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Bold_iqms pipeline

Compute no-reference IQMs (image quality metrics) from functional (BOLD)

• Used in bold_mriqc pipeline.

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Pipeline insight

Bold_iqms pipeline combines the following pipelines and processes:

- Outlier Count

- Carpet parcellation

- Compute frame wise displacement

- Spikes

- Compute GCor

- Compute DVARS

- Compute FWHMX

- Compute quality index

- Compute IQMs

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Mandatory inputs parameters

• brainmask (a string representing an existing file)

  Brain mask. An existing file (valid extensions: [.nii, .nii.gz]).

  ex. '/home/username/data/raw_data/automask_mean_reg_func_valid.nii'
  

• epi_mean (a string representing an existing file)

  Mean functional image (BOLD). An existing file (valid extensions: [.nii, .nii.gz]).

  ex. '/home/username/data/raw_data/mean_reg_func_valid.nii'
  

• epi_parc (a string representing an existing file)

  Template data in bold space (extensions: [.nii, .nii.gz]).

  ex. '/home/username/data/derived_data/t_tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii'
  

• hmc_motion (a string representing an existing file)

  Movement parameters file (extensions: [.txt]).

  ex. '/home/username/data/derived_data/reg_d_func_oned.txt'
  

• ras_epi (a string representing an existing file)

  Functional image (BOLD). An existing file (valid extensions: [.nii, .nii.gz]).

  ex. '/home/username/data/raw_data/func_valid.nii'
  

Optional inputs parameters

• dummy_TRS (an integer, optional)

  Volume to discard

  ex. 3
  

• dvars_intensity_normalization (a float, optional)

  See dvars brick

  ex. 1000.0
  

• dvars_remove_zero_variance (a boolean, optional)

  See dvars brick

  ex. True
  

• epi_tsnr (a string representing an existing file, optional)

  See TSNR brick

  ex. '/home/username/data/derived_data/reg_func_valid_tsnr.nii'
  

• fd_normalize (a boolean, optional)

  See Frame displacement brick

  ex. False
  

• fd_parameter_source (optional)

  See Frame displacement brick

  ex. 'AFNI'
  

• fd_radius (a float, optional)

  See Frame displacement brick

  ex. 50.0
  

• fd_thresh (a float, optional)

  Frame displacement threshold

  ex. 0.2
  

• fwhm_combine (a boolean, optional)

  See FWHMx brick

  ex. True
  

• fwhm_detrend (a boolean, optional)

  See FWHMx brick

  ex. True
  

• hmc_epi (a string representing an existing file, optional)

  Head motion corrected functional image

  ex. '/home/username/data/raw_data/reg_func_valid.nii'
  

• quality_index_automask (a boolean, optional)

  See quality index brick

  ex. True
  

• outlier_fraction (a boolean, optional)

  See Outlier Count brick

  ex. True
  

• spikes_detrend (a boolean, optional)

  See Spikes brick

  ex. False
  

• spikes_no_zscore (a boolean, optional)

  See Spikes brick

  ex. True
  

• spikes_skip_frames (an integer, optional)

  See Spikes brick

  ex. 0
  

• spikes_skipe_thresh (a float, optional)

  See Spikes brick

  ex. 6.0
  

Outputs parameters:

• BoldQC_out_file

  Functional Image-Quality Metrics summary json file.

  ex. '/home/username/data/derived_data/mean_reg_func_valid_bold_qc.json'
  

• carpet_seg

  Carpet segmentation.

  ex. '/home/username/data/derived_data/cseg_t_tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz'
  

• dvars_file

  DVARS out file.

  ex. '/home/username/data/derived_data/dvars_reg_func_valid.out'
  

• fd_file

  Framewise displacement out file.

  ex. '/home/username/data/derived_data/fd_reg_func_valid_oned.out'
  

• outliercount_file

  Outlier count out file.

  ex. '/home/username/data/derived_data/outliers_reg_func_valid.out'
  

• spike_file

  File with all the spkies detected.

  ex. '/home/username/data/derived_data/spikes_func.out'
  

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Useful links:

mriqc 22.06