Example 2: 1st-level Analysis¶

In this example, we will take the preprocessed output from the first example and run for each subject a 1st-level analysis. For this we need to do the following steps:

Extract onset times of stimuli from TVA file
Specify the model (TR, high pass filter, onset times, etc.)
Specify contrasts to compute
Estimate contrasts

In the previous example, we used two different smoothing kernels of fwhm=4 and fwhm=8. Therefore, let us also run the 1st-level analysis for those two versions.

So, let's begin!

Imports¶

First, we need to import all the modules we later want to use.

%matplotlib inline
from os.path import join as opj
import json
from nipype.interfaces.spm import Level1Design, EstimateModel, EstimateContrast
from nipype.algorithms.modelgen import SpecifySPMModel
from nipype.interfaces.utility import Function, IdentityInterface
from nipype.interfaces.io import SelectFiles, DataSink
from nipype import Workflow, Node

Experiment parameters¶

It's always a good idea to specify all parameters that might change between experiments at the beginning of your script.

experiment_dir = '/output'
output_dir = 'datasink'
working_dir = 'workingdir'

# list of subject identifiers
subject_list = ['01', '02', '03', '04', '05', '06', '07', '08', '09', '10']

# TR of functional images
with open('/data/ds000114/task-fingerfootlips_bold.json', 'rt') as fp:
    task_info = json.load(fp)
TR = task_info['RepetitionTime']

# Smoothing withds used during preprocessing
fwhm = [4, 8]

Specify Nodes¶

Initiate all the different interfaces (represented as nodes) that you want to use in your workflow.

# SpecifyModel - Generates SPM-specific Model
modelspec = Node(SpecifySPMModel(concatenate_runs=False,
                                 input_units='secs',
                                 output_units='secs',
                                 time_repetition=TR,
                                 high_pass_filter_cutoff=128),
                 name="modelspec")

# Level1Design - Generates an SPM design matrix
level1design = Node(Level1Design(bases={'hrf': {'derivs': [1, 0]}},
                                 timing_units='secs',
                                 interscan_interval=TR,
                                 model_serial_correlations='FAST'),
                    name="level1design")

# EstimateModel - estimate the parameters of the model
level1estimate = Node(EstimateModel(estimation_method={'Classical': 1}),
                      name="level1estimate")

# EstimateContrast - estimates contrasts
level1conest = Node(EstimateContrast(), name="level1conest")

Specify GLM contrasts¶

To do any GLM analysis, we need to also define the contrasts that we want to investigate. If we recap, we had three different conditions in the fingerfootlips task in this dataset:

finger
foot
lips

Therefore, we could create the following contrasts (seven T-contrasts and two F-contrasts):

# Condition names
condition_names = ['Finger', 'Foot', 'Lips']

# Contrasts
cont01 = ['average',        'T', condition_names, [1/3., 1/3., 1/3.]]
cont02 = ['Finger',         'T', condition_names, [1, 0, 0]]
cont03 = ['Foot',           'T', condition_names, [0, 1, 0]]
cont04 = ['Lips',           'T', condition_names, [0, 0, 1]]
cont05 = ['Finger > others','T', condition_names, [1, -0.5, -0.5]]
cont06 = ['Foot > others',  'T', condition_names, [-0.5, 1, -0.5]]
cont07 = ['Lips > others',  'T', condition_names, [-0.5, -0.5, 1]]

cont08 = ['activation',     'F', [cont02, cont03, cont04]]
cont09 = ['differences',    'F', [cont05, cont06, cont07]]

contrast_list = [cont01, cont02, cont03, cont04, cont05, cont06, cont07, cont08, cont09]

Specify GLM Model¶

The next step is now to get information such as stimuli onset, duration and other regressors into the GLM model. For this we need to create a helper function, in our case called subjectinfo.

To recap, let's see what we have in the TSV file for each run:

!cat /data/ds000114/task-fingerfootlips_events.tsv

onset	duration	weight	trial_type
10	15.0	1	Finger
40	15.0	1	Foot
70	15.0	1	Lips
100	15.0	1	Finger
130	15.0	1	Foot
160	15.0	1	Lips
190	15.0	1	Finger
220	15.0	1	Foot
250	15.0	1	Lips
280	15.0	1	Finger
310	15.0	1	Foot
340	15.0	1	Lips
370	15.0	1	Finger
400	15.0	1	Foot
430	15.0	1	Lips

We can also create a data frame using pandas library.

import pandas as pd
trialinfo = pd.read_table('/data/ds000114/task-fingerfootlips_events.tsv')
trialinfo

And finally we need to separate the onsets of the three conditions, i.e. group by trial_type. This can be done as follows:

for group in trialinfo.groupby('trial_type'):
    print(group)
    print("")

('Finger',     onset  duration  weight trial_type
0      10      15.0       1     Finger
3     100      15.0       1     Finger
6     190      15.0       1     Finger
9     280      15.0       1     Finger
12    370      15.0       1     Finger)

('Foot',     onset  duration  weight trial_type
1      40      15.0       1       Foot
4     130      15.0       1       Foot
7     220      15.0       1       Foot
10    310      15.0       1       Foot
13    400      15.0       1       Foot)

('Lips',     onset  duration  weight trial_type
2      70      15.0       1       Lips
5     160      15.0       1       Lips
8     250      15.0       1       Lips
11    340      15.0       1       Lips
14    430      15.0       1       Lips)

Now, let us incorporate all this in the helper function subjectinfo.

def subjectinfo(subject_id):

    import pandas as pd
    from nipype.interfaces.base import Bunch

    trialinfo = pd.read_table('/data/ds000114/task-fingerfootlips_events.tsv')
    trialinfo.head()
    conditions = []
    onsets = []
    durations = []

    for group in trialinfo.groupby('trial_type'):
        conditions.append(group[0])
        onsets.append(list(group[1].onset - 10)) # subtracting 10s due to removing of 4 dummy scans
        durations.append(group[1].duration.tolist())

    subject_info = [Bunch(conditions=conditions,
                          onsets=onsets,
                          durations=durations,
                          #amplitudes=None,
                          #tmod=None,
                          #pmod=None,
                          #regressor_names=None,
                          #regressors=None
                         )]

    return subject_info  # this output will later be returned to infosource

# Get Subject Info - get subject specific condition information
getsubjectinfo = Node(Function(input_names=['subject_id'],
                               output_names=['subject_info'],
                               function=subjectinfo),
                      name='getsubjectinfo')

Specify input & output stream¶

Specify where the input data can be found & where and how to save the output data.

# Infosource - a function free node to iterate over the list of subject names
infosource = Node(IdentityInterface(fields=['subject_id',
                                            'fwhm_id',
                                            'contrasts'],
                                    contrasts=contrast_list),
                  name="infosource")
infosource.iterables = [('subject_id', subject_list),
                        ('fwhm_id', fwhm)]

# SelectFiles - to grab the data (alternativ to DataGrabber)
templates = {'func': opj(output_dir, 'preproc', 'sub-{subject_id}', 'task-{task_id}',
                         'fwhm-{fwhm_id}_ssub-{subject_id}_ses-test_task-{task_id}_bold.nii'),
             'mc_param': opj(output_dir, 'preproc', 'sub-{subject_id}', 'task-{task_id}',
                             'sub-{subject_id}_ses-test_task-{task_id}_bold.par'),
             'outliers': opj(output_dir, 'preproc', 'sub-{subject_id}', 'task-{task_id}',
                             'art.sub-{subject_id}_ses-test_task-{task_id}_bold_outliers.txt')}
selectfiles = Node(SelectFiles(templates,
                               base_directory=experiment_dir,
                               sort_filelist=True),
                   name="selectfiles")
selectfiles.inputs.task_id = 'fingerfootlips'

# Datasink - creates output folder for important outputs
datasink = Node(DataSink(base_directory=experiment_dir,
                         container=output_dir),
                name="datasink")

# Use the following DataSink output substitutions
substitutions = [('_subject_id_', 'sub-')]
subjFolders = [('_fwhm_id_%ssub-%s' % (f, sub), 'sub-%s/fwhm-%s' % (sub, f))
               for f in fwhm
               for sub in subject_list]
substitutions.extend(subjFolders)
datasink.inputs.substitutions = substitutions

Specify Workflow¶

Create a workflow and connect the interface nodes and the I/O stream to each other.

