Hi all,

I have a problem when I tried to run CPAC,
the errors are as following:


outputSubjectListLocation : '/home/peter/fcon_1000/%s/%s/anat/mprage_anonymized.nii.gz'

outputSubjectListLocation : '/home/peter/fcon_1000/%s/%s/func/rest.nii.gz'
outputSubjectListLocation : None
outputSubjectListLocation : None
outputSubjectListLocation : ['NYU']
outputSubjectListLocation : None
outputSubjectListLocation : /home/peter/fcon_1000/NYU
saving /home/peter/fcon_1000/NYU_data_config.yaml
executing extract data
For any errors or messages check the log file - /home/peter/extract_data_logs.log
Extraction Successfully Completed...Input Subjects_list for CPAC - /home/peter/fcon_1000/NYU/CPAC_subject_list.yml
Template Phenotypic file for group analysis - /home/peter/fcon_1000/NYU/phenotypic_template.csv
Subject list required later for group analysis - /home/peter/fcon_1000/NYU/subject_list_group_analysis.txt
['wm,csf,motion']
['wm,csf,motion', 'gm']
['wm,csf,motion']
[]
['gm']
['gm', 'wm,csf,motion']
['[0.01, 0.1]']
pipeline_id == NorthHodge
running for configuration, subject list, pipeline_id --> /home/peter/fcon_1000/pipeline_config_NYU123.yml /home/peter/fcon_1000/NYU/CPAC_subject_list.yml DAVID
corrections dictionary list:
[{'global': 0, 'linear': 0, 'wm': 0, 'pc1': 0, 'motion': 0, 'quadratic': 0, 'gm': 1, 'compcor': 0, 'csf': 0}, {'global': 0, 'linear': 0, 'wm': 1, 'pc1': 0, 'motion': 1, 'quadratic': 0, 'gm': 0, 'compcor': 0, 'csf': 1}]
Paths:
["['ncomponents_5_selector_pc10.linear0.wm0.global0.motion0.quadratic0.gm1.compcor0.csf0', 'ncomponents_5_selector_pc10.linear0.wm1.global0.motion1.quadratic0.gm0.compcor0.csf1']#['0.96']#['0.7']#[90]#['0.2']#['0.96']"]
sub entries:
['_compcor_ncomponents_5_selector_pc10.linear0.wm0.global0.motion0.quadratic0.gm1.compcor0.csf0.ncomponents_5_selector_pc10.linear0.wm1.global0.motion1.quadratic0.gm0.compcor0.csf1', '_csf_threshold_0.96', '_gm_threshold_0.7', '_target_angle_deg_90', '_threshold_0.2', '_wm_threshold_0.96']
strategies --->
[['_compcor_ncomponents_5_selector_pc10.linear0.wm0.global0.motion0.quadratic0.gm1.compcor0.csf0.ncomponents_5_selector_pc10.linear0.wm1.global0.motion1.quadratic0.gm0.compcor0.csf1', '_csf_threshold_0.96', '_gm_threshold_0.7', '_target_angle_deg_90', '_threshold_0.2', '_wm_threshold_0.96']]
subject list:
[{'subject_id': 'sub19738', 'anat': '/home/peter/fcon_1000/NYU/sub19738/anat/mprage_anonymized.nii.gz', 'unique_id': '', 'rest': {'func_rest': '/home/peter/fcon_1000/NYU/sub19738/func/rest.nii.gz'}}, {'subject_id': 'sub17017', 'anat': '/home/peter/fcon_1000/NYU/sub17017/anat/mprage_anonymized.nii.gz', 'unique_id': '', 'rest': {'func_rest': '/home/peter/fcon_1000/NYU/sub17017/func/rest.nii.gz'}}]
/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py:376: UserWarning: Input apply_xfm requires inputs: in_matrix_file
warn(msg)
/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py:376: UserWarning: Input apply_xfm requires inputs: in_matrix_file
warn(msg)
/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py:376: UserWarning: Input apply_xfm requires inputs: in_matrix_file
warn(msg)
/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py:376: UserWarning: Input apply_xfm requires inputs: in_matrix_file
warn(msg)
/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py:376: UserWarning: Input apply_xfm requires inputs: in_matrix_file
warn(msg)
/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py:376: UserWarning: Input apply_xfm requires inputs: in_matrix_file
warn(msg)
anat_preproc  ~~~  1
seg_preproc  ~~~  4
func_preproc  ~~~  8
fristons_parameter_model  ~~~  16
