Node: workflow_enumerator.funcMRIQC.ReportsWorkflow.GenerateReport
Working directory: /CALM_BIDS_New_2/derivatives/mriqcwork-fft/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..CALM_BIDS_New_2..sub-128..func..sub-128_task-rest_bold.nii.gz/GenerateReport

Node inputs:

function_str = def individual_html(in_iqms, in_plots=None, api_id=None):
    from pathlib import Path
    import datetime
    from json import load
    from mriqc import logging, __version__ as ver
    from mriqc.utils.misc import BIDS_COMP
    from mriqc.reports import REPORT_TITLES
    from mriqc.reports.utils import iqms2html, read_report_snippet
    from mriqc.data import IndividualTemplate

    report_log = logging.getLogger('mriqc.report')

    def _get_details(in_iqms, modality):
        in_prov = in_iqms.pop('provenance', {})
        warn_dict = in_prov.pop('warnings', None)
        sett_dict = in_prov.pop('settings', None)

        wf_details = []
        if modality == 'bold':
            bold_exclude_index = in_iqms.get('dumb_trs')
            if bold_exclude_index is None:
                report_log.warning('Building bold report: no exclude index was found')
            elif bold_exclude_index > 0:
                msg = """\
<span class="problematic">Non-steady state (strong T1 contrast) has been detected in the \
first {} volumes</span>. They were excluded before generating any QC measures and plots."""
                wf_details.append(msg.format(bold_exclude_index))

            hmc_fsl = sett_dict.pop('hmc_fsl')
            if hmc_fsl is not None:
                msg = 'Framewise Displacement was computed using '
                if hmc_fsl:
                    msg += 'FSL <code>mcflirt</code>'
                else:
                    msg += 'AFNI <code>3dvolreg</code>'
                wf_details.append(msg)

            fd_thres = sett_dict.pop('fd_thres')
            if fd_thres is not None:
                wf_details.append(
                    'Framewise Displacement threshold was defined at %f mm' % fd_thres)
        elif modality in ('T1w', 'T2w'):
            if warn_dict.pop('small_air_mask', False):
                wf_details.append(
                    '<span class="problematic">Detected hat mask was too small</span>')

            if warn_dict.pop('large_rot_frame', False):
                wf_details.append(
                    '<span class="problematic">Detected a zero-filled frame, has the original '
                    'image been rotated?</span>')

        return in_prov, wf_details, sett_dict

    in_iqms = Path(in_iqms)
    with in_iqms.open() as jsonfile:
        iqms_dict = load(jsonfile)

    # Now, the in_iqms file should be correctly named
    out_file = str(Path(in_iqms.with_suffix(".html").name).resolve())

    # Extract and prune metadata
    metadata = iqms_dict.pop('bids_meta', None)
    mod = metadata.pop('modality', None)
    prov, wf_details, _ = _get_details(iqms_dict, mod)

    file_id = [metadata.pop(k, None)
               for k in list(BIDS_COMP.keys())]
    file_id = [comp for comp in file_id if comp is not None]

    if in_plots is None:
        in_plots = []
    else:
        if any(('melodic_reportlet' in k for k in in_plots)):
            REPORT_TITLES['bold'].insert(3, 'ICA components')

        in_plots = [(REPORT_TITLES[mod][i], read_report_snippet(v))
                    for i, v in enumerate(in_plots)]

    pred_qa = None  # metadata.pop('mriqc_pred', None)
    config = {
        'modality': mod,
        'dataset': metadata.pop('dataset', None),
        'bids_name': in_iqms.with_suffix("").name,
        'timestamp': datetime.datetime.now().strftime("%Y-%m-%d, %H:%M"),
        'version': ver,
        'imparams': iqms2html(iqms_dict, 'iqms-table'),
        'svg_files': in_plots,
        'workflow_details': wf_details,
        'webapi_url': prov.pop('webapi_url'),
        'webapi_port': prov.pop('webapi_port'),
        'provenance': iqms2html(prov, 'provenance-table'),
        'md5sum': prov['md5sum'],
        'metadata': iqms2html(metadata, 'metadata-table'),
        'pred_qa': pred_qa
    }

    if config['metadata'] is None:
        config['workflow_details'].append(
            '<span class="warning">File has no metadata</span> '
            '<span>(sidecar JSON file missing or empty)</span>')

    tpl = IndividualTemplate()
    tpl.generate_conf(config, out_file)

    report_log.info('Generated individual log (%s)', out_file)
    return out_file

in_iqms = /CALM_BIDS_New_2/derivatives/mriqc-fft/sub-128/func/sub-128_task-rest_bold.json
in_plots = ['/CALM_BIDS_New_2/derivatives/mriqcwork-fft/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..CALM_BIDS_New_2..sub-128..func..sub-128_task-rest_bold.nii.gz/PlotMosaicMean/plot_func_mean_mosaic1.svg', '/CALM_BIDS_New_2/derivatives/mriqcwork-fft/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..CALM_BIDS_New_2..sub-128..func..sub-128_task-rest_bold.nii.gz/PlotMosaicSD/plot_func_stddev_mosaic2_stddev.svg', '/CALM_BIDS_New_2/derivatives/mriqcwork-fft/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..CALM_BIDS_New_2..sub-128..func..sub-128_task-rest_bold.nii.gz/BigPlot/sub-128_task-rest_bold_valid_volreg_fmriplot.svg', '/CALM_BIDS_New_2/derivatives/mriqcwork-fft/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..CALM_BIDS_New_2..sub-128..func..sub-128_task-rest_bold.nii.gz/PlotSpikes/plot_spikes.svg', '/CALM_BIDS_New_2/derivatives/mriqcwork-fft/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..CALM_BIDS_New_2..sub-128..func..sub-128_task-rest_bold.nii.gz/PlotMosaicZoomed/plot_anat_mosaic1_zoomed.svg', '/CALM_BIDS_New_2/derivatives/mriqcwork-fft/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..CALM_BIDS_New_2..sub-128..func..sub-128_task-rest_bold.nii.gz/PlotMosaicNoise/plot_anat_mosaic2_noise.svg', '/CALM_BIDS_New_2/derivatives/mriqcwork-fft/workflow_enumerator/funcMRIQC/ReportsWorkflow/_in_file_..CALM_BIDS_New_2..sub-128..func..sub-128_task-rest_bold.nii.gz/PlotBrainmask/plot_bmask_contours.svg', '/CALM_BIDS_New_2/derivatives/mriqcwork-fft/workflow_enumerator/funcMRIQC/SpatialNormalization/_in_file_..CALM_BIDS_New_2..sub-128..func..sub-128_task-rest_bold.nii.gz/EPI2MNI/report.svg']

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 521, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/utility/wrappers.py", line 144, in _run_interface
    out = function_handle(**args)
  File "<string>", line 77, in individual_html
  File "<string>", line 77, in <listcomp>
IndexError: list index out of range