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Extract_roi_param pipeline

Produces gray matter masks for various ROIs and means, standard deviations, laterality indices for beta and spmT values in these ROIs

Pipeline insight

• Extract_roi_param pipeline combines the following bricks:

  • Concat_to_list_of_list

  • Import_Data

  • Find_In_List

  • Files_To_List

  • ConvROI

  • Mean_stdDev_calc

  • Concat_to_list

  • Result_collector

---

Inputs parameters:

• spmT_images

  A list of T-statistics images, previously obtained from the EstimateContrast brick.

  ex. ['/home/username/data/raw_data/spmT_0001.nii']
  

• beta_images

  A list of estimated regression coefficients images (beta_000k.nii, where k indexes the kth regression coefficient), previously obtained from the EstimateModel brick.

  ex. ['/home/username/data/raw_data/beta_0001.nii',
       '/home/username/data/raw_data/beta_0002.nii',
       '/home/username/data/raw_data/beta_0003.nii',
       '/home/username/data/raw_data/beta_0004.nii',
       '/home/username/data/raw_data/beta_0005.nii',
       '/home/username/data/raw_data/beta_0006.nii',
       '/home/username/data/raw_data/beta_0007.nii',
       '/home/username/data/raw_data/beta_0008.nii']
  

• mask_003

  A grey matter mask with a resolution defined previously in the Spatial_mask.

  ex. /home/username/data/raw_data/mask_anat_002.nii
  

• patient_info

  A dictionary whose keys/values correspond to information about the patient. If the value for a key is not defined, the corresponding tag and its value will be searched for in the database. patient_info keys/values therefore take precedence over database tags, allowing the user to force patient data.

  ex. {'PatientName': <undefined>,
       'Pathology': <undefined>,
       'Age': <undefined>,
       'Sex': <undefined>,
       'MR': <undefined>,
       'Gas': <undefined>,
       'GasAdmin': <undefined>}
  

Outputs parameters:

• xls_files

  A list of xls files containing the means and standard deviations of the parameters in the ROIs defined by the Concat_to_list_of_list brick. The laterality index between the two hemispheres is also calculated (files with IL in the name).

  ex. ['/home/username/data/derived_data/patient-name_data/results_aggregation/BOLD_IL_mean_beta.xls',
       '/home/username/data/derived_data/patient-name_data/results_aggregation/BOLD_mean_spmT.xls',
       '/home/username/data/derived_data/patient-name_data/results_aggregation/BOLD_mean_beta.xls',
       '/home/username/data/derived_data/patient-name_data/results_aggregation/BOLD_IL_std_spmT.xls',
       '/home/username/data/derived_data/patient-name_data/results_aggregation/BOLD_IL_mean_spmT.xls',
       '/home/username/data/derived_data/patient-name_data/results_aggregation/BOLD_std_spmT.xls',
       '/home/username/data/derived_data/patient-name_data/results_aggregation/BOLD_std_beta.xls',
       '/home/username/data/derived_data/patient-name_data/results_aggregation/BOLD_IL_std_beta.xls']
  

• conv_roi_maks

  A list of images, resulting from the convolution of mask_003 with the ROIs defined by the Concat_to_list_of_list brick.

  ex. ['/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convACA_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convACA_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convACM_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_dat/convROI_BOLD/convACM_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convACP_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convACP_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convPICA_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convPICA_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-CING_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-CING_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-FRON_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-FRON_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-INSULA_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-INSULA_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-OCC_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-OCC_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-PAR_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-PAR_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-STR_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-STR_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-TEMP_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-TEMP_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-THA_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convROI-THA_R.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convSCA_L.nii',
       '/home/username/data/derived_data/patient-name_data/ROI_data/convROI_BOLD/convSCA_R.nii']