963472 | 0.26334 |
| 0.048722 | -0.963472 | 0.26334 |
| -0.21719 | 0.081357 | 0.972733 |
| 0.21719 | -0.081357 | 0.972733 |
| -0.139571 | -0.372602 | 0.917435 |
| 0.139571 | 0.372602 | 0.917435 |
| -0.074942 | -0.750611 | 0.656481 |
| 0.074942 | 0.750611 | 0.656481 |
| -0.25242 | -0.963472 | -0.089475 |
| 0.25242 | 0.963472 | -0.089475 |
| -0.107651 | -0.20543 | -0.972733 |
| 0.107651 | 0.20543 | -0.972733 |
| -0.094674 | -0.853927 | -0.511708 |
| 0.094674 | 0.853927 | -0.511708 |
| -0.951008 | -0.081357 | -0.298269 |
| 0.951008 | 0.081357 | -0.298269 |
| -0.763081 | -0.573361 | 0.29827 |
| 0.763081 | 0.573361 | 0.29827 |
| -0.970739 | -0.184669 | 0.153499 |
| 0.970739 | 0.184669 | 0.153499 |
| -0.618304 | 0.184671 | 0.763935 |
| 0.618304 | -0.184671 | 0.763935 |
| -0.846662 | -0.509511 | -0.1535 |
| 0.846662 | 0.509511 | -0.1535 |
| -0.2904 | 0.50951 | 0.80998 |
| 0.2904 | -0.50951 | 0.80998 |
| -0.492719 | -0.549849 | 0.674459 |
| 0.492719 | 0.549849 | 0.674459 |
| -0.896235 | 0.205431 | 0.393143 |
| 0.896235 | -0.205431 | 0.393143 |
| -0.53106 | -0.75061 | -0.393141 |
| 0.53106 | 0.75061 | -0.393141 |
| -0.733817 | 0.081357 | -0.674458 |
| 0.733817 | -0.081357 | -0.674458 |
| -0.490489 | 0.853928 | 0.173859 |
| 0.490489 | -0.853928 | 0.173859 |
| -0.2037 | 0.963472 | -0.17386 |
| 0.2037 | -0.963472 | -0.17386 |
| -0.724734 | -0.372602 | -0.579593 |
| 0.724734 | 0.372602 | -0.579593 |
| -0.864311 | 0.372601 | -0.33784 |
| 0.864311 | -0.372601 | -0.33784 |
| -0.78859 | -0.20543 | 0.57959 |
| 0.78859 | 0.20543 | 0.57959 |
| -0.337742 | -0.549852 | -0.763933 |
| 0.337742 | 0.549852 | -0.763933 |
| -0.123231 | 0.573362 | -0.809982 |
| 0.123231 | -0.573362 | -0.809982 |
| -0.352432 | 0.184671 | -0.917436 |
| 0.352432 | -0.184671 | -0.917436 |
| -0.556269 | 0.509509 | -0.656479 |
| 0.556269 | -0.509509 | -0.656479 |
| -0.830458 | 0.549849 | 0.089475 |
| 0.830458 | -0.549849 | 0.089475 |
| -0.606 | 0.75061 | -0.26334 |
| 0.606 | -0.75061 | -0.26334 |
| -0.395811 | -0.853931 | 0.33784 |
| 0.395811 | 0.853931 | 0.33784 |
| -0.639851 | 0.573361 | 0.511711 |
| 0.639851 | -0.573361 | 0.511711 |
| -0.048722 | 0.963472 | 0.26334 |
| 0.048722 | -0.963472 | 0.26334 |
| -0.21719 | 0.081357 | 0.972733 |
| 0.21719 | -0.081357 | 0.972733 |
| -0.139571 | -0.372602 | 0.917435 |
| 0.139571 | 0.372602 | 0.917435 |
| -0.074942 | -0.750611 | 0.656481 |
| 0.074942 | 0.750611 | 0.656481 |
| -0.25242 | -0.963472 | -0.089475 |
| 0.25242 | 0.963472 | -0.089475 |
| -0.107651 | -0.20543 | -0.972733 |
| 0.107651 | 0.20543 | -0.972733 |
| -0.094674 | -0.853927 | -0.511708 |
| 0.094674 | 0.853927 | -0.511708 |
| -0.951008 | -0.081357 | -0.298269 |
| 0.951008 | 0.081357 | -0.298269 |
| -0.763081 | -0.573361 | 0.29827 |
| 0.763081 | 0.573361 | 0.29827 |
| -0.970739 | -0.184669 | 0.153499 |
| 0.970739 | 0.184669 | 0.153499 |
| -0.618304 | 0.184671 | 0.763935 |
| 0.618304 | -0.184671 | 0.763935 |
| -0.846662 | -0.509511 | -0.1535 |
| 0.846662 | 0.509511 | -0.1535 |
| -0.2904 | 0.50951 | 0.80998 |
| 0.2904 | -0.50951 | 0.80998 |
| -0.492719 | -0.549849 | 0.674459 |
| 0.492719 | 0.549849 | 0.674459 |
| -0.896235 | 0.205431 | 0.393143 |
| 0.896235 | -0.205431 | 0.393143 |
| -0.53106 | -0.75061 | -0.393141 |
| 0.53106 | 0.75061 | -0.393141 |
| -0.733817 | 0.081357 | -0.674458 |
| 0.733817 | -0.081357 | -0.674458 |
| -0.490489 | 0.853928 | 0.173859 |
| 0.490489 | -0.853928 | 0.173859 |
| -0.2037 | 0.963472 | -0.17386 |
