Mean_stdDev_calc brick¶

Makes the mean and standard deviation of parametric maps¶

The rois_files are first resized, if necessary, to the size of the parametric_maps.

Next, the parametric_maps and the rois_files are convolved.

Finally, the mean and standard deviation are calculated for the corresponding ROIs.

The “PatientName_data/ROI_data/ROI_analysis” directory is created to receive the results. If this directory exists at runtime, it is overwritten.

Output file names are built like this:

roi_ calculation_ parameter_ contrast.txt

roi is deducted from each rois_files after deleting the extension. If prefix_to_delete is defined and if it corresponds to the beginning of roi, this beginning of string is deleted.

calculation corresponds to “mean” (mean calculation) or “std” (standard deviation calculation).

parameter is deducted from each parametric_maps file name. This is the string before the first underscore. If there is no underscore, this is the file name after removing the extension.

contrast is contrast_type.

To work correctly, the database entry for the first element of parametric_maps must have the PatientName tag filled in.

Mandatory inputs parameters:

parametric_maps

A list of uncompressed file.

ex. ['/home/username/data/raw_data/spmT_0001.nii',
     '/home/username/data/raw_data/beta_0001.nii']

rois_files

A list of regions of interest (a list of uncompressed file), which will be applied to the parametric maps before calculating the mean and standard deviation of the parameters in the corresponding regions.

ex. ['/home/username/data/raw_data/convACA_L.nii',
     '/home/username/data/raw_data/convACA_R.nii',
     '/home/username/data/raw_data/convACM_L.nii',
     '/home/username/data/raw_data/convACM_R.nii']

contrast_type
The contrast used (a string).
ex. BOLD
prefix_to_delete
The string to be deleted from the deduced ROI name, when creating the mean_out_files and the std_out_files.
ex. conv

Outputs parameters:

mean_out_files

A list of .txt files with the calculated mean for each ROI convolved with each parametric map.

ex. ['/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACA_L_mean_spmT_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACA_R_mean_spmT_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACM_L_mean_spmT_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACM_R_mean_spmT_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACA_L_mean_beta_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACA_R_mean_beta_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACM_L_mean_beta_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACM_R_mean_beta_BOLD.txt']

std_out_files

A list of .txt files with the calculated standard deviation for each ROI convolved with each parametric map.

ex. ['/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACA_L_std_spmT_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACA_R_std_spmT_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACM_L_std_spmT_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACM_R_std_spmT_BOLD.txt'
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACA_L_std_beta_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACA_R_std_beta_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACM_L_std_beta_BOLD.txt',
     '/home/username/data/derived_data/patient-name_data/ROI_data/ROI_analysis/ACM_R_std_beta_BOLD.txt']