Merge pull request #5 from ftdc-picsl/longitudinal

Longitudinal processing

Dockerfile

@@ -20,7 +20,7 @@ ENV ANTSPATH="/opt/ants/bin/" \
     LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH"
 
 RUN mkdir -p /opt/scripts
-COPY runAntsCT_nonBIDS.pl /opt/scripts/runAntsCT_nonBIDS.pl
+COPY run*.pl /opt/scripts/
 COPY trim_neck.sh /opt/scripts/trim_neck.sh
 # BIDS script when it's ready to use
 # COPY runANTsCT.py /opt/scripts/runANTsCT.py
@@ -35,4 +35,4 @@ WORKDIR /data
 # ENTRYPOINT ["/opt/scripts/runANTsCT.py"]
 #
 # For now, use a legacy interface
-ENTRYPOINT ["/opt/scripts/runAntsCT_nonBIDS.pl"]
+ENTRYPOINT ["/opt/scripts/run.pl"]

README.md

@@ -52,6 +52,17 @@ Custom labels defined at run time must be aligned to the MNI152NLin2009cAsym
 template in templateflow v1.4.1.
 
 
+## Running the container
+
+```
+# For cross-sectional processing
+docker run --rm -it cookpa/antsct-aging:0.4.1 --help
+
+# For longitudinal processing
+docker run --rm -it cookpa/antsct-aging:0.4.1 --help --longitudinal
+```
+
+
 ## References
 
 For ANTs cortical thickness: [Tustison, et al 2014](http://dx.doi.org/10.1016/j.neuroimage.2014.05.044).

run.pl

@@ -0,0 +1,43 @@
+#!/usr/bin/perl -w
+#
+# Wrapper script, just figures out if longitudinal and then runs
+# the appropriate script.
+
+use strict;
+use Getopt::Long;
+
+my $runLongitudinal = 0;
+
+if ($#ARGV < 0) {
+    print qq{
+  antsct-aging run script
+
+  For help, run with "--help" or "--longitudinal --help".
+
+};
+
+    exit 1;
+}
+
+my $printHelp = 0;
+
+Getopt::Long::Configure("pass_through");
+
+GetOptions("help" => \$printHelp,
+           "longitudinal" => \$runLongitudinal);
+
+
+if ($printHelp) {
+    if ($runLongitudinal) {
+        system("/opt/scripts/runAntsLongCT_nonBIDS.pl --help");
+    } else {
+        system("/opt/scripts/runAntsCT_nonBIDS.pl --help");
+    }
+    exit 0;
+}
+
+if ($runLongitudinal) {
+    system("/opt/scripts/runAntsLongCT_nonBIDS.pl --longitudinal @ARGV");
+} else {
+    system("/opt/scripts/runAntsCT_nonBIDS.pl @ARGV");
+}

runAntsCT_nonBIDS.pl

@@ -175,6 +175,7 @@
            "brain-mask-image=s" => \$brainMaskImage,
            "brain-mask-mode=s" => \$brainMaskMode,
            "denoise=i" => \$denoise,
+           "help" => sub { print $usage; exit(0); },
            "keep-files=i" => \$keepTmp,
            "mni-cortical-labels=s{1,}" => \@userMNICorticalLabels,
            "mni-labels=s{1,}" => \@userMNILabels,