# Initiation of the 1st-level analysis workflow
l1analysis = Workflow(name='l1analysis')
l1analysis.base_dir = opj(experiment_dir, working_dir)

# Connect up the 1st-level analysis components
l1analysis.connect([(infosource, selectfiles, [('subject_id', 'subject_id'),
                                               ('fwhm_id', 'fwhm_id')]),
                    (infosource, getsubjectinfo, [('subject_id',
                                                   'subject_id')]),
                    (getsubjectinfo, modelspec, [('subject_info',
                                                  'subject_info')]),
                    (infosource, level1conest, [('contrasts', 'contrasts')]),
                    (selectfiles, modelspec, [('func', 'functional_runs')]),
                    (selectfiles, modelspec, [('mc_param', 'realignment_parameters'),
                                              ('outliers', 'outlier_files')]),
                    (modelspec, level1design, [('session_info',
                                                'session_info')]),
                    (level1design, level1estimate, [('spm_mat_file',
                                                     'spm_mat_file')]),
                    (level1estimate, level1conest, [('spm_mat_file',
                                                     'spm_mat_file'),
                                                    ('beta_images',
                                                     'beta_images'),
                                                    ('residual_image',
                                                     'residual_image')]),
                    (level1conest, datasink, [('spm_mat_file', '1stLevel.@spm_mat'),
                                              ('spmT_images', '1stLevel.@T'),
                                              ('con_images', '1stLevel.@con'),
                                              ('spmF_images', '1stLevel.@F'),
                                              ('ess_images', '1stLevel.@ess'),
                                              ]),
                    ])

Visualize the workflow¶

It always helps to visualize your workflow.

# Create 1st-level analysis output graph
l1analysis.write_graph(graph2use='colored', format='png', simple_form=True)

# Visualize the graph
from IPython.display import Image
Image(filename=opj(l1analysis.base_dir, 'l1analysis', 'graph.png'))

180514-10:47:53,876 workflow INFO:
	 Generated workflow graph: /output/workingdir/l1analysis/graph.png (graph2use=colored, simple_form=True).

Run the Workflow¶

Now that everything is ready, we can run the 1st-level analysis workflow. Change n_procs to the number of jobs/cores you want to use.

l1analysis.run('MultiProc', plugin_args={'n_procs': 8})

180514-10:47:53,944 workflow INFO:
	 Workflow l1analysis settings: ['check', 'execution', 'logging', 'monitoring']
180514-10:47:54,75 workflow INFO:
	 Running in parallel.
180514-10:47:54,82 workflow INFO:
	 [MultiProc] Running 0 tasks, and 40 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:47:54,140 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_10/getsubjectinfo".
180514-10:47:54,143 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_10/selectfiles".
180514-10:47:54,150 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_09/getsubjectinfo".180514-10:47:54,149 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")180514-10:47:54,152 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:47:54,154 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_09/selectfiles".


180514-10:47:54,160 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")180514-10:47:54,161 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:47:54,163 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".

180514-10:47:54,147 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_10/selectfiles".180514-10:47:54,171 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".180514-10:47:54,145 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_10/getsubjectinfo".180514-10:47:54,148 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_09/selectfiles".180514-10:47:54,147 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_09/getsubjectinfo".


180514-10:47:54,175 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".
180514-10:47:54,183 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")

180514-10:47:54,186 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:47:54,183 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")180514-10:47:54,185 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")

180514-10:47:54,187 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".

180514-10:47:54,194 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".180514-10:47:54,198 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".


180514-10:47:54,207 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".
180514-10:47:54,213 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".
180514-10:47:56,84 workflow INFO:
	 [Job 0] Completed (l1analysis.getsubjectinfo).
180514-10:47:56,90 workflow INFO:
	 [Job 1] Completed (l1analysis.selectfiles).
180514-10:47:56,95 workflow INFO:
	 [Job 7] Completed (l1analysis.getsubjectinfo).
180514-10:47:56,102 workflow INFO:
	 [Job 8] Completed (l1analysis.selectfiles).
180514-10:47:56,109 workflow INFO:
	 [Job 14] Completed (l1analysis.getsubjectinfo).
180514-10:47:56,116 workflow INFO:
	 [Job 15] Completed (l1analysis.selectfiles).
180514-10:47:56,122 workflow INFO:
	 [Job 21] Completed (l1analysis.getsubjectinfo).
180514-10:47:56,127 workflow INFO:
	 [Job 22] Completed (l1analysis.selectfiles).
180514-10:47:56,133 workflow INFO:
	 [MultiProc] Running 0 tasks, and 36 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:47:56,189 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_10/modelspec".
180514-10:47:56,194 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_10/modelspec".
180514-10:47:56,198 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")180514-10:47:56,200 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_09/modelspec".

180514-10:47:56,206 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")180514-10:47:56,210 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")
180514-10:47:56,211 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_09/modelspec".
180514-10:47:56,214 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_08/getsubjectinfo".

180514-10:47:56,222 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")180514-10:47:56,220 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")

180514-10:47:56,229 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_08/selectfiles".
180514-10:47:56,219 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_08/selectfiles".
180514-10:47:56,224 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_08/getsubjectinfo".180514-10:47:56,241 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
180514-10:47:56,236 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:47:56,254 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".
180514-10:47:56,245 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".

180514-10:47:56,262 workflow INFO:
	 [Node] Finished "l1analysis.modelspec".180514-10:47:56,259 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")180514-10:47:56,263 workflow INFO:
	 [Node] Finished "l1analysis.modelspec".
180514-10:47:56,268 workflow INFO:
	 [Node] Finished "l1analysis.modelspec".
180514-10:47:56,270 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".


180514-10:47:56,286 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".
180514-10:47:56,296 workflow INFO:
	 [Node] Finished "l1analysis.modelspec".
180514-10:47:58,85 workflow INFO:
	 [Job 2] Completed (l1analysis.modelspec).
180514-10:47:58,87 workflow INFO:
	 [Job 9] Completed (l1analysis.modelspec).
180514-10:47:58,90 workflow INFO:
	 [Job 16] Completed (l1analysis.modelspec).
180514-10:47:58,92 workflow INFO:
	 [Job 23] Completed (l1analysis.modelspec).
180514-10:47:58,94 workflow INFO:
	 [Job 28] Completed (l1analysis.getsubjectinfo).
180514-10:47:58,96 workflow INFO:
	 [Job 29] Completed (l1analysis.selectfiles).
180514-10:47:58,98 workflow INFO:
	 [Job 35] Completed (l1analysis.getsubjectinfo).
180514-10:47:58,100 workflow INFO:
	 [Job 36] Completed (l1analysis.selectfiles).
180514-10:47:58,103 workflow INFO:
	 [MultiProc] Running 0 tasks, and 34 jobs ready. Free memory (GB): 53.94/53.94, Free processors: 8/8.
180514-10:47:58,173 workflow INFO:
	 [Node] Setting-up "l1analysis.level1design" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_10/level1design".
180514-10:47:58,205 workflow INFO:
	 [Node] Setting-up "l1analysis.level1design" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_10/level1design".
180514-10:47:58,226 workflow INFO:
	 [Node] Running "level1design" ("nipype.interfaces.spm.model.Level1Design")
180514-10:47:58,229 workflow INFO:
	 [Node] Setting-up "l1analysis.level1design" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_09/level1design".
180514-10:47:58,247 workflow INFO:
	 [Node] Running "level1design" ("nipype.interfaces.spm.model.Level1Design")
180514-10:47:58,264 workflow INFO:
	 [Node] Setting-up "l1analysis.level1design" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_09/level1design".
180514-10:47:58,270 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_08/modelspec".
180514-10:47:58,271 workflow INFO:
	 [Node] Running "level1design" ("nipype.interfaces.spm.model.Level1Design")
180514-10:47:58,277 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_08/modelspec".
180514-10:47:58,279 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_07/getsubjectinfo".180514-10:47:58,280 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")180514-10:47:58,284 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_07/selectfiles".
180514-10:47:58,288 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")