| 0.2037 | -0.963472 | -0.17386 |
| -0.724734 | -0.372602 | -0.579593 |
| 0.724734 | 0.372602 | -0.579593 |
| -0.864311 | 0.372601 | -0.33784 |
| 0.864311 | -0.372601 | -0.33784 |
| -0.78859 | -0.20543 | 0.57959 |
| 0.78859 | 0.20543 | 0.57959 |
| -0.337742 | -0.549852 | -0.763933 |
| 0.337742 | 0.549852 | -0.763933 |
| -0.123231 | 0.573362 | -0.809982 |
| 0.123231 | -0.573362 | -0.809982 |
| -0.352432 | 0.184671 | -0.917436 |
| 0.352432 | -0.184671 | -0.917436 |
| -0.556269 | 0.509509 | -0.656479 |
| 0.556269 | -0.509509 | -0.656479 |
| -0.830458 | 0.549849 | 0.089475 |
| 0.830458 | -0.549849 | 0.089475 |
| -0.606 | 0.75061 | -0.26334 |
| 0.606 | -0.75061 | -0.26334 |
| -0.395811 | -0.853931 | 0.33784 |
| 0.395811 | 0.853931 | 0.33784 |
| -0.639851 | 0.573361 | 0.511711 |
| 0.639851 | -0.573361 | 0.511711 |
| -0.048722 | 0.963472 | 0.26334 |
| 0.048722 | -0.963472 | 0.26334 |
| -0.21719 | 0.081357 | 0.972733 |
| 0.21719 | -0.081357 | 0.972733 |
| -0.139571 | -0.372602 | 0.917435 |
| 0.139571 | 0.372602 | 0.917435 |
| -0.074942 | -0.750611 | 0.656481 |
| 0.074942 | 0.750611 | 0.656481 |
| -0.25242 | -0.963472 | -0.089475 |
| 0.25242 | 0.963472 | -0.089475 |
| -0.107651 | -0.20543 | -0.972733 |
| 0.107651 | 0.20543 | -0.972733 |
| -0.094674 | -0.853927 | -0.511708 |
| 0.094674 | 0.853927 | -0.511708 |
| -0.951008 | -0.081357 | -0.298269 |
| 0.951008 | 0.081357 | -0.298269 |
| -0.763081 | -0.573361 | 0.29827 |
| 0.763081 | 0.573361 | 0.29827 |
| -0.970739 | -0.184669 | 0.153499 |
| 0.970739 | 0.184669 | 0.153499 |
| -0.618304 | 0.184671 | 0.763935 |
| 0.618304 | -0.184671 | 0.763935 |
| -0.846662 | -0.509511 | -0.1535 |
| 0.846662 | 0.509511 | -0.1535 |
| -0.2904 | 0.50951 | 0.80998 |
| 0.2904 | -0.50951 | 0.80998 |
| -0.492719 | -0.549849 | 0.674459 |
| 0.492719 | 0.549849 | 0.674459 |
| -0.896235 | 0.205431 | 0.393143 |
| 0.896235 | -0.205431 | 0.393143 |
| -0.53106 | -0.75061 | -0.393141 |
| 0.53106 | 0.75061 | -0.393141 |
| -0.733817 | 0.081357 | -0.674458 |
| 0.733817 | -0.081357 | -0.674458 |
| -0.490489 | 0.853928 | 0.173859 |
| 0.490489 | -0.853928 | 0.173859 |
| -0.2037 | 0.963472 | -0.17386 |
| 0.2037 | -0.963472 | -0.17386 |
| -0.724734 | -0.372602 | -0.579593 |
| 0.724734 | 0.372602 | -0.579593 |
| -0.864311 | 0.372601 | -0.33784 |
| 0.864311 | -0.372601 | -0.33784 |
| -0.78859 | -0.20543 | 0.57959 |
| 0.78859 | 0.20543 | 0.57959 |
| -0.337742 | -0.549852 | -0.763933 |
| 0.337742 | 0.549852 | -0.763933 |
| -0.123231 | 0.573362 | -0.809982 |
| 0.123231 | -0.573362 | -0.809982 |
| -0.352432 | 0.184671 | -0.917436 |
| 0.352432 | -0.184671 | -0.917436 |
| -0.556269 | 0.509509 | -0.656479 |
| 0.556269 | -0.509509 | -0.656479 |
| -0.830458 | 0.549849 | 0.089475 |
| 0.830458 | -0.549849 | 0.089475 |
| -0.606 | 0.75061 | -0.26334 |
| 0.606 | -0.75061 | -0.26334 |
| -0.395811 | -0.853931 | 0.33784 |
| 0.395811 | 0.853931 | 0.33784 |
| -0.639851 | 0.573361 | 0.511711 |
| 0.639851 | -0.573361 | 0.511711 |
| -0.048722 | 0.963472 | 0.26334 |
| 0.048722 | -0.963472 | 0.26334 |
| -0.21719 | 0.081357 | 0.972733 |
| 0.21719 | -0.081357 | 0.972733 |
| -0.139571 | -0.372602 | 0.917435 |
| 0.139571 | 0.372602 | 0.917435 |
| -0.074942 | -0.750611 | 0.656481 |
| 0.074942 | 0.750611 | 0.656481 |
| -0.25242 | -0.963472 | -0.089475 |
| 0.25242 | 0.963472 | -0.089475 |
| -0.107651 | -0.20543 | -0.972733 |
| 0.107651 | 0.20543 | -0.972733 |
| -0.094674 | -0.853927 | -0.511708 |
| 0.094674 | 0.853927 | -0.511708 |