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Error running episodes_reg

Open Leprimaire opened this issue 1 year ago • 9 comments

Hello, I try to use Synbo-DISCO for the first time with Docker. I set my T1raw + first b0 +acqparams.txt (0 -1 0 0.0351891 and create the second line : 0 -1 0 0.000).

Finally it show: Failed to read volume /OUTPUTS/b0_all.nii.gz Error : No image files match: /OUTPUTS/b0_all

Looking inside the process, the first error seem to occur at this time, line 320, when running the FAST segmentation:

epi_reg distorted b0 to T1 epi_reg --epi=/INPUTS/b0.nii.gz --t1=/INPUTS/T1.nii.gz --t1brain=/tmp/tmp.M7wXzCLbwv/T1_mask.nii.gz --out=/tmp/tmp.M7wXzCLbwv/epi_reg_d Running FAST segmentation /extra/fsl/bin/epi_reg: line 320: 1401 Killed $FSLDIR/bin/fast -o ${vout}_fast ${vrefbrain} Image Exception : #63 :: No image files match: /tmp/tmp.M7wXzCLbwv/epi_reg_d_fast_pve_2 terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /tmp/tmp.M7wXzCLbwv/epi_reg_d_fast_pve_2 /extra/fsl/bin/epi_reg: line 320: 1402 Aborted $FSLDIR/bin/fslmaths ${vout}_fast_pve_2 -thr 0.5 -bin ${vout}_fast_wmseg Image Exception : #63 :: No image files match: /tmp/tmp.M7wXzCLbwv/epi_reg_d_fast_wmseg terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: /tmp/tmp.M7wXzCLbwv/epi_reg_d_fast_wmseg /extra/fsl/bin/epi_reg: line 329: 1427 Aborted $FSLDIR/bin/fslmaths ${vout}_fast_wmseg -edge -bin -mas ${vout}_fast_wmseg ${vout}_fast_wmedge FLIRT pre-alignment Running BBR Image Exception : #63 :: No image files match: /tmp/tmp.M7wXzCLbwv/epi_reg_d_fast_wmseg Image Exception : #22 :: Failed to read volume /tmp/tmp.M7wXzCLbwv/epi_reg_d_fast_wmseg Error : No image files match: /tmp/tmp.M7wXzCLbwv/epi_reg_d_fast_wmseg Failed to read volume /tmp/tmp.M7wXzCLbwv/epi_reg_d_fast_wmseg Error : No image files match: /tmp/tmp.M7wXzCLbwv/epi_reg_d_fast_wmseg Could not open matrix file /tmp/tmp.M7wXzCLbwv/epi_reg_d.mat /extra/fsl/bin/epi_reg: line 399: 1430 Segmentation fault $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline

Do you know how can I fix this?

Thank you very much Charles

Leprimaire avatar Dec 10 '22 01:12 Leprimaire