tckgen: [ERROR] Cannot use image /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz for rejection sampling - image is empty

[sebastientourbier]

How we can get the error

The error is raised while using:

• Lausanne2018 parcellation with no extra structures selected (no thalamic nuclei, no brainstem substructures, no hippocampal subfields)
• MRtrix anatomically-constrained tractography

For more details, below are the configuration file of the pipelines as well as the complete crash report generated by tckgen interface:

Anatomical pipeline

[Global]
subject_session = ses-1
subjects = ['sub-01']
process_type = anatomical
subject = sub-01

[parcellation_stage]
parcellation_scheme = Lausanne2018
brain_file = 
segment_hippocampal_subfields = False
segment_brainstem = False
ants_precision_type = double
thalamic_nuclei_maps = app/connectomemapper3/cmtklib/data/segmentation/thalamus2018/Thalamus_Nuclei-HCP-4DSPAMs.nii.gz
include_thalamic_nuclei_parcellation = False
template_thalamus = app/connectomemapper3/cmtklib/data/segmentation/thalamus2018/mni_icbm152_t1_tal_nlin_sym_09b_hires_1.nii.gz
pipeline_mode = Diffusion
atlas_nifti_file = 
parcellation_scheme_editor = ['NativeFreesurfer', 'Lausanne2008', 'Lausanne2018', 'Custom']
number_of_regions = 0
graphml_file = 
atlas_info = {}
pre_custom = Lausanne2008
csf_file = 

[segmentation_stage]
ants_templatefile = 
make_isotropic = True
freesurfer_subject_id = 
isotropic_interpolation = cubic
isotropic_vox_size = 1.0
freesurfer_subjects_dir = 
brain_mask_extraction_tool = Freesurfer
freesurfer_args = 
white_matter_mask = 
ants_regmaskfile = 
seg_tool = Freesurfer
use_fsl_brain_mask = False
brain_mask_path = 
ants_probmaskfile = 
use_existing_freesurfer_data = False

[Multi-processing]
number_of_cores = 1

Diffusion pipeline

[Global]
modalities = []
process_type = diffusion
subject_session = ses-1
diffusion_imaging_model = DSI
dmri_bids_acq = dsiNdir129
subjects = ['sub-01']
subject = sub-01

