INFO:nipype.workflow:QSIRecon workflow graph with 53 nodes built successfully.
INFO:cli:Generating an HTML version of the citation boilerplate...
INFO:cli:Generating a LaTeX version of the citation boilerplate...
IMPORTANT:nipype.workflow:QSIRecon started!
WARNING:nipype.interface:Changing /output/sub-261814/dwi/sub-261814_space-ACPC_desc-brain_mask.nii.gz dtype from float64 to float64
INFO:nipype.workflow:[Node] Setting-up "qsirecon_1_1_wf.sub-261814_mrtrix_multishell_msmt_pyafq_tractometry.sub_261814_space_ACPC_desc_preproc_recon_wf.pyafq_tractometry.run_afq" in "/work/qsirecon_1_1_wf/sub-261814_mrtrix_multishell_msmt_pyafq_tractometry/sub_261814_space_ACPC_desc_preproc_recon_wf/pyafq_tractometry/run_afq".
INFO:nipype.workflow:[Node] Executing "run_afq" <qsirecon.interfaces.pyafq.PyAFQRecon>
INFO:AFQ:No seed mask given, using FA (or first scalar if none are FA)thresholded to 0.2
INFO:AFQ:No stop mask given, using FA (or first scalar if none are FA)thresholded to 0.2
INFO:AFQ:Saving /work/qsirecon_1_1_wf/sub-261814_mrtrix_multishell_msmt_pyafq_tractometry/sub_261814_space_ACPC_desc_preproc_recon_wf/pyafq_tractometry/run_afq/study/subject/PYAFQ/models/sub-261814_desc-brain_mask.nii.gz
WARNING:AFQ:Failed to export warped b0. This could be because your mapping type is only compatible with transformation from template to subject space. The error is: Could not compute CSD response function for file: 
<class 'nibabel.nifti1.Nifti1Image'>
data shape (161, 197, 171, 99)
affine:
[[ -1.   0.   0.  80.]
 [  0.  -1.   0.  81.]
 [  0.   0.   1. -80.]
 [  0.   0.   0.   1.]]
metadata:
<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
sizeof_hdr      : 348
data_type       : b''
db_name         : b''
extents         : 0
session_error   : 0
regular         : b''
dim_info        : 0
dim             : [  4 161 197 171  99   1   1   1]
intent_p1       : 0.0
intent_p2       : 0.0
intent_p3       : 0.0
intent_code     : none
datatype        : float64
bitpix          : 64
slice_start     : 0
pixdim          : [1. 1. 1. 1. 1. 1. 1. 1.]
vox_offset      : 0.0
scl_slope       : nan
scl_inter       : nan
slice_end       : 0
slice_code      : unknown
xyzt_units      : 0
cal_max         : 0.0
cal_min         : 0.0
slice_duration  : 0.0
toffset         : 0.0
glmax           : 0
glmin           : 0
descrip         : b''
aux_file        : b''
qform_code      : unknown
sform_code      : aligned
quatern_b       : 0.0
quatern_c       : 0.0
quatern_d       : 1.0
qoffset_x       : 80.0
qoffset_y       : 81.0
qoffset_z       : -80.0
srow_x          : [-1.  0.  0. 80.]
srow_y          : [ 0. -1.  0. 81.]
srow_z          : [  0.   0.   1. -80.]
intent_name     : b''
magic           : b'n+1'
.
INFO:nipype.workflow:[Node] Finished "run_afq", elapsed time 10.541488s.
WARNING:nipype.workflow:Storing result file without outputs
WARNING:nipype.workflow:[Node] Error on "qsirecon_1_1_wf.sub-261814_mrtrix_multishell_msmt_pyafq_tractometry.sub_261814_space_ACPC_desc_preproc_recon_wf.pyafq_tractometry.run_afq" (/work/qsirecon_1_1_wf/sub-261814_mrtrix_multishell_msmt_pyafq_tractometry/sub_261814_space_ACPC_desc_preproc_recon_wf/pyafq_tractometry/run_afq)
ERROR:nipype.workflow:Node run_afq failed to run on host cn1631.hw.accre.vu.
ERROR:nipype.workflow:Saving crash info to /output/sub-261814/log/20250927-075905_ba3dc4de-3246-4384-9ae6-d07b312b76d6/crash-20250927-102920-harrioem-run_afq-409eb250-bb4f-44df-8acf-e622fc93f67c.txt
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node run_afq.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/data.py", line 340, in csd_params
	    csdf = csd_fit_model(
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/models/csd.py", line 67, in _fit
	    return _model(gtab, data, response, sh_order, csd_fa_thr).fit(
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/models/csd.py", line 56, in _model
	    raise CsdNanResponseError
	AFQ.models.csd.CsdNanResponseError