180514-10:47:58,291 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:47:58,294 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")

180514-10:47:58,314 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".180514-10:47:58,315 workflow INFO:
	 [Node] Running "level1design" ("nipype.interfaces.spm.model.Level1Design")

/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/modelgen.py:423: UserWarning: loadtxt: Empty input file: "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_08/modelspec/art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt"
  outindices = np.loadtxt(filename, dtype=int)

180514-10:47:58,323 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".

/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/modelgen.py:423: UserWarning: loadtxt: Empty input file: "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_08/modelspec/art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt"
  outindices = np.loadtxt(filename, dtype=int)

180514-10:47:58,349 workflow INFO:
	 [Node] Finished "l1analysis.modelspec".
180514-10:47:58,381 workflow INFO:
	 [Node] Finished "l1analysis.modelspec".
180514-10:48:00,87 workflow INFO:
	 [Job 30] Completed (l1analysis.modelspec).
180514-10:48:00,89 workflow INFO:
	 [Job 37] Completed (l1analysis.modelspec).
180514-10:48:00,93 workflow INFO:
	 [Job 42] Completed (l1analysis.getsubjectinfo).
180514-10:48:00,95 workflow INFO:
	 [Job 43] Completed (l1analysis.selectfiles).
180514-10:48:00,101 workflow INFO:
	 [MultiProc] Running 4 tasks, and 29 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
                     Currently running:
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
180514-10:48:00,197 workflow INFO:
	 [Node] Setting-up "l1analysis.level1design" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_08/level1design".
180514-10:48:00,228 workflow INFO:
	 [Node] Running "level1design" ("nipype.interfaces.spm.model.Level1Design")180514-10:48:00,232 workflow INFO:
	 [Node] Setting-up "l1analysis.level1design" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_08/level1design".

180514-10:48:00,250 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_07/getsubjectinfo".
180514-10:48:00,264 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")180514-10:48:00,248 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_07/modelspec".

180514-10:48:00,298 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")180514-10:48:00,293 workflow INFO:
	 [Node] Running "level1design" ("nipype.interfaces.spm.model.Level1Design")
180514-10:48:00,303 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".

/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/modelgen.py:423: UserWarning: loadtxt: Empty input file: "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_07/modelspec/art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt"
  outindices = np.loadtxt(filename, dtype=int)

180514-10:48:00,376 workflow INFO:
	 [Node] Finished "l1analysis.modelspec".
180514-10:48:02,89 workflow INFO:
	 [Job 44] Completed (l1analysis.modelspec).
180514-10:48:02,96 workflow INFO:
	 [Job 49] Completed (l1analysis.getsubjectinfo).
180514-10:48:02,104 workflow INFO:
	 [MultiProc] Running 6 tasks, and 26 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
                     Currently running:
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
180514-10:48:02,204 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_07/selectfiles".180514-10:48:02,200 workflow INFO:
	 [Node] Setting-up "l1analysis.level1design" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_07/level1design".

180514-10:48:02,245 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:48:02,272 workflow INFO:
	 [Node] Running "level1design" ("nipype.interfaces.spm.model.Level1Design")
180514-10:48:02,284 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".

180514-10:48:04,93 workflow INFO:
	 [Job 50] Completed (l1analysis.selectfiles).
180514-10:48:04,100 workflow INFO:
	 [MultiProc] Running 7 tasks, and 25 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
                     Currently running:
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
180514-10:48:04,162 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_07/modelspec".
180514-10:48:04,179 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")

/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/modelgen.py:423: UserWarning: loadtxt: Empty input file: "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_07/modelspec/art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt"
  outindices = np.loadtxt(filename, dtype=int)

180514-10:48:04,227 workflow INFO:
	 [Node] Finished "l1analysis.modelspec".
180514-10:48:06,94 workflow INFO:
	 [Job 51] Completed (l1analysis.modelspec).
180514-10:48:06,97 workflow INFO:
	 [MultiProc] Running 7 tasks, and 25 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
                     Currently running:
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
180514-10:48:06,173 workflow INFO:
	 [Node] Setting-up "l1analysis.level1design" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_07/level1design".
180514-10:48:06,204 workflow INFO:
	 [Node] Running "level1design" ("nipype.interfaces.spm.model.Level1Design")
180514-10:48:08,98 workflow INFO:
	 [MultiProc] Running 8 tasks, and 24 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
                     Currently running:
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
180514-10:48:31,405 workflow INFO:
	 [Node] Finished "l1analysis.level1design".
180514-10:48:32,121 workflow INFO:
	 [Job 24] Completed (l1analysis.level1design).
180514-10:48:32,135 workflow INFO:
	 [MultiProc] Running 7 tasks, and 25 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
                     Currently running:
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
180514-10:48:32,214 workflow INFO:
	 [Node] Setting-up "l1analysis.level1estimate" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_09/level1estimate".
180514-10:48:32,253 workflow INFO:
	 [Node] Running "level1estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-10:48:33,58 workflow INFO:
	 [Node] Finished "l1analysis.level1design".
180514-10:48:33,358 workflow INFO:
	 [Node] Finished "l1analysis.level1design".
180514-10:48:33,484 workflow INFO:
	 [Node] Finished "l1analysis.level1design".
180514-10:48:34,125 workflow INFO:
	 [Job 3] Completed (l1analysis.level1design).
180514-10:48:34,128 workflow INFO:
	 [Job 10] Completed (l1analysis.level1design).
180514-10:48:34,131 workflow INFO:
	 [Job 17] Completed (l1analysis.level1design).
180514-10:48:34,135 workflow INFO:
	 [MultiProc] Running 5 tasks, and 27 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
                     Currently running:
                       * l1analysis.level1estimate
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
                       * l1analysis.level1design
180514-10:48:34,195 workflow INFO:
	 [Node] Setting-up "l1analysis.level1estimate" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_10/level1estimate".
180514-10:48:34,202 workflow INFO:
	 [Node] Setting-up "l1analysis.level1estimate" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_10/level1estimate".
180514-10:48:34,208 workflow INFO:
	 [Node] Setting-up "l1analysis.level1estimate" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_09/level1estimate".180514-10:48:34,216 workflow INFO:
	 [Node] Running "level1estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-10:48:34,226 workflow INFO:
	 [Node] Running "level1estimate" ("nipype.interfaces.spm.model.EstimateModel")

180514-10:48:34,246 workflow INFO:
	 [Node] Running "level1estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-10:48:34,790 workflow INFO:
	 [Node] Finished "l1analysis.level1design".
180514-10:48:34,893 workflow INFO:
	 [Node] Finished "l1analysis.level1design".
180514-10:48:36,127 workflow INFO:
	 [Job 31] Completed (l1analysis.level1design).
180514-10:48:36,135 workflow INFO:
	 [Job 38] Completed (l1analysis.level1design).
180514-10:48:36,145 workflow INFO:
	 [MultiProc] Running 6 tasks, and 26 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
                     Currently running:
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1design
                       * l1analysis.level1design
180514-10:48:36,231 workflow INFO:
	 [Node] Setting-up "l1analysis.level1estimate" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_08/level1estimate".180514-10:48:36,237 workflow INFO:
	 [Node] Setting-up "l1analysis.level1estimate" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_08/level1estimate".