[diffusion_stage]
tracking_processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']
tracking_processing_tool = MRtrix
dilation_kernel = Box
recon_processing_tool_editor = ['Dipy', 'Custom']
custom_track_file = 
dilation_radius = 1
diffusion_model = Deterministic
dilate_rois = True
recon_processing_tool = Dipy
dipy_tracking_config.fa_thresh = 0.2
dipy_tracking_config.seed_density = 1.0
dipy_tracking_config.number_of_seeds = 1000
dipy_tracking_config.tracking_mode = Deterministic
dipy_tracking_config.use_act = False
dipy_tracking_config.imaging_model = DSI
dipy_tracking_config.sh_order = 8
dipy_tracking_config.curvature = 0.0
dipy_tracking_config.step_size = 0.5
dipy_tracking_config.seed_from_gmwmi = False
dipy_tracking_config.sd = True
dipy_tracking_config.max_angle = 25.0
diffusion_imaging_model_editor = ['DSI', 'DTI', 'HARDI']
mrtrix_tracking_config.min_length = 5.0
mrtrix_tracking_config.angle = 45.0
mrtrix_tracking_config.tracking_mode = Deterministic
mrtrix_tracking_config.use_act = True
mrtrix_tracking_config.cutoff_value = 0.05
mrtrix_tracking_config.backtrack = False
mrtrix_tracking_config.curvature = 0.0
mrtrix_tracking_config.crop_at_gmwmi = True
mrtrix_tracking_config.step_size = 0.5
mrtrix_tracking_config.max_length = 500.0
mrtrix_tracking_config.desired_number_of_tracks = 200000
mrtrix_tracking_config.seed_from_gmwmi = True
mrtrix_tracking_config.sd = True
mrtrix_recon_config.recon_mode = Probabilistic
mrtrix_recon_config.imaging_model = DSI
mrtrix_recon_config.single_fib_thr = 0.7
mrtrix_recon_config.lmax_order = Auto
mrtrix_recon_config.flip_table_axis = []
mrtrix_recon_config.local_model_editor = {True: 'Constrained Spherical Deconvolution'}
mrtrix_recon_config.local_model = True
mrtrix_recon_config.normalize_to_b0 = False
diffusion_model_editor = ['Deterministic', 'Probabilistic']
dipy_recon_config.shore_radial_order = 4
dipy_recon_config.shore_constrain_e0 = False
dipy_recon_config.positivity_constraint = True
dipy_recon_config.tracking_processing_tool = MRtrix
dipy_recon_config.imaging_model = DSI
dipy_recon_config.small_delta = 0.02
dipy_recon_config.big_delta = 0.5
dipy_recon_config.lmax_order = Auto
dipy_recon_config.shore_lambdal = 1e-08
dipy_recon_config.shore_lambdan = 1e-08
dipy_recon_config.local_model_editor = {False: '1:Tensor', True: '2:Constrained Spherical Deconvolution'}
dipy_recon_config.shore_zeta = 700
dipy_recon_config.local_model = True
dipy_recon_config.radial_order = 8
dipy_recon_config.radial_order_values = [2, 4, 6, 8, 10, 12]
dipy_recon_config.single_fib_thr = 0.7
dipy_recon_config.recon_mode = Probabilistic
dipy_recon_config.flip_table_axis = []
dipy_recon_config.shore_tau = 0.0338336
dipy_recon_config.laplacian_regularization = True
dipy_recon_config.mapmri = False
dipy_recon_config.laplacian_weighting = 0.05
dipy_recon_config.shore_positive_constraint = True
diffusion_imaging_model = DSI
processing_tool_editor = ['Dipy', 'MRtrix', 'Custom']

[preprocessing_stage]
eddy_current_and_motion_correction = True
description = description
denoising = False
total_readout = 0.0
eddy_correct_motion_correction = True
dipy_noise_model = Rician
denoising_algo = MRtrix (MP-PCA)
bias_field_algo = ANTS N4
bias_field_correction = False
fast_use_priors = True
resampling = (1, 1, 1)
partial_volume_estimation = True
eddy_correction_algo = FSL eddy_correct
interpolation = interpolate

[connectome_stage]
circular_layout = False
probtrackx = False
output_types = ['gPickle', 'cff']
compute_curvature = False
log_visualization = True
connectivity_metrics = ['Fiber number', 'Fiber length', 'Fiber density', 'Fiber proportion', 'Normalized fiber density', 'ADC', 'gFA']
subject = sub-01

[registration_stage]
ants_convergence_winsize = 10
ants_nonlinear_update_field_variance = 3.0
flirt_args = 
contrast_type = dti
ants_upper_quantile = 0.995
use_float_precision = False
ants_nonlinear_total_field_variance = 0.0
registration_mode = ANTs
init = header
ants_interpolation = BSpline
ants_linear_sampling_perc = 0.25
apply_to_eroded_wm = True
ants_convergence_thresh = 1e-06
ants_multilab_interpolation_parameters = (5.0, 5.0)
ants_gauss_interpolation_parameters = (5.0, 5.0)
ants_nonlinear_cost = CC
ants_bspline_interpolation_parameters = (5,)
apply_to_eroded_brain = False
uses_qform = True
pipeline = Diffusion
ants_lower_quantile = 0.005
no_search = True
ants_linear_cost = MI
ants_linear_gradient_step = 0.1
apply_to_eroded_csf = True
ants_perform_syn = True
ants_linear_sampling_strategy = Regular
dof = 6
diffusion_imaging_model = 
fsl_cost = normmi
ants_nonlinear_gradient_step = 0.1

[Multi-processing]
number_of_cores = 1

Complete crash report

Node: diffusion_pipeline.diffusion_stage.tracking.mrtrix_deterministic_tracking
Working directory: /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/diffusion_stage/tracking/mrtrix_deterministic_tracking

