PET HRRT insertion pipeline

[cmadjar]

New dependencies:

sudo cpan install Digest::BLAKE2
sudo cpan install File::Type
sudo cpan install String::ShellQuote

Note for projects using the MNI HRRT PET scanner:

If you are acquiring datasets using the MNI HRRT PET scanner, ensure that:

• when running HRRT_PET_insertion.pl, the option -bic. Note, the flag is automatically set on the call to HRRT_PET_insertion.pl from imaging_upload_file.pl based on the number of files that contains the BIC string for the moment.
• ensure to add the following function to your profile file (typically called prod, see dicom-archive/profileTemplate.pl for example)

sub determineHRRTprotocol {
    my ( $protocol, $ecat_file ) = @_;

    $protocol =~ s/'|\\|_|"|\s//g; # remove weird characters from protocol name

    if ( $ecat_file =~ /Dfbp/i ) {
        $protocol .= "FBP"; # add FBP reconstruction to filename
    } else {
        $protocol .= "OSEM"; # add OSEM reconstruction to filename
    }

    if ( $ecat_file =~ /_MC01/i ) {
        $protocol .= "mc"; # add mc acronym for motion corrected datasets
    }

    return $protocol;
}

• to add the proper scan type to the table mri_scan_type based on the information present in the PROTOCOL variable of the Matlab file of the BIC HRRT study. Example: for an acquisition acquired using the PROTOCOL F18_NAV_6fr the following scan types need to be created based on the reconstruction technique (OSEM or FBP) and whether motion correction was applied to the image or not:
  • F18NAV6frOSEM: OSEM (Ordered Suspect Expectation Maximization) reconstruction
  • F18NAV6frFBP: FBP (Filter Back Projection) reconstruction
  • F18NAV6frOSEMmc: OSEM reconstruction and motion correction applied
  • F18NAV6frFBPmc: FBP reconstruction and motion correction applied

Issues and link to other PRs

• [SQL/imaging] Adding SQL code for the new HRRT PET insertion scripts Loris#6142
• [PET insertion] HRRT PET insertion scripts #480

[laemtl]

I tested the PET pipeline with success.