	The above exception was the direct cause of the following exception:

	Traceback (most recent call last):
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    runtime = self._run_interface(runtime)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/interfaces/pyafq.py", line 114, in _run_interface
	    myafq.export_all()
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/api/participant.py", line 201, in export_all
	    export_all_helper(self, xforms, indiv, viz)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/api/utils.py", line 121, in export_all_helper
	    api_afq_object.export("template_xform")
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/api/participant.py", line 155, in export
	    return self.wf_dict[section][attr_name]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 90, in __call__
	    args.append(opts[name])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 889, in __getitem__
	    return self._examine_val(k, ps.PMap.__getitem__(self, k))
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 885, in _examine_val
	    val = val()
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1164, in <lambda>
	    def curry_choice(k, args): return lambda:choose_fn(k, args)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1133, in _choose_last
	    return vs[-1][k]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 90, in __call__
	    args.append(opts[name])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 889, in __getitem__
	    return self._examine_val(k, ps.PMap.__getitem__(self, k))
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 885, in _examine_val
	    val = val()
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1164, in <lambda>
	    def curry_choice(k, args): return lambda:choose_fn(k, args)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1133, in _choose_last
	    return vs[-1][k]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 91, in __call__
	    result = self.function(*args)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/mapping.py", line 212, in get_reg_subject
	    reg_subject_spec = data_imap[filename_dict[reg_subject_spec]]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 90, in __call__
	    args.append(opts[name])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 889, in __getitem__
	    return self._examine_val(k, ps.PMap.__getitem__(self, k))
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 885, in _examine_val
	    val = val()
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1164, in <lambda>
	    def curry_choice(k, args): return lambda:choose_fn(k, args)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1133, in _choose_last
	    return vs[-1][k]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 91, in __call__
	    result = self.function(*args)
	  File "<string>", line 2, in wrapper_has_args_func
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/decorators.py", line 146, in wrapper_as_file
	    gen, meta = func(*args[:og_arg_count], **kwargs)
	  File "<string>", line 2, in wrapper_has_args_func
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/decorators.py", line 216, in wrapper_as_img
	    data, meta = func(*args[:og_arg_count], **kwargs)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/data.py", line 347, in csd_params
	    raise CsdNanResponseError(
	AFQ.models.csd.CsdNanResponseError: Could not compute CSD response function for file: 
	<class 'nibabel.nifti1.Nifti1Image'>
	data shape (161, 197, 171, 99)
	affine:
	[[ -1.   0.   0.  80.]
	 [  0.  -1.   0.  81.]
	 [  0.   0.   1. -80.]
	 [  0.   0.   0.   1.]]
	metadata:
	<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
	sizeof_hdr      : 348
	data_type       : b''
	db_name         : b''
	extents         : 0
	session_error   : 0
	regular         : b''
	dim_info        : 0
	dim             : [  4 161 197 171  99   1   1   1]
	intent_p1       : 0.0
	intent_p2       : 0.0
	intent_p3       : 0.0
	intent_code     : none
	datatype        : float64
	bitpix          : 64
	slice_start     : 0
	pixdim          : [1. 1. 1. 1. 1. 1. 1. 1.]
	vox_offset      : 0.0
	scl_slope       : nan
	scl_inter       : nan
	slice_end       : 0
	slice_code      : unknown
	xyzt_units      : 0
	cal_max         : 0.0
	cal_min         : 0.0
	slice_duration  : 0.0
	toffset         : 0.0
	glmax           : 0
	glmin           : 0
	descrip         : b''
	aux_file        : b''
	qform_code      : unknown
	sform_code      : aligned
	quatern_b       : 0.0
	quatern_c       : 0.0
	quatern_d       : 1.0
	qoffset_x       : 80.0
	qoffset_y       : 81.0
	qoffset_z       : -80.0
	srow_x          : [-1.  0.  0. 80.]
	srow_y          : [ 0. -1.  0. 81.]
	srow_z          : [  0.   0.   1. -80.]
	intent_name     : b''
	magic           : b'n+1'
	.


ERROR:nipype.workflow:could not run node: qsirecon_1_1_wf.sub-261814_mrtrix_multishell_msmt_pyafq_tractometry.sub_261814_space_ACPC_desc_preproc_recon_wf.pyafq_tractometry.run_afq
CRITICAL:nipype.workflow:QSIRecon failed: Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node run_afq.