180514-10:48:36,286 workflow INFO:
	 [Node] Running "level1estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-10:48:36,315 workflow INFO:
	 [Node] Running "level1estimate" ("nipype.interfaces.spm.model.EstimateModel")180514-10:48:36,318 workflow INFO:
	 [Node] Finished "l1analysis.level1design".

180514-10:48:38,130 workflow INFO:
	 [Job 45] Completed (l1analysis.level1design).
180514-10:48:38,140 workflow INFO:
	 [MultiProc] Running 7 tasks, and 25 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
                     Currently running:
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1design
180514-10:48:38,207 workflow INFO:
	 [Node] Setting-up "l1analysis.level1estimate" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_07/level1estimate".
180514-10:48:38,236 workflow INFO:
	 [Node] Running "level1estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-10:48:39,70 workflow INFO:
	 [Node] Finished "l1analysis.level1design".
180514-10:48:40,135 workflow INFO:
	 [Job 52] Completed (l1analysis.level1design).
180514-10:48:40,160 workflow INFO:
	 [MultiProc] Running 7 tasks, and 25 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
                     Currently running:
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
180514-10:48:40,261 workflow INFO:
	 [Node] Setting-up "l1analysis.level1estimate" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_07/level1estimate".
180514-10:48:40,363 workflow INFO:
	 [Node] Running "level1estimate" ("nipype.interfaces.spm.model.EstimateModel")
180514-10:48:42,140 workflow INFO:
	 [MultiProc] Running 8 tasks, and 24 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
                     Currently running:
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
180514-10:49:06,722 workflow INFO:
	 [Node] Finished "l1analysis.level1estimate".
180514-10:49:08,165 workflow INFO:
	 [Job 25] Completed (l1analysis.level1estimate).
180514-10:49:08,213 workflow INFO:
	 [MultiProc] Running 7 tasks, and 25 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
                     Currently running:
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
180514-10:49:08,301 workflow INFO:
	 [Node] Setting-up "l1analysis.level1conest" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_09/level1conest".
180514-10:49:08,356 workflow INFO:
	 [Node] Running "level1conest" ("nipype.interfaces.spm.model.EstimateContrast")
180514-10:49:08,453 workflow INFO:
	 [Node] Finished "l1analysis.level1estimate".
180514-10:49:09,210 workflow INFO:
	 [Node] Finished "l1analysis.level1estimate".
180514-10:49:10,167 workflow INFO:
	 [Job 4] Completed (l1analysis.level1estimate).
180514-10:49:10,171 workflow INFO:
	 [Job 11] Completed (l1analysis.level1estimate).
180514-10:49:10,177 workflow INFO:
	 [MultiProc] Running 6 tasks, and 26 jobs ready. Free memory (GB): 52.74/53.94, Free processors: 2/8.
                     Currently running:
                       * l1analysis.level1conest
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
180514-10:49:10,258 workflow INFO:
	 [Node] Setting-up "l1analysis.level1conest" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_10/level1conest".
180514-10:49:10,272 workflow INFO:
	 [Node] Setting-up "l1analysis.level1conest" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_10/level1conest".
180514-10:49:10,291 workflow INFO:
	 [Node] Running "level1conest" ("nipype.interfaces.spm.model.EstimateContrast")
180514-10:49:10,306 workflow INFO:
	 [Node] Running "level1conest" ("nipype.interfaces.spm.model.EstimateContrast")
180514-10:49:11,46 workflow INFO:
	 [Node] Finished "l1analysis.level1estimate".
180514-10:49:12,169 workflow INFO:
	 [Job 32] Completed (l1analysis.level1estimate).
180514-10:49:12,173 workflow INFO:
	 [MultiProc] Running 7 tasks, and 25 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
                     Currently running:
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
                       * l1analysis.level1estimate
180514-10:49:12,246 workflow INFO:
	 [Node] Setting-up "l1analysis.level1conest" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_08/level1conest".
180514-10:49:12,283 workflow INFO:
	 [Node] Running "level1conest" ("nipype.interfaces.spm.model.EstimateContrast")
180514-10:49:12,657 workflow INFO:
	 [Node] Finished "l1analysis.level1estimate".
180514-10:49:13,244 workflow INFO:
	 [Node] Finished "l1analysis.level1estimate".
180514-10:49:13,866 workflow INFO:
	 [Node] Finished "l1analysis.level1estimate".
180514-10:49:14,170 workflow INFO:
	 [Job 18] Completed (l1analysis.level1estimate).
180514-10:49:14,172 workflow INFO:
	 [Job 39] Completed (l1analysis.level1estimate).
180514-10:49:14,175 workflow INFO:
	 [Job 46] Completed (l1analysis.level1estimate).
180514-10:49:14,183 workflow INFO:
	 [MultiProc] Running 5 tasks, and 27 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
                     Currently running:
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1estimate
180514-10:49:14,245 workflow INFO:
	 [Node] Setting-up "l1analysis.level1conest" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_09/level1conest".
180514-10:49:14,261 workflow INFO:
	 [Node] Setting-up "l1analysis.level1conest" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_08/level1conest".
180514-10:49:14,279 workflow INFO:
	 [Node] Running "level1conest" ("nipype.interfaces.spm.model.EstimateContrast")180514-10:49:14,273 workflow INFO:
	 [Node] Setting-up "l1analysis.level1conest" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_07/level1conest".

