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[Everything] DIE MRI ALIAS DIE #1227

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[Everything] DIE MRI ALIAS DIE #1227

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adb2614
[Everything] DIE MRI ALIAS DIE
ridz1208 Feb 7, 2025
3ee1790
Update MRIProcessingUtility.pm
ridz1208 Feb 7, 2025
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2 changes: 1 addition & 1 deletion docs/scripts_md/MRIProcessingUtility.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ utilities

%tarchiveInfo = $utility->createTarchiveArray($ArchiveLocation);

my ($center_name, $centerID) = $utility->determinePSC(\%tarchiveInfo,0);
my $centerID = $utility->determinePSC(\%tarchiveInfo,0);

my $projectID = $utility->determineProjectID(\%tarchiveInfo);
my $scannerID = $utility->determineScannerID(\%tarchiveInfo, 0, $centerID, $projectID);
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44 changes: 37 additions & 7 deletions uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm
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Expand Up @@ -19,7 +19,7 @@ utilities

%tarchiveInfo = $utility->createTarchiveArray($ArchiveLocation);

my ($center_name, $centerID) = $utility->determinePSC(\%tarchiveInfo,0);
my $centerID = $utility->determinePSC(\%tarchiveInfo,0);

my $projectID = $utility->determineProjectID(\%tarchiveInfo);
my $scannerID = $utility->determineScannerID(\%tarchiveInfo, 0, $centerID, $projectID);
Expand Down Expand Up @@ -613,14 +613,13 @@ sub determinePSC {
my $lookupCenterNameUsing = $configOB->getLookupCenterNameUsing();


my ($center_name, $centerID) =
NeuroDB::MRI::getPSC(
my $centerID = NeuroDB::MRI::getPSC(
$tarchiveInfo->{$lookupCenterNameUsing},
$this->{dbhr},
$this->{'db'}
);
if ($to_log) {
if (!$center_name) {
if (!$centerID) {

my $message = "\nERROR: No center found for this candidate \n\n";
$this->writeErrorLog(
Expand All @@ -630,13 +629,12 @@ sub determinePSC {
exit $NeuroDB::ExitCodes::SELECT_FAILURE;
}
my $message = "\n==> Verifying acquisition center\n-> " .
"Center Name : $center_name\n-> CenterID ".
" : $centerID\n";
"CenterID: $centerID\n";
$this->{LOG}->print($message);
$this->spool($message, 'N', $upload_id, $notify_detailed);
}

return ($center_name, $centerID);
return $centerID;
}


Expand Down Expand Up @@ -2289,6 +2287,38 @@ sub getUploadIDUsingTarchiveSrcLoc {
return $upload_id;
}

=pod

=head3 getCenterNameFromCenterID($centerID)

Gets the MRI ALIAS form the C<psc> table using the center ID.

INPUT: Center ID

RETURNS: MRI ALIAS

=cut


sub getCenterNameFromCenterID {
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Personal opinion: I would prefer this function to be named getSiteMRIAliasFromSiteID.

  • "center" is used pervasively in the LORIS code but Samir said in some LORIS / LORIS-MRI meeting that "site" is the preferred terminology. Since it does against the current code I guess this is somewhat controversial.
  • A "site name" refers to another column in the database, so I think it would be less confusing to specify "MRIAlias" directly.

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I'll avoid the entire situation and change it to getMRIAliasFromCenterID()

my $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db);

my $centerID = shift;
my $query = '';
my $alias = undef;

if ($centerID) {
$query = "SELECT MRI_alias FROM psc "
. "WHERE CenterID =?";
my $sth = $dbh->prepare($query);
$sth->execute($centerID);
if ( $sth->rows > 0 ) {
$alias = $sth->fetchrow_array;
}
}
return $alias;
}


=pod

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2 changes: 1 addition & 1 deletion uploadNeuroDB/imaging_non_minc_insertion.pl
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Expand Up @@ -407,7 +407,7 @@ =head2 Methods


# determine Center ID
my ($center_name, $centerID) = $utility->determinePSC(\%info, 0, undef);
my $centerID = $utility->determinePSC(\%info, 0, undef);



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2 changes: 1 addition & 1 deletion uploadNeuroDB/minc_insertion.pl
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Expand Up @@ -498,7 +498,7 @@ =head2 Methods
$studyInfo{'DateAcquired'} //= $file->getParameter('study:start_date');

## Determine PSC, ScannerID and Subject IDs
my ($center_name, $centerID) = $utility->determinePSC(\%studyInfo, 0, $upload_id);
my $centerID = $utility->determinePSC(\%studyInfo, 0, $upload_id);
my $projectID = $utility->determineProjectID(\%studyInfo);
my $scannerID = $utility->determineScannerID(\%studyInfo, 0, $centerID, $projectID, $upload_id);
my $subjectIDsref = $utility->determineSubjectID(
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9 changes: 4 additions & 5 deletions uploadNeuroDB/register_processed_data.pl
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Expand Up @@ -231,7 +231,7 @@ =head2 Methods

# ----- STEP 2: Verify PSC information using whatever field contains the site string
# (only for minc files)
my ($center_name,$centerID);
my $centerID;
if ($file->getFileDatum('FileType') eq 'mnc') {
my $patientInfo;
if ($lookupCenterName eq 'PatientName') {
Expand All @@ -243,13 +243,12 @@ =head2 Methods
$filename, 'patient:identification'
);
}
($center_name, $centerID) = NeuroDB::MRI::getPSC($patientInfo, \$dbh, $db);
my $psc = $center_name;
if (!$psc) {
$centerID = NeuroDB::MRI::getPSC($patientInfo, \$dbh, $db);
if (!$centerID) {
print LOG "\nERROR: No center found for this candidate \n\n";
exit $NeuroDB::ExitCodes::SELECT_FAILURE;
}
print LOG "\n==> Verifying acquisition center\n - Center Name : $center_name\n - CenterID : $centerID\n";
print LOG "\n==> Verifying acquisition center\n - CenterID: $centerID\n";
}


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7 changes: 4 additions & 3 deletions uploadNeuroDB/tarchiveLoader.pl
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Expand Up @@ -373,10 +373,11 @@ =head2 Methods
}

################################################################
########## Get the $center_name, $centerID ################
#################### Get the $centerID #########################
################################################################
my ($center_name, $centerID) =
my $centerID =
$utility->determinePSC(\%tarchiveInfo, 0, $upload_id);
my $mri_alias = $utility->getCenterNameFromCenterID($centerID);

################################################################
######### Determine the ScannerID ##############################
Expand Down Expand Up @@ -605,7 +606,7 @@ =head2 Methods
################################################################
# make final logfile name without overwriting phantom logs #####
################################################################
my $final_logfile = $center_name;
my $final_logfile = $mri_alias;
unless ($tarchiveInfo{'DateAcquired'} && $subjectIDsref->{'CandID'}) {
### if something went wrong and there is no acq date or CandID
$final_logfile .= '_'.$temp[$#temp];
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2 changes: 1 addition & 1 deletion uploadNeuroDB/tarchive_validation.pl
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Expand Up @@ -282,7 +282,7 @@ =head2 Methods
### Verify PSC information using whatever field ################
### contains site string #######################################
################################################################
my ($center_name, $centerID) = $utility->determinePSC(\%tarchiveInfo, 1, $upload_id);
my $centerID = $utility->determinePSC(\%tarchiveInfo, 1, $upload_id);

################################################################
################################################################
Expand Down
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