Added creation of bvec and bval files when creating NIfTI files (#335)

* added creation of bvec and bval files when creating NIfTI files for DWI files (when bvalue and direction are found in the MINC header)

* script to back populate bval/bvec files

* Corrected a typo

* Nicolas' feedback

* harmonization of the 'die' statement

docs/scripts_md/MRI.md

@@ -346,6 +346,46 @@ INPUTS:
   - $fileref : file hash ref
   - $data\_dir: data directory (e.g. `/data/$PROJECT/data`)
 
+### create\_dwi\_nifti\_bval\_file($file\_ref, $bval\_file)
+
+Creates the NIfTI `.bval` file required for DWI acquisitions based on the
+returned value of `acquisition:bvalues`.
+
+INPUTS:
+  - $file\_ref : file hash ref
+  - $bval\_file: path to the `.bval` file to write into
+
+RETURNS:
+  - undef if no `acquisition:bvalues` were found (skipping the creation
+    of the `.bval` file since there is nothing to write into)
+  - 1 after the `.bval` file was created
+
+### create\_dwi\_nifti\_bvec\_file($file\_ref, $bvec\_file)
+
+Creates the NIfTI `.bvec` file required for DWI acquisitions based on the
+returned value of `acquisition:direction_x`, `acquisition:direction_y` and
+`acquisition:direction_z`.
+
+INPUTS:
+  - $file\_ref : file hash ref
+  - $bvec\_file: path to the `.bvec` file to write into
+
+RETURNS:
+  - undef if no `acquisition:direction_x`, `acquisition:direction_y` and
+    `acquisition:direction_z` were found (skipping the creation
+    of the `.bvec` file since there is nothing to write into)
+  - 1 after the `.bvec` file was created
+
+### write\_to\_file($file, $value, $mode)
+
+This method writes into a file `$file` values stored in `$value`. The mode
+in which the file should be open with is specified in `$mode`.
+
+INPUTS:
+  - $file : output file to write into
+  - $value: value that needs to be written in the file
+  - $mode : mode with which the file should be open with (`'\`'> or `'\`\\>'>)
+
 ### make\_minc\_pics($dbhr, $TarchiveSource, $profile, $minFileID, $debug, $verbose)
 
 Creates pics associated with MINC files.

docs/scripts_md/create_nifti_bval_bvec.md

@@ -0,0 +1,27 @@
+# NAME
+
+create\_nifti\_bval\_bvec.pl -- a script that creates the missing bval and bvec
+files for DWI NIfTI acquisitions.
+
+# SYNOPSIS
+
+perl tools/create\_nifti\_bval\_bvec.pl `[options]`
+
+Available options are:
+
+\-profile: name of the config file in `../dicom-archive/.loris_mri`
+\-verbose: be verbose
+
+# DESCRIPTION
+
+This script will create the missing NIfTI bval and bvec files for DWI
+acquisitions.
+
+# LICENSING
+
+License: GPLv3
+
+# AUTHORS
+
+LORIS community <loris.info@mcin.ca> and McGill Centre for Integrative
+Neuroscience