180514-10:49:14,307 workflow INFO:
	 [Node] Running "level1conest" ("nipype.interfaces.spm.model.EstimateContrast")
180514-10:49:14,330 workflow INFO:
	 [Node] Running "level1conest" ("nipype.interfaces.spm.model.EstimateContrast")
180514-10:49:14,927 workflow INFO:
	 [Node] Finished "l1analysis.level1estimate".
180514-10:49:16,173 workflow INFO:
	 [Job 53] Completed (l1analysis.level1estimate).
180514-10:49:16,185 workflow INFO:
	 [MultiProc] Running 7 tasks, and 25 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
                     Currently running:
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
180514-10:49:16,273 workflow INFO:
	 [Node] Setting-up "l1analysis.level1conest" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_07/level1conest".
180514-10:49:16,344 workflow INFO:
	 [Node] Running "level1conest" ("nipype.interfaces.spm.model.EstimateContrast")
180514-10:49:18,178 workflow INFO:
	 [MultiProc] Running 8 tasks, and 24 jobs ready. Free memory (GB): 52.34/53.94, Free processors: 0/8.
                     Currently running:
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
180514-10:49:31,755 workflow INFO:
	 [Node] Finished "l1analysis.level1conest".
180514-10:49:32,190 workflow INFO:
	 [Job 26] Completed (l1analysis.level1conest).
180514-10:49:32,215 workflow INFO:
	 [MultiProc] Running 7 tasks, and 25 jobs ready. Free memory (GB): 52.54/53.94, Free processors: 1/8.
                     Currently running:
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
180514-10:49:32,295 workflow INFO:
	 [Node] Setting-up "l1analysis.datasink" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_09/datasink".
180514-10:49:32,311 workflow INFO:
	 [Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:49:32,321 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/SPM.mat -> /output/datasink/1stLevel/sub-09/fwhm-4/SPM.mat
180514-10:49:32,328 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmT_0001.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmT_0001.nii
180514-10:49:32,339 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmT_0002.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmT_0002.nii
180514-10:49:32,354 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmT_0003.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmT_0003.nii
180514-10:49:32,369 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmT_0004.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmT_0004.nii
180514-10:49:32,376 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmT_0005.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmT_0005.nii
180514-10:49:32,383 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmT_0006.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmT_0006.nii
180514-10:49:32,391 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmT_0007.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmT_0007.nii
180514-10:49:32,397 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmF_0008.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmF_0008.nii
180514-10:49:32,413 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmF_0009.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmF_0009.nii
180514-10:49:32,420 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/con_0001.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/con_0001.nii
180514-10:49:32,442 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/con_0002.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/con_0002.nii
180514-10:49:32,453 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/con_0003.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/con_0003.nii
180514-10:49:32,462 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/con_0004.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/con_0004.nii
180514-10:49:32,470 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/con_0005.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/con_0005.nii
180514-10:49:32,477 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/con_0006.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/con_0006.nii
180514-10:49:32,489 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/con_0007.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/con_0007.nii
180514-10:49:32,497 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/ess_0008.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/ess_0008.nii
180514-10:49:32,511 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/ess_0009.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/ess_0009.nii
180514-10:49:32,530 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmF_0008.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmF_0008.nii
180514-10:49:32,541 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/spmF_0009.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/spmF_0009.nii
180514-10:49:32,554 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/ess_0008.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/ess_0008.nii
180514-10:49:32,572 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_09/ess_0009.nii -> /output/datasink/1stLevel/sub-09/fwhm-4/ess_0009.nii
180514-10:49:32,594 workflow INFO:
	 [Node] Finished "l1analysis.datasink".
180514-10:49:33,813 workflow INFO:
	 [Node] Finished "l1analysis.level1conest".
180514-10:49:33,849 workflow INFO:
	 [Node] Finished "l1analysis.level1conest".
180514-10:49:34,192 workflow INFO:
	 [Job 5] Completed (l1analysis.level1conest).
180514-10:49:34,194 workflow INFO:
	 [Job 12] Completed (l1analysis.level1conest).
180514-10:49:34,196 workflow INFO:
	 [Job 27] Completed (l1analysis.datasink).
180514-10:49:34,200 workflow INFO:
	 [MultiProc] Running 5 tasks, and 26 jobs ready. Free memory (GB): 52.94/53.94, Free processors: 3/8.
                     Currently running:
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
180514-10:49:34,267 workflow INFO:
	 [Node] Setting-up "l1analysis.datasink" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_10/datasink".
180514-10:49:34,287 workflow INFO:
	 [Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-10:49:34,282 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_06/getsubjectinfo".180514-10:49:34,281 workflow INFO:
	 [Node] Setting-up "l1analysis.datasink" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_10/datasink".

180514-10:49:34,295 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")180514-10:49:34,305 workflow INFO:
	 [Node] Running "datasink" ("nipype.interfaces.io.DataSink")

180514-10:49:34,310 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/SPM.mat -> /output/datasink/1stLevel/sub-10/fwhm-8/SPM.mat
180514-10:49:34,315 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmT_0001.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmT_0001.nii180514-10:49:34,318 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".


180514-10:49:34,329 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmT_0002.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmT_0002.nii180514-10:49:34,331 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/SPM.mat -> /output/datasink/1stLevel/sub-10/fwhm-4/SPM.mat
180514-10:49:34,334 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmT_0001.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmT_0001.nii

180514-10:49:34,342 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmT_0003.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmT_0003.nii180514-10:49:34,343 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmT_0002.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmT_0002.nii

180514-10:49:34,348 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmT_0003.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmT_0003.nii180514-10:49:34,350 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmT_0004.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmT_0004.nii
180514-10:49:34,354 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmT_0005.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmT_0005.nii
180514-10:49:34,357 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmT_0004.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmT_0004.nii
180514-10:49:34,366 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmT_0006.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmT_0006.nii
180514-10:49:34,371 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmT_0005.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmT_0005.nii
180514-10:49:34,378 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmT_0007.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmT_0007.nii
180514-10:49:34,383 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmF_0008.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmF_0008.nii

180514-10:49:34,391 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmF_0009.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmF_0009.nii
180514-10:49:34,388 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmT_0006.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmT_0006.nii180514-10:49:34,398 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/con_0001.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/con_0001.nii
180514-10:49:34,406 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmT_0007.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmT_0007.nii

180514-10:49:34,414 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/con_0002.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/con_0002.nii180514-10:49:34,414 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmF_0008.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmF_0008.nii
180514-10:49:34,422 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmF_0009.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmF_0009.nii

180514-10:49:34,426 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/con_0003.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/con_0003.nii
180514-10:49:34,433 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/con_0001.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/con_0001.nii180514-10:49:34,434 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/con_0004.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/con_0004.nii
180514-10:49:34,442 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/con_0002.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/con_0002.nii

180514-10:49:34,449 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/con_0003.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/con_0003.nii
180514-10:49:34,454 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/con_0005.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/con_0005.nii180514-10:49:34,457 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/con_0004.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/con_0004.nii
180514-10:49:34,471 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/con_0006.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/con_0006.nii
180514-10:49:34,476 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/con_0005.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/con_0005.nii
180514-10:49:34,479 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/con_0007.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/con_0007.nii

180514-10:49:34,490 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/con_0006.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/con_0006.nii
180514-10:49:34,497 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/con_0007.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/con_0007.nii180514-10:49:34,501 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/ess_0008.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/ess_0008.nii

180514-10:49:34,510 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/ess_0008.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/ess_0008.nii
180514-10:49:34,516 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/ess_0009.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/ess_0009.nii180514-10:49:34,513 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/ess_0009.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/ess_0009.nii

180514-10:49:34,527 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmF_0008.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmF_0008.nii
180514-10:49:34,531 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/spmF_0009.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/spmF_0009.nii180514-10:49:34,524 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmF_0008.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmF_0008.nii

180514-10:49:34,540 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/spmF_0009.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/spmF_0009.nii180514-10:49:34,546 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/ess_0008.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/ess_0008.nii

180514-10:49:34,553 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_10/ess_0009.nii -> /output/datasink/1stLevel/sub-10/fwhm-8/ess_0009.nii180514-10:49:34,555 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/ess_0008.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/ess_0008.nii

180514-10:49:34,562 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_4_subject_id_10/ess_0009.nii -> /output/datasink/1stLevel/sub-10/fwhm-4/ess_0009.nii
180514-10:49:34,577 workflow INFO:
	 [Node] Finished "l1analysis.datasink".180514-10:49:34,572 workflow INFO:
	 [Node] Finished "l1analysis.datasink".

180514-10:49:35,994 workflow INFO:
	 [Node] Finished "l1analysis.level1conest".
180514-10:49:36,194 workflow INFO:
	 [Job 33] Completed (l1analysis.level1conest).
180514-10:49:36,197 workflow INFO:
	 [Job 6] Completed (l1analysis.datasink).
180514-10:49:36,199 workflow INFO:
	 [Job 13] Completed (l1analysis.datasink).
180514-10:49:36,201 workflow INFO:
	 [Job 56] Completed (l1analysis.getsubjectinfo).
180514-10:49:36,205 workflow INFO:
	 [MultiProc] Running 4 tasks, and 24 jobs ready. Free memory (GB): 53.14/53.94, Free processors: 4/8.
                     Currently running:
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
180514-10:49:36,265 workflow INFO:
	 [Node] Setting-up "l1analysis.datasink" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_08/datasink".180514-10:49:36,266 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_06/selectfiles".180514-10:49:36,267 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_06/getsubjectinfo".