Node inputs:

act_file = /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz
angle = 45.0
args = <undefined>
backtrack = False
crop_at_gmwmi = True
cutoff_value = 0.05
desired_number_of_tracks = 200000
do_not_precompute = <undefined>
environ = {}
gradient_encoding_file = /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/extract_grad/grad.txt
in_file = /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/diffusion_stage/reconstruction/dipy_SHORE/shore_fodf.nii.gz
initial_cutoff_value = <undefined>
initial_direction = <undefined>
inputmodel = SD_Stream
mask_file = <undefined>
maximum_number_of_seeds = <undefined>
maximum_tract_length = 500.0
minimum_tract_length = 5.0
out_file = <undefined>
rk4 = <undefined>
seed_file = <undefined>
seed_gmwmi = /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz
seed_spec = <undefined>
step_size = 0.5
stop = <undefined>
unidirectional = <undefined>

Traceback (most recent call last):
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 48, in run
    node.run(updatehash=updatehash)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 369, in run
    runtime = self._run_interface(runtime)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 752, in _run_interface
    self.raise_exception(runtime)
  File "/opt/conda/envs/py27cmp-core/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 689, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
tckgen /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/diffusion_stage/reconstruction/dipy_SHORE/shore_fodf.nii.gz -act /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz -angle 45.0 -crop_at_gmwmi -cutoff 0.05 -select 200000 -grad /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/extract_grad/grad.txt -maxlength 500.0 -minlength 5.0 -seed_gmwmi /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz -step 0.5 -algorithm SD_Stream shore_fodf_tracked.tck
Standard output:

Standard error:

tckgen: [  0%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [  1%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [  2%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [  3%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [  4%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [  5%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [  6%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [  7%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [  8%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [  9%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 10%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 11%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 12%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 13%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 14%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 15%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 16%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 17%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 18%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 19%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 20%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 21%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 22%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 23%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 24%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 25%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 26%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 27%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 28%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 29%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 30%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 31%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 32%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 33%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 34%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 35%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 36%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 37%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 38%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 39%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 40%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 41%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 42%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 43%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 44%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 45%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 46%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 47%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 48%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 49%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 50%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 51%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 52%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 53%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 54%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 55%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 56%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 57%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 58%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 59%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 60%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 61%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 62%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 63%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 64%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 65%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 66%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 67%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 68%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 69%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 70%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 71%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 72%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 73%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 74%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 75%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 76%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 77%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 78%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 79%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 80%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 81%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 82%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 83%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 84%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 85%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 86%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 87%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 88%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 89%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 90%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 91%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 92%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 93%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 94%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 95%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 96%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 97%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 98%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [ 99%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [100%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"... 
tckgen: [100%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_5tt/act_5tt_resampled_warped.nii.gz"

tckgen: [  0%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [  2%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [  3%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [  5%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [  7%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [  8%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 10%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 12%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 13%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 15%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 17%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 18%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 20%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 22%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 23%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 25%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 27%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 28%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 30%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 32%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 33%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 35%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 37%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 38%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 40%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 42%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 43%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 45%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 47%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 48%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 50%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 52%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 53%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 55%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 57%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 58%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 60%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 62%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 63%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 65%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 67%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 68%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 70%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 72%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 73%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 75%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 77%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 78%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 80%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 82%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 83%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 85%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 87%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 88%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 90%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 92%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 93%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 95%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 97%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [ 98%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [100%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"... 
tckgen: [100%] uncompressing image "/tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz"
tckgen: [ERROR] Cannot use image /tmp/derivatives/nipype/sub-01/ses-1/diffusion_pipeline/registration_stage/apply_warp_gmwmi/gmwmi_resampled_warped.nii.gz for rejection sampling - image is empty
Return code: 1

[sebastientourbier]

Reason aparc+aseg (in .../derivatives/cmp/sub-01/ses-1/anat/sub-01_ses-1_desc-aparcaseg_dseg.nii.gz) generated by CMP3 which is used as input to the mrtrix 5ttgen has label values shifted by 1 (e.g. 1 instead of 2) which causes 5ttgen failing in generating the 5tt image and consequently the GMWM interface image