tools/create_nifti_bval_bvec.pl

@@ -0,0 +1,204 @@
+#! /usr/bin/perl
+
+=pod
+
+=head1 NAME
+
+create_nifti_bval_bvec.pl -- a script that creates the missing bval and bvec
+files for DWI NIfTI acquisitions.
+
+
+=head1 SYNOPSIS
+
+perl tools/create_nifti_bval_bvec.pl C<[options]>
+
+Available options are:
+
+-profile: name of the config file in C<../dicom-archive/.loris_mri>
+-verbose: be verbose
+
+
+=head1 DESCRIPTION
+
+This script will create the missing NIfTI bval and bvec files for DWI
+acquisitions.
+
+
+=head1 LICENSING
+
+License: GPLv3
+
+
+=head1 AUTHORS
+
+LORIS community <loris.info@mcin.ca> and McGill Centre for Integrative
+Neuroscience
+
+=cut
+
+
+
+use strict;
+use warnings;
+use Getopt::Tabular;
+
+use NeuroDB::File;
+use NeuroDB::MRI;
+use NeuroDB::DBI;
+use NeuroDB::ExitCodes;
+
+
+
+
+### Set up Getopt::Tabular
+
+my $profile;
+my $verbose      = 0;
+my $profile_desc = "Name of the config file in ../dicom-archive/.loris_mri";
+
+my @opt_table = (
+    [ "-profile", "string",  1, \$profile, $profile_desc ],
+    [ "-verbose", "boolean", 1, \$verbose, "Be verbose"  ]
+);
+
+my $Help = <<HELP;
+******************************************************************************
+CREATE NIFTI BVAL BVEC DWI FILES
+******************************************************************************
+
+This will check if the configuration flag for NIfTI files creation is set to
+'yes' and will create .bvec and .bval files for the DWI acquisitions that
+need to accompany the NIfTI DWI files (bug in mnc2nii that do not create
+those files so we create them ourselves based on values present in the MINC
+header for acquisition:bvalues, acquisition:direction_x,
+acquisition:direction_y and acquisition:direction_z).
+
+Documentation: perldoc create_nifti_bval_bvec.pl
+
+HELP
+
+my $Usage = <<USAGE;
+Usage: $0 [options]
+       $0 -help to list options
+USAGE
+
+&Getopt::Tabular::SetHelp($Help, $Usage);
+&Getopt::Tabular::GetOptions(\@opt_table, \@ARGV)
+    || exit $NeuroDB::ExitCodes::GETOPT_FAILURE;
+
+
+
+## input error checking
+
+if (!$ENV{LORIS_CONFIG}) {
+    print STDERR "\n\tERROR: Environment variable 'LORIS_CONFIG' not set\n\n";
+    exit $NeuroDB::ExitCodes::INVALID_ENVIRONMENT_VAR;
+}
+
+if (!defined $profile || !-e "$ENV{LORIS_CONFIG}/.loris_mri/$profile") {
+    print $Help;
+    print STDERR "$Usage\n\tERROR: You must specify a valid and existing profile.\n\n";
+    exit $NeuroDB::ExitCodes::PROFILE_FAILURE;
+}
+
+{ package Settings; do "$ENV{LORIS_CONFIG}/.loris_mri/$profile" }
+
+if ( !@Settings::db ) {
+    print STDERR "\n\tERROR: You don't have a \@db setting in the file "
+        . "$ENV{LORIS_CONFIG}/.loris_mri/$profile \n\n";
+    exit $NeuroDB::ExitCodes::DB_SETTINGS_FAILURE;
+}
+
+
+
+## establish database connection
+
+my $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db);
+print "\n==> Successfully connected to the database \n" if $verbose;
+
+
+
+## get config settings
+
+my $data_dir   = NeuroDB::DBI::getConfigSetting(\$dbh, 'dataDirBasepath');
+my $create_nii = NeuroDB::DBI::getConfigSetting(\$dbh, 'create_nii');
+
+
+
+## exit if create_nii is set to No
+
+unless ($create_nii) {
+    print "\nConfig option 'create_nii' set to no. bvec/bval files will not be "
+          . "created as NIfTI files are not created by the imaging pipeline\n\n";
+    exit $NeuroDB::ExitCodes::SUCCESS;
+}
+
+
+
+## grep all FileIDs for which acquisition:bvalues are set
+
+print "\n==> Fetching all FileIDs with acquisition:bvalues. \n" if $verbose;
+
+( my $query = <<QUERY ) =~ s/\n/ /g;
+  SELECT
+    FileID
+  FROM
+    parameter_file
+    JOIN parameter_type USING (ParameterTypeID)
+  WHERE
+    parameter_type.Name=?
+QUERY
+
+my $sth = $dbh->prepare($query);
+$sth->execute('acquisition:bvalues');
+
+my @file_ids = map { $_->{'FileID'} }  @{ $sth->fetchall_arrayref( {} ) };
+
+unless (@file_ids) {
+    print "\n No files were found with header 'acquisition:bvalues' so no need "
+          . "to create bval/bvec files \n";
+    exit $NeuroDB::ExitCodes::SUCCESS;
+}
+
+
+
+## loop through all FileIDs and create bvec/bval files
+foreach my $file_id (@file_ids) {
+
+    # load the file based on the FileID
+    my $file = NeuroDB::File->new(\$dbh);
+    $file->loadFile($file_id);
+
+    # determine paths for bval/bvec files
+    my $minc = $file->getFileDatum('File');
+    my ($bval_file, $bvec_file) = ($minc) x 2;
+    $bval_file =~ s/mnc$/bval/;
+    $bvec_file =~ s/mnc$/bvec/;
+
+    # create complementary nifti files for DWI acquisitions
+    my $bval_success = NeuroDB::MRI::create_dwi_nifti_bval_file(
+        \$file, "$data_dir/$bval_file"
+    );
+    my $bvec_success = NeuroDB::MRI::create_dwi_nifti_bvec_file(
+        \$file, "$data_dir/$bvec_file"
+    );
+
+    # check if bval/bvec created & update parameter_file table with their paths
+    if ($bval_success) {
+        print "\n==> Successfully created bval file for $minc \n";
+        # update parameter_file table with bval path
+        $file->setParameter('check_bval_filename', $bval_file);
+    }
+    if ($bvec_success) {
+        print "\n==> Successfully created bvec file for $minc \n";
+        # update parameter_file table with bvec path
+        $file->setParameter('check_bvec_filename', $bvec_file);
+    }
+
+}
+
+
+
+## disconnect from the database and exit the script with SUCCESS exit code
+$dbh->disconnect();
+exit $NeuroDB::ExitCodes::SUCCESS;