180514-10:49:36,270 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_06/selectfiles".
180514-10:49:36,273 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")180514-10:49:36,277 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")

180514-10:49:36,280 workflow INFO:
	 [Node] Running "datasink" ("nipype.interfaces.io.DataSink")
180514-10:49:36,284 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".180514-10:49:36,290 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/SPM.mat -> /output/datasink/1stLevel/sub-08/fwhm-8/SPM.mat


180514-10:49:36,295 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:49:36,297 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".
180514-10:49:36,298 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmT_0001.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmT_0001.nii

180514-10:49:36,302 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmT_0002.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmT_0002.nii
180514-10:49:36,305 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmT_0003.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmT_0003.nii180514-10:49:36,305 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".

180514-10:49:36,309 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmT_0004.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmT_0004.nii
180514-10:49:36,313 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmT_0005.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmT_0005.nii
180514-10:49:36,316 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmT_0006.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmT_0006.nii
180514-10:49:36,320 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmT_0007.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmT_0007.nii
180514-10:49:36,323 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmF_0008.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmF_0008.nii
180514-10:49:36,327 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmF_0009.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmF_0009.nii
180514-10:49:36,330 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/con_0001.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/con_0001.nii
180514-10:49:36,332 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/con_0002.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/con_0002.nii
180514-10:49:36,335 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/con_0003.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/con_0003.nii
180514-10:49:36,338 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/con_0004.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/con_0004.nii
180514-10:49:36,342 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/con_0005.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/con_0005.nii
180514-10:49:36,346 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/con_0006.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/con_0006.nii
180514-10:49:36,349 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/con_0007.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/con_0007.nii
180514-10:49:36,351 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/ess_0008.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/ess_0008.nii
180514-10:49:36,354 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/ess_0009.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/ess_0009.nii
180514-10:49:36,358 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmF_0008.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmF_0008.nii
180514-10:49:36,361 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/spmF_0009.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/spmF_0009.nii
180514-10:49:36,364 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/ess_0008.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/ess_0008.nii
180514-10:49:36,368 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_08/ess_0009.nii -> /output/datasink/1stLevel/sub-08/fwhm-8/ess_0009.nii
180514-10:49:36,375 workflow INFO:
	 [Node] Finished "l1analysis.datasink".
180514-10:49:38,178 workflow INFO:
	 [Node] Finished "l1analysis.level1conest".
180514-10:49:38,196 workflow INFO:
	 [Job 19] Completed (l1analysis.level1conest).
180514-10:49:38,199 workflow INFO:
	 [Job 34] Completed (l1analysis.datasink).
180514-10:49:38,201 workflow INFO:
	 [Job 57] Completed (l1analysis.selectfiles).
180514-10:49:38,203 workflow INFO:
	 [Job 63] Completed (l1analysis.getsubjectinfo).
180514-10:49:38,205 workflow INFO:
	 [Job 64] Completed (l1analysis.selectfiles).
180514-10:49:38,208 workflow INFO:
	 [MultiProc] Running 3 tasks, and 23 jobs ready. Free memory (GB): 53.34/53.94, Free processors: 5/8.
                     Currently running:
                       * l1analysis.level1conest
                       * l1analysis.level1conest
                       * l1analysis.level1conest
180514-10:49:38,243 workflow INFO:
	 [Node] Finished "l1analysis.level1conest".
180514-10:49:38,267 workflow INFO:
	 [Node] Setting-up "l1analysis.datasink" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_09/datasink".
180514-10:49:38,272 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_06/modelspec".
180514-10:49:38,277 workflow INFO:
	 [Node] Setting-up "l1analysis.modelspec" in "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_06/modelspec".180514-10:49:38,278 workflow INFO:
	 [Node] Setting-up "l1analysis.getsubjectinfo" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_05/getsubjectinfo".

180514-10:49:38,280 workflow INFO:
	 [Node] Setting-up "l1analysis.selectfiles" in "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_05/selectfiles".
180514-10:49:38,330 workflow INFO:
	 [Node] Finished "l1analysis.level1conest".
180514-10:49:38,563 workflow INFO:
	 [Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")180514-10:49:38,564 workflow INFO:
	 [Node] Running "getsubjectinfo" ("nipype.interfaces.utility.wrappers.Function")

180514-10:49:38,570 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")180514-10:49:38,574 workflow INFO:
	 [Node] Running "modelspec" ("nipype.algorithms.modelgen.SpecifySPMModel")

180514-10:49:38,586 workflow INFO:
	 [Node] Running "datasink" ("nipype.interfaces.io.DataSink")180514-10:49:38,589 workflow INFO:
	 [Node] Finished "l1analysis.selectfiles".

180514-10:49:38,603 interface INFO:
	 sub: /output/datasink/1stLevel/_fwhm_id_8_subject_id_09/SPM.mat -> /output/datasink/1stLevel/sub-09/fwhm-8/SPM.mat180514-10:49:38,605 workflow INFO:
	 [Node] Finished "l1analysis.getsubjectinfo".

/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/modelgen.py:423: UserWarning: loadtxt: Empty input file: "/output/workingdir/l1analysis/_fwhm_id_4_subject_id_06/modelspec/art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt"
  outindices = np.loadtxt(filename, dtype=int)
/opt/conda/envs/neuro/lib/python3.6/site-packages/nipype/algorithms/modelgen.py:423: UserWarning: loadtxt: Empty input file: "/output/workingdir/l1analysis/_fwhm_id_8_subject_id_06/modelspec/art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt"
  outindices = np.loadtxt(filename, dtype=int)

Inspect output¶

Let's check the structure of the output folder, to see if we have everything we wanted to save. You should have nine contrast images (con_*.nii for T-contrasts and ess_*.nii for T-contrasts) and nine statistic images (spmT_*.nii and spmF_*.nii) for every subject and smoothing kernel.