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/data.py", line 340, in csd_params
	    csdf = csd_fit_model(
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/models/csd.py", line 67, in _fit
	    return _model(gtab, data, response, sh_order, csd_fa_thr).fit(
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/models/csd.py", line 56, in _model
	    raise CsdNanResponseError
	AFQ.models.csd.CsdNanResponseError

	The above exception was the direct cause of the following exception:

	Traceback (most recent call last):
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    runtime = self._run_interface(runtime)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/interfaces/pyafq.py", line 114, in _run_interface
	    myafq.export_all()
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/api/participant.py", line 201, in export_all
	    export_all_helper(self, xforms, indiv, viz)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/api/utils.py", line 121, in export_all_helper
	    api_afq_object.export("template_xform")
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/api/participant.py", line 155, in export
	    return self.wf_dict[section][attr_name]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 90, in __call__
	    args.append(opts[name])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 889, in __getitem__
	    return self._examine_val(k, ps.PMap.__getitem__(self, k))
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 885, in _examine_val
	    val = val()
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1164, in <lambda>
	    def curry_choice(k, args): return lambda:choose_fn(k, args)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1133, in _choose_last
	    return vs[-1][k]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 90, in __call__
	    args.append(opts[name])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 889, in __getitem__
	    return self._examine_val(k, ps.PMap.__getitem__(self, k))
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 885, in _examine_val
	    val = val()
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1164, in <lambda>
	    def curry_choice(k, args): return lambda:choose_fn(k, args)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1133, in _choose_last
	    return vs[-1][k]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 91, in __call__
	    result = self.function(*args)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/mapping.py", line 212, in get_reg_subject
	    reg_subject_spec = data_imap[filename_dict[reg_subject_spec]]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 90, in __call__
	    args.append(opts[name])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 889, in __getitem__
	    return self._examine_val(k, ps.PMap.__getitem__(self, k))
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 885, in _examine_val
	    val = val()
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1164, in <lambda>
	    def curry_choice(k, args): return lambda:choose_fn(k, args)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/util.py", line 1133, in _choose_last
	    return vs[-1][k]
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 470, in __getitem__
	    self._run_node(self.plan.efferents[k])
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 534, in _run_node
	    if not found: res = node(self)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pimms/calculation.py", line 91, in __call__
	    result = self.function(*args)
	  File "<string>", line 2, in wrapper_has_args_func
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/decorators.py", line 146, in wrapper_as_file
	    gen, meta = func(*args[:og_arg_count], **kwargs)
	  File "<string>", line 2, in wrapper_has_args_func
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/decorators.py", line 216, in wrapper_as_img
	    data, meta = func(*args[:og_arg_count], **kwargs)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/AFQ/tasks/data.py", line 347, in csd_params
	    raise CsdNanResponseError(
	AFQ.models.csd.CsdNanResponseError: Could not compute CSD response function for file: 
	<class 'nibabel.nifti1.Nifti1Image'>
	data shape (161, 197, 171, 99)
	affine:
	[[ -1.   0.   0.  80.]
	 [  0.  -1.   0.  81.]
	 [  0.   0.   1. -80.]
	 [  0.   0.   0.   1.]]
	metadata:
	<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
	sizeof_hdr      : 348
	data_type       : b''
	db_name         : b''
	extents         : 0
	session_error   : 0
	regular         : b''
	dim_info        : 0
	dim             : [  4 161 197 171  99   1   1   1]
	intent_p1       : 0.0
	intent_p2       : 0.0
	intent_p3       : 0.0
	intent_code     : none
	datatype        : float64
	bitpix          : 64
	slice_start     : 0
	pixdim          : [1. 1. 1. 1. 1. 1. 1. 1.]
	vox_offset      : 0.0
	scl_slope       : nan
	scl_inter       : nan
	slice_end       : 0
	slice_code      : unknown
	xyzt_units      : 0
	cal_max         : 0.0
	cal_min         : 0.0
	slice_duration  : 0.0
	toffset         : 0.0
	glmax           : 0
	glmin           : 0
	descrip         : b''
	aux_file        : b''
	qform_code      : unknown
	sform_code      : aligned
	quatern_b       : 0.0
	quatern_c       : 0.0
	quatern_d       : 1.0
	qoffset_x       : 80.0
	qoffset_y       : 81.0
	qoffset_z       : -80.0
	srow_x          : [-1.  0.  0. 80.]
	srow_y          : [ 0. -1.  0. 81.]
	srow_z          : [  0.   0.   1. -80.]
	intent_name     : b''
	magic           : b'n+1'
	.


WARNING:nipype.utils:DatasetType key not in /data/dataset_description.json. Assuming 'derivative'.
WARNING:nipype.utils:DatasetType key not in /data/dataset_description.json. Assuming 'derivative'.
WARNING:nipype.utils:DatasetType key not in /data/dataset_description.json. Assuming 'derivative'.