uploadNeuroDB/NeuroDB/MRI.pm

@@ -1394,19 +1394,109 @@ sub make_nii {
     # Get MINC filename and NIfTI filename
     my $file = $$fileref;
     my $minc  = $file->getFileDatum('File');
-    my $nifti = $minc;
-    $nifti    =~ s/mnc$/nii/g;
+    my ($nifti, $bval_file, $bvec_file) = ($minc) x 3;
+    $nifti     =~ s/mnc$/nii/;
+    $bval_file =~ s/mnc$/bval/;
+    $bvec_file =~ s/mnc$/bvec/;
 
     #  mnc2nii command
-    my $m2n_cmd = "mnc2nii -nii -quiet " .
-                    $data_dir . "/" . $minc . " " .
-                    $data_dir . "/" . $nifti;
+    my $m2n_cmd = "mnc2nii -nii -quiet $data_dir/$minc $data_dir/$nifti";
     system($m2n_cmd);
 
+    # create complementary nifti files for DWI acquisitions
+    my $bval_success = create_dwi_nifti_bval_file($fileref, "$data_dir/$bval_file");
+    my $bvec_success = create_dwi_nifti_bvec_file($fileref, "$data_dir/$bvec_file");
+
     # update mri table (parameter_file table)
     $file->setParameter('check_nii_filename', $nifti);
+    $file->setParameter('check_bval_filename', $bval_file) if $bval_success;
+    $file->setParameter('check_bvec_filename', $bvec_file) if $bvec_success;
+}
+
+
+=pod
+
+=head3 create_dwi_nifti_bval_file($file_ref, $bval_file)
+
+Creates the NIfTI C<.bval> file required for DWI acquisitions based on the
+returned value of C<acquisition:bvalues>.
+
+INPUTS:
+  - $file_ref : file hash ref
+  - $bval_file: path to the C<.bval> file to write into
+
+RETURNS:
+  - undef if no C<acquisition:bvalues> were found (skipping the creation
+    of the C<.bval> file since there is nothing to write into)
+  - 1 after the C<.bval> file was created
+
+=cut
+
+sub create_dwi_nifti_bval_file {
+    my ($file_ref, $bval_file) = @_;
+
+    # grep bvals from the header acquisition:bvalues
+    my $file  = $$file_ref;
+    my $bvals = $file->getParameter('acquisition:bvalues');
+
+    return undef unless $bvals;
+
+    # clean up the bvals string
+    $bvals =~ s/\.\,//g; # remove all '.,' from the string
+    $bvals =~ s/\.$//;   # remove the last trailing '.' from the string
+
+    # print bvals into bval_file
+    open(FILE, '>', $bval_file) or die "Could not open file $bval_file: $!\n";
+    print FILE $bvals;
+    close FILE;
+
+    return -e $bval_file;
 }
 
+
+=pod
+
+=head3 create_dwi_nifti_bvec_file($file_ref, $bvec_file)
+
+Creates the NIfTI C<.bvec> file required for DWI acquisitions based on the
+returned value of C<acquisition:direction_x>, C<acquisition:direction_y> and
+C<acquisition:direction_z>.
+
+INPUTS:
+  - $file_ref : file hash ref
+  - $bvec_file: path to the C<.bvec> file to write into
+
+RETURNS:
+  - undef if no C<acquisition:direction_x>, C<acquisition:direction_y> and
+    C<acquisition:direction_z> were found (skipping the creation
+    of the C<.bvec> file since there is nothing to write into)
+  - 1 after the C<.bvec> file was created
+
+=cut
+
+sub create_dwi_nifti_bvec_file {
+    my ($file_ref, $bvec_file) = @_;
+
+    # grep bvecs from headers acquisition:direction_x, y and z
+    my $file  = $$file_ref;
+    my @bvecs = (
+        $file->getParameter('acquisition:direction_x'),
+        $file->getParameter('acquisition:direction_y'),
+        $file->getParameter('acquisition:direction_z')
+    );
+
+    return undef unless ($bvecs[0] && $bvecs[1] && $bvecs[2]);
+
+    # loop through all bvecs, clean them up and print them into the bvec file
+    s/^\"+|\"$//g for @bvecs;
+    open(OUT, '>', $bvec_file) or die "Cannot write to file $bvec_file: $!\n";
+    print OUT map { "$_\n" } @bvecs;
+    close(OUT);
+
+    return -e $bvec_file;
+}
+
+
 =pod
 
 =head3 make_minc_pics($dbhr, $TarchiveSource, $profile, $minFileID, $debug, $verbose)