!tree /output/datasink/1stLevel

/output/datasink/1stLevel
├── sub-01
│   ├── fwhm-4
│   │   ├── con_0001.nii
│   │   ├── con_0002.nii
│   │   ├── con_0003.nii
│   │   ├── con_0004.nii
│   │   ├── con_0005.nii
│   │   ├── con_0006.nii
│   │   ├── con_0007.nii
│   │   ├── ess_0008.nii
│   │   ├── ess_0009.nii
│   │   ├── spmF_0008.nii
│   │   ├── spmF_0009.nii
│   │   ├── SPM.mat
│   │   ├── spmT_0001.nii
│   │   ├── spmT_0002.nii
│   │   ├── spmT_0003.nii
│   │   ├── spmT_0004.nii
│   │   ├── spmT_0005.nii
│   │   ├── spmT_0006.nii
│   │   └── spmT_0007.nii
│   └── fwhm-8
│       ├── con_0001.nii
│       ├── con_0002.nii
│       ├── con_0003.nii
│       ├── con_0004.nii
│       ├── con_0005.nii
│       ├── con_0006.nii
│       ├── con_0007.nii
│       ├── ess_0008.nii
│       ├── ess_0009.nii
│       ├── spmF_0008.nii
│       ├── spmF_0009.nii
│       ├── SPM.mat
│       ├── spmT_0001.nii
│       ├── spmT_0002.nii
│       ├── spmT_0003.nii
│       ├── spmT_0004.nii
│       ├── spmT_0005.nii
│       ├── spmT_0006.nii
│       └── spmT_0007.nii
├── sub-02
│   ├── fwhm-4
│   │   ├── con_0001.nii
│   │   ├── con_0002.nii
│   │   ├── con_0003.nii
│   │   ├── con_0004.nii
│   │   ├── con_0005.nii
│   │   ├── con_0006.nii
│   │   ├── con_0007.nii
│   │   ├── ess_0008.nii
│   │   ├── ess_0009.nii
│   │   ├── spmF_0008.nii
│   │   ├── spmF_0009.nii
│   │   ├── SPM.mat
│   │   ├── spmT_0001.nii
│   │   ├── spmT_0002.nii
│   │   ├── spmT_0003.nii
│   │   ├── spmT_0004.nii
│   │   ├── spmT_0005.nii
│   │   ├── spmT_0006.nii
│   │   └── spmT_0007.nii
│   └── fwhm-8
│       ├── con_0001.nii
│       ├── con_0002.nii
│       ├── con_0003.nii
│       ├── con_0004.nii
│       ├── con_0005.nii
│       ├── con_0006.nii
│       ├── con_0007.nii
│       ├── ess_0008.nii
│       ├── ess_0009.nii
│       ├── spmF_0008.nii
│       ├── spmF_0009.nii
│       ├── SPM.mat
│       ├── spmT_0001.nii
│       ├── spmT_0002.nii
│       ├── spmT_0003.nii
│       ├── spmT_0004.nii
│       ├── spmT_0005.nii
│       ├── spmT_0006.nii
│       └── spmT_0007.nii
├── sub-03
│   ├── fwhm-4
│   │   ├── con_0001.nii
│   │   ├── con_0002.nii
│   │   ├── con_0003.nii
│   │   ├── con_0004.nii
│   │   ├── con_0005.nii
│   │   ├── con_0006.nii
│   │   ├── con_0007.nii
│   │   ├── ess_0008.nii
│   │   ├── ess_0009.nii
│   │   ├── spmF_0008.nii
│   │   ├── spmF_0009.nii
│   │   ├── SPM.mat
│   │   ├── spmT_0001.nii
│   │   ├── spmT_0002.nii
│   │   ├── spmT_0003.nii
│   │   ├── spmT_0004.nii
│   │   ├── spmT_0005.nii
│   │   ├── spmT_0006.nii
│   │   └── spmT_0007.nii
│   └── fwhm-8
│       ├── con_0001.nii
│       ├── con_0002.nii
│       ├── con_0003.nii
│       ├── con_0004.nii
│       ├── con_0005.nii
│       ├── con_0006.nii
│       ├── con_0007.nii
│       ├── ess_0008.nii
│       ├── ess_0009.nii
│       ├── spmF_0008.nii
│       ├── spmF_0009.nii
│       ├── SPM.mat
│       ├── spmT_0001.nii
│       ├── spmT_0002.nii
│       ├── spmT_0003.nii
│       ├── spmT_0004.nii
│       ├── spmT_0005.nii
│       ├── spmT_0006.nii
│       └── spmT_0007.nii
├── sub-04
│   ├── fwhm-4
│   │   ├── con_0001.nii
│   │   ├── con_0002.nii
│   │   ├── con_0003.nii
│   │   ├── con_0004.nii
│   │   ├── con_0005.nii
│   │   ├── con_0006.nii
│   │   ├── con_0007.nii
│   │   ├── ess_0008.nii
│   │   ├── ess_0009.nii
│   │   ├── spmF_0008.nii
│   │   ├── spmF_0009.nii
│   │   ├── SPM.mat
│   │   ├── spmT_0001.nii
│   │   ├── spmT_0002.nii
│   │   ├── spmT_0003.nii
│   │   ├── spmT_0004.nii
│   │   ├── spmT_0005.nii
│   │   ├── spmT_0006.nii
│   │   └── spmT_0007.nii
│   └── fwhm-8
│       ├── con_0001.nii
│       ├── con_0002.nii
│       ├── con_0003.nii
│       ├── con_0004.nii
│       ├── con_0005.nii
│       ├── con_0006.nii
│       ├── con_0007.nii
│       ├── ess_0008.nii
│       ├── ess_0009.nii
│       ├── spmF_0008.nii
│       ├── spmF_0009.nii
│       ├── SPM.mat
│       ├── spmT_0001.nii
│       ├── spmT_0002.nii
│       ├── spmT_0003.nii
│       ├── spmT_0004.nii
│       ├── spmT_0005.nii
│       ├── spmT_0006.nii
│       └── spmT_0007.nii
├── sub-05
│   ├── fwhm-4
│   │   ├── con_0001.nii
│   │   ├── con_0002.nii
│   │   ├── con_0003.nii
│   │   ├── con_0004.nii
│   │   ├── con_0005.nii
│   │   ├── con_0006.nii
│   │   ├── con_0007.nii
│   │   ├── ess_0008.nii
│   │   ├── ess_0009.nii
│   │   ├── spmF_0008.nii
│   │   ├── spmF_0009.nii
│   │   ├── SPM.mat
│   │   ├── spmT_0001.nii
│   │   ├── spmT_0002.nii
│   │   ├── spmT_0003.nii
│   │   ├── spmT_0004.nii
│   │   ├── spmT_0005.nii
│   │   ├── spmT_0006.nii
│   │   └── spmT_0007.nii
│   └── fwhm-8
│       ├── con_0001.nii
│       ├── con_0002.nii
│       ├── con_0003.nii
│       ├── con_0004.nii
│       ├── con_0005.nii
│       ├── con_0006.nii
│       ├── con_0007.nii
│       ├── ess_0008.nii
│       ├── ess_0009.nii
│       ├── spmF_0008.nii
│       ├── spmF_0009.nii
│       ├── SPM.mat
│       ├── spmT_0001.nii
│       ├── spmT_0002.nii
│       ├── spmT_0003.nii
│       ├── spmT_0004.nii
│       ├── spmT_0005.nii
│       ├── spmT_0006.nii
│       └── spmT_0007.nii
├── sub-06
│   ├── fwhm-4
│   │   ├── con_0001.nii
│   │   ├── con_0002.nii
│   │   ├── con_0003.nii
│   │   ├── con_0004.nii
│   │   ├── con_0005.nii
│   │   ├── con_0006.nii
│   │   ├── con_0007.nii
│   │   ├── ess_0008.nii
│   │   ├── ess_0009.nii
│   │   ├── spmF_0008.nii
│   │   ├── spmF_0009.nii
│   │   ├── SPM.mat
│   │   ├── spmT_0001.nii
│   │   ├── spmT_0002.nii
│   │   ├── spmT_0003.nii
│   │   ├── spmT_0004.nii
│   │   ├── spmT_0005.nii
│   │   ├── spmT_0006.nii
│   │   └── spmT_0007.nii
│   └── fwhm-8
│       ├── con_0001.nii
│       ├── con_0002.nii
│       ├── con_0003.nii
│       ├── con_0004.nii
│       ├── con_0005.nii
│       ├── con_0006.nii
│       ├── con_0007.nii
│       ├── ess_0008.nii
│       ├── ess_0009.nii
│       ├── spmF_0008.nii
│       ├── spmF_0009.nii
│       ├── SPM.mat
│       ├── spmT_0001.nii
│       ├── spmT_0002.nii
│       ├── spmT_0003.nii
│       ├── spmT_0004.nii
│       ├── spmT_0005.nii
│       ├── spmT_0006.nii
│       └── spmT_0007.nii
├── sub-07
│   ├── fwhm-4
│   │   ├── con_0001.nii
│   │   ├── con_0002.nii
│   │   ├── con_0003.nii
│   │   ├── con_0004.nii
│   │   ├── con_0005.nii
│   │   ├── con_0006.nii
│   │   ├── con_0007.nii
│   │   ├── ess_0008.nii
│   │   ├── ess_0009.nii
│   │   ├── spmF_0008.nii
│   │   ├── spmF_0009.nii
│   │   ├── SPM.mat
│   │   ├── spmT_0001.nii
│   │   ├── spmT_0002.nii
│   │   ├── spmT_0003.nii
│   │   ├── spmT_0004.nii
│   │   ├── spmT_0005.nii
│   │   ├── spmT_0006.nii
│   │   └── spmT_0007.nii
│   └── fwhm-8
│       ├── con_0001.nii
│       ├── con_0002.nii
│       ├── con_0003.nii
│       ├── con_0004.nii
│       ├── con_0005.nii
│       ├── con_0006.nii
│       ├── con_0007.nii
│       ├── ess_0008.nii
│       ├── ess_0009.nii
│       ├── spmF_0008.nii
│       ├── spmF_0009.nii
│       ├── SPM.mat
│       ├── spmT_0001.nii
│       ├── spmT_0002.nii
│       ├── spmT_0003.nii
│       ├── spmT_0004.nii
│       ├── spmT_0005.nii
│       ├── spmT_0006.nii
│       └── spmT_0007.nii
├── sub-08
│   ├── fwhm-4
│   │   ├── con_0001.nii
│   │   ├── con_0002.nii
│   │   ├── con_0003.nii
│   │   ├── con_0004.nii
│   │   ├── con_0005.nii
│   │   ├── con_0006.nii
│   │   ├── con_0007.nii
│   │   ├── ess_0008.nii
│   │   ├── ess_0009.nii
│   │   ├── spmF_0008.nii
│   │   ├── spmF_0009.nii
│   │   ├── SPM.mat
│   │   ├── spmT_0001.nii
│   │   ├── spmT_0002.nii
│   │   ├── spmT_0003.nii
│   │   ├── spmT_0004.nii
│   │   ├── spmT_0005.nii
│   │   ├── spmT_0006.nii
│   │   └── spmT_0007.nii
│   └── fwhm-8
│       ├── con_0001.nii
│       ├── con_0002.nii
│       ├── con_0003.nii
│       ├── con_0004.nii
│       ├── con_0005.nii
│       ├── con_0006.nii
│       ├── con_0007.nii
│       ├── ess_0008.nii
│       ├── ess_0009.nii
│       ├── spmF_0008.nii
│       ├── spmF_0009.nii
│       ├── SPM.mat
│       ├── spmT_0001.nii
│       ├── spmT_0002.nii
│       ├── spmT_0003.nii
│       ├── spmT_0004.nii
│       ├── spmT_0005.nii
│       ├── spmT_0006.nii
│       └── spmT_0007.nii
├── sub-09
│   ├── fwhm-4
│   │   ├── con_0001.nii
│   │   ├── con_0002.nii
│   │   ├── con_0003.nii
│   │   ├── con_0004.nii
│   │   ├── con_0005.nii
│   │   ├── con_0006.nii
│   │   ├── con_0007.nii
│   │   ├── ess_0008.nii
│   │   ├── ess_0009.nii
│   │   ├── spmF_0008.nii
│   │   ├── spmF_0009.nii
│   │   ├── SPM.mat
│   │   ├── spmT_0001.nii
│   │   ├── spmT_0002.nii
│   │   ├── spmT_0003.nii
│   │   ├── spmT_0004.nii
│   │   ├── spmT_0005.nii
│   │   ├── spmT_0006.nii
│   │   └── spmT_0007.nii
│   └── fwhm-8
│       ├── con_0001.nii
│       ├── con_0002.nii
│       ├── con_0003.nii
│       ├── con_0004.nii
│       ├── con_0005.nii
│       ├── con_0006.nii
│       ├── con_0007.nii
│       ├── ess_0008.nii
│       ├── ess_0009.nii
│       ├── spmF_0008.nii
│       ├── spmF_0009.nii
│       ├── SPM.mat
│       ├── spmT_0001.nii
│       ├── spmT_0002.nii
│       ├── spmT_0003.nii
│       ├── spmT_0004.nii
│       ├── spmT_0005.nii
│       ├── spmT_0006.nii
│       └── spmT_0007.nii
└── sub-10
    ├── fwhm-4
    │   ├── con_0001.nii
    │   ├── con_0002.nii
    │   ├── con_0003.nii
    │   ├── con_0004.nii
    │   ├── con_0005.nii
    │   ├── con_0006.nii
    │   ├── con_0007.nii
    │   ├── ess_0008.nii
    │   ├── ess_0009.nii
    │   ├── spmF_0008.nii
    │   ├── spmF_0009.nii
    │   ├── SPM.mat
    │   ├── spmT_0001.nii
    │   ├── spmT_0002.nii
    │   ├── spmT_0003.nii
    │   ├── spmT_0004.nii
    │   ├── spmT_0005.nii
    │   ├── spmT_0006.nii
    │   └── spmT_0007.nii
    └── fwhm-8
        ├── con_0001.nii
        ├── con_0002.nii
        ├── con_0003.nii
        ├── con_0004.nii
        ├── con_0005.nii
        ├── con_0006.nii
        ├── con_0007.nii
        ├── ess_0008.nii
        ├── ess_0009.nii
        ├── spmF_0008.nii
        ├── spmF_0009.nii
        ├── SPM.mat
        ├── spmT_0001.nii
        ├── spmT_0002.nii
        ├── spmT_0003.nii
        ├── spmT_0004.nii
        ├── spmT_0005.nii
        ├── spmT_0006.nii
        └── spmT_0007.nii

