resolving script name conflicts

diff --git a/scripts/common.sh b/scripts/midp_common.sh
similarity index 100%
rename from scripts/common.sh
rename to scripts/midp_common.sh

diff --git a/scripts/midp_template.conf b/scripts/midp_template.conf
new file mode 100644 (file)
index 0000000..8fde2c8
--- /dev/null
+++ b/scripts/midp_template.conf
@@ -0,0 +1,67 @@
+###############################################################################
+#
+# FILE: midp_template.conf
+# AUTHOR: Rômulo Pinho 05/08/2011
+#
+# Template configuration file for create_midP-2.0.sh. Values between <> must be
+# changed according to the methods.
+#
+###############################################################################
+
+# output directories
+vf_dir="<VFDIR>"
+midp_dir="<MIDPDIR>"
+output_dir="<OUTDIR>"
+log_dir="<LOGDIR>"
+
+# script step to be executed (mask, registration, midp, all)
+# midp depends on registration, which depends on mask
+step="all"
+
+# mask parameters
+#
+# interpolation algorithm for resampling (see clitkResampleImage)
+mask_interpolation_algorithm="<MASK_INTERPