Hi. I run the QSIPrep to do recon. But some subjects stuck in track_ifod2/tractography.
There are no error to merge. Because this problem didn’t merge for some subjects.
So, I didn’t know what I can do next. Could someone help me?
This is my qsiprep command:
qsiprep-docker /mnt/workdir/DCM/BIDS /mnt/workdir/DCM/BIDS/derivatives/qsiprep participant --participant_label sub-060 sub-065 sub-076 --output-resolution 2
--recon-only --recon_input /mnt/workdir/DCM/BIDS/derivatives/qsiprep --recon_spec /mnt/workdir/DCM/Docs/Reference/qsiprep/mrtrix_multishell_msmt_ACT-hsvs.json --fs-license-file /mnt/data/license.txt --freesurfer-input /mnt/workdir/DCM/BIDS/derivatives/freesurfer -w /mnt/workdir/DCM/working --custom_atlases /mnt/workdir/DCM/Docs/Reference/qsiprep/qsirecon_atlases --nthreads 88 --gpus all --stop-on-first-crash
This is the output log:
log.txt (195.1 KB)
This is what I found in the stucking subjects.
[
[
"act_file",
[
"/scratch/qsirecon_wf/sub-060_mrtrix_multishell_msmt_hsvs/anat_ingress_wf/apply_header_to_5tt/sub-060_5tt_hdrxform.nii.gz",
"d300b38f25cb2462f9f618a34a6edcc0"
]
],
[
"algorithm",
"iFOD2"
],
[
"backtrack",
true
],
[
"crop_at_gmwmi",
true
],
[
"in_file",
[
"/scratch/qsirecon_wf/sub-060_mrtrix_multishell_msmt_hsvs/sub_060_dir_PA_space_T1w_desc_preproc_recon_wf/msmt_csd/intensity_norm/sub-060_dir-PA_space-T1w_desc-preproc_dwi_wm_mtnorm.mif",
"674ae541d71d67a3d073818541110b11"
]
],
[
"max_length",
"250.0000000000"
],
[
"min_length",
"30.0000000000"
],
[
"n_samples",
4
],
[
"out_file",
"tracked.tck"
],
[
"out_seeds",
"out_seeds.nii.gz"
],
[
"power",
"0.3300000000"
],
[
"quiet",
true
],
[
"seed_dynamic",
[
"/scratch/qsirecon_wf/sub-060_mrtrix_multishell_msmt_hsvs/sub_060_dir_PA_space_T1w_desc_preproc_recon_wf/msmt_csd/intensity_norm/sub-060_dir-PA_space-T1w_desc-preproc_dwi_wm_mtnorm.mif",
"674ae541d71d67a3d073818541110b11"
]
],
[
"select",
10000000
]
]