30 directories, 380 files

Visualize results¶

Let's look at the contrasts of one subject that we've just computed. First, let's see what the difference of smoothing is for the contrast average

from nilearn.plotting import plot_stat_map
%matplotlib inline
anatimg = '/data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz'

plot_stat_map(
    '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0001.nii', title='average - fwhm=4',
    bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-02/fwhm-8/spmT_0001.nii', title='average - fwhm=8',
    bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);

Now, let's look at the three contrasts Finger, Foot, Lips.

plot_stat_map(
    '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0002.nii', title='finger - fwhm=4',
    bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0003.nii', title='foot - fwhm=4',
    bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0004.nii', title='lips - fwhm=4',
    bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);

We can also check three additional contrasts Finger > others, Foot > others and Lips > others.

plot_stat_map(
    '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0005.nii', title='finger - fwhm=4',
    bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0006.nii', title='foot - fwhm=4',
    bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0007.nii', title='lips - fwhm=4',
    bg_img=anatimg, threshold=3, display_mode='y', cut_coords=(-5, 0, 5, 10, 15), dim=-1);

Special case¶

There is something special with the Finger contrast in all subjects. So let's take a look at all of them.

plot_stat_map(
    '/output/datasink/1stLevel/sub-01/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-01',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-02/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-02',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-03/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-03',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-04/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-04',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-05/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-05',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-06/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-06',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-07/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-07',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-08/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-08',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-09/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-09',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

plot_stat_map(
    '/output/datasink/1stLevel/sub-10/fwhm-4/spmT_0002.nii', title='finger - fwhm=4 - sub-10',
    bg_img='/data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_preproc.nii.gz',
    threshold=3, display_mode='y', cut_coords=(5, 10, 15, 20), dim=-1);

What you might see is that the hemisphere of the main cluster differs significantly between subjects. This is because all subjects were asked to use the dominant hand, either right or left. There were three subjects (sub-01, sub-06 and sub-10) that were left-handed. This can be seen in the pictures above, where we find the main cluster in the left hemisphere for right-handed subject and on the right hemisphere for left-handed subjects.

Because of this, We will use only right-handed subjects for the following anlysis.

	onset	duration	weight	trial_type
0	10	15.0	1	Finger
1	40	15.0	1	Foot
2	70	15.0	1	Lips
3	100	15.0	1	Finger
4	130	15.0	1	Foot
5	160	15.0	1	Lips
6	190	15.0	1	Finger
7	220	15.0	1	Foot
8	250	15.0	1	Lips
9	280	15.0	1	Finger
10	310	15.0	1	Foot
11	340	15.0	1	Lips
12	370	15.0	1	Finger
13	400	15.0	1	Foot
14	430	15.0	1	Lips