I am getting following error on running the tractoflow pipeline:
[66/94972d] NOTE: Process Bet_Prelim_DWI (S1) terminated with an error exit status (1) -- Execution is retried (1)
Here’s the command I ran:
nextflow run tractoflow -r 2.4.3 --input /home/turing/tractoflow/via_direct_input/on_ismrm -with-singularity /home/turing/tractoflow/bids_project/scilus_1.6.0.sif -profile use_gpu -resume --run_local_tracking true
whole output log:
N E X T F L O W ~ version 21.12.1-edge
Launching `scilus/tractoflow` [cheesy_varahamihira] - revision: 2ca9dad434 [2.4.3]
TractoFlow pipeline
===================
Start time: 2024-01-06T12:35:56.486694+05:30
Max DTI shell extracted: 1200
Min FODF shell extracted: 700
Input: /home/turing/tractoflow/via_direct_input/on_ismrm
executor > local (2)
executor > local (2)
executor > local (3)
[65/dd03f0] process > README (README) [100%] 1 of 1 ✔
[9d/38f449] process > Bet_Prelim_DWI (S1) [ 50%] 1 of 2, failed: 1, retries: 1
executor > local (4)
[65/dd03f0] process > README (README) [100%] 1 of 1 ✔
[8f/5c4652] process > Bet_Prelim_DWI (S1) [ 66%] 2 of 3, failed: 2, retries: 2
[97/c79597] process > Denoise_DWI (S1) [100%] 1 of 1, cached: 1 ✔
[- ] process > Gibbs_correction -
executor > local (4)
[65/dd03f0] process > README (README) [100%] 1 of 1 ✔
[8f/5c4652] process > Bet_Prelim_DWI (S1) [ 66%] 2 of 3, failed: 2, retries: 2
[97/c79597] process > Denoise_DWI (S1) [100%] 1 of 1, cached: 1 ✔
[- ] process > Gibbs_correction -
executor > local (5)
[65/dd03f0] process > README (README) [100%] 1 of 1 ✔
[d3/48ff24] process > Bet_Prelim_DWI (S1) [ 75%] 3 of 4, failed: 3, retries: 3
[97/c79597] process > Denoise_DWI (S1) [100%] 1 of 1, cached: 1 ✔
[- ] process > Gibbs_correction -
[- ] process > Prepare_for_Topup -
[- ] process > Topup -
executor > local (5)
[65/dd03f0] process > README (README) [100%] 1 of 1 ✔
[d3/48ff24] process > Bet_Prelim_DWI (S1) [100%] 4 of 4, failed: 4, retries: 3 ✔
[97/c79597] process > Denoise_DWI (S1) [100%] 1 of 1, cached: 1 ✔
[- ] process > Gibbs_correction -
[- ] process > Prepare_for_Topup -
[- ] process > Topup -
[- ] process > Prepare_dwi_for_eddy -
[- ] process > Eddy_Topup -
[- ] process > Eddy -
[- ] process > Bet_DWI -
[- ] process > N4_DWI -
[- ] process > Crop_DWI -
[- ] process > Denoise_T1 -
[c9/5f565b] process > N4_T1 (S1) [100%] 1 of 1, cached: 1 ✔
[7a/90d97a] process > Resample_T1 (S1) [100%] 1 of 1, cached: 1 ✔
[6c/de3242] process > Bet_T1 (S1) [100%] 1 of 1, cached: 1 ✔
[6b/42873c] process > Crop_T1 (S1) [100%] 1 of 1, cached: 1 ✔
[- ] process > Normalize_DWI -
[- ] process > Resample_DWI -
[- ] process > Extract_B0 -
[- ] process > Extract_SH_Fitting_Shell -
[- ] process > SH_Fitting -
[- ] process > Extract_DTI_Shell -
[- ] process > DTI_Metrics -
[- ] process > Extract_FODF_Shell -
[- ] process > Register_T1 -
[- ] process > Register_Freesurfer -
[- ] process > Segment_Freesurfer -
[- ] process > Segment_Tissues -
[- ] process > Compute_FRF -
[- ] process > Mean_FRF -
[- ] process > FODF_Metrics -
[- ] process > PFT_Tracking_Maps -
[- ] process > PFT_Seeding_Mask -
[- ] process > PFT_Tracking -
[- ] process > Local_Tracking_Mask -
[- ] process > Local_Seeding_Mask -
[- ] process > Local_Tracking -
Pipeline completed at: 2024-01-06T12:36:15.888949+05:30
Execution status: OK
Execution duration: 19.4s
[66/94972d] NOTE: Process `Bet_Prelim_DWI (S1)` terminated with an error exit status (1) -- Execution is retried (1)
[9d/38f449] NOTE: Process `Bet_Prelim_DWI (S1)` terminated with an error exit status (1) -- Execution is retried (2)
[8f/5c4652] NOTE: Process `Bet_Prelim_DWI (S1)` terminated with an error exit status (1) -- Execution is retried (3)
[d3/48ff24] NOTE: Process `Bet_Prelim_DWI (S1)` terminated with an error exit status (1) -- Error is ignored
Here is the log file: (tractoflow/via_direct_input/work/d3/48ff2466a7d638e2fad8ea69b731c1/.command.log)
nxf-scratch-dir turing:/tmp/nxf.NVD7rMTrOF
/fsl/bin/bet: line 399: 2571036 Segmentation fault (core dumped) ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
/fsl/bin/bet failed during command:S1__b0.nii.gz S1__b0_bet.nii.gz -m -R -f 0.16