func_to_anat_bbreg  ~~~  64
gen_motion_stats  ~~~  128
nuisance  ~~~  256
frequency_filter  ~~~  1024
anat_preproc  ~~~  1
seg_preproc  ~~~  4
func_preproc  ~~~  8
fristons_parameter_model  ~~~  16
func_to_anat_bbreg  ~~~  64
gen_motion_stats  ~~~  128
nuisance  ~~~  256
frequency_filter  ~~~  1024
Process Process-2:
Traceback (most recent call last):
File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/lib/python2.7/dist-packages/CPAC/pipeline/cpac_pipeline.py", line 4069, in prep_workflow
workflow.run(plugin='MultiProc', plugin_args={'n_procs': c.numCoresPerSubject})
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 679, in run
Process Process-1:
Traceback (most recent call last):
File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/lib/python2.7/dist-packages/CPAC/pipeline/cpac_pipeline.py", line 4069, in prep_workflow
workflow.run(plugin='MultiProc', plugin_args={'n_procs': c.numCoresPerSubject})
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 679, in run
execgraph = generate_expanded_graph(deepcopy(flatgraph))
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/utils.py", line 572, in generate_expanded_graph
execgraph = generate_expanded_graph(deepcopy(flatgraph))
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/utils.py", line 572, in generate_expanded_graph
graph_in = _remove_nonjoin_identity_nodes(graph_in, keep_iterables=True)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/utils.py", line 471, in _remove_nonjoin_identity_nodes
_remove_identity_node(graph, node)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/utils.py", line 492, in _remove_identity_node
graph_in = _remove_nonjoin_identity_nodes(graph_in, keep_iterables=True)
portinputs)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/utils.py", line 561, in _propagate_internal_output
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/utils.py", line 471, in _remove_nonjoin_identity_nodes
destnode.set_input(inport, value)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1244, in set_input
setattr(self.inputs, parameter, deepcopy(val))
_remove_identity_node(graph, node)
File "/usr/lib/python2.7/dist-packages/traits/trait_handlers.py", line 170, in error
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/utils.py", line 492, in _remove_identity_node
portinputs)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/utils.py", line 561, in _propagate_internal_output
destnode.set_input(inport, value)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1244, in set_input
setattr(self.inputs, parameter, deepcopy(val))
File "/usr/lib/python2.7/dist-packages/traits/trait_handlers.py", line 170, in error
value )
value )
TraitError: The 'config_file' trait of a FNIRTInputSpec instance must be 'T1_2_MNI152_2mm' or 'FA_2_FMRIB58_1mm' or an existing file name, but a value of '/usr/share/fsl/5.0/etc/flirtsch/T1_2_MNI152_3mm.cnf' was specified.
TraitError: The 'config_file' trait of a FNIRTInputSpec instance must be 'T1_2_MNI152_2mm' or 'FA_2_FMRIB58_1mm' or an existing file name, but a value of '/usr/share/fsl/5.0/etc/flirtsch/T1_2_MNI152_3mm.cnf' was specified.


what's wrong happened? and how to fix it?

Thank you so much.

Best

Peter

then I rerun the cpac setup.py, but I get the  " customize UnixCCompiler", what does this mean?


BUT I STILL GET THE WRONG MESSAGE.


In [1]: import CPAC
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
in ()
----> 1 import CPAC

ImportError: No module named CPAC

WHO CAN HELP ME TO FIX?

THANK YOU IN ADVANCE.

I have solved this...

Dear Peter

I am having the exact same issue. How did you solve it?

Kind regards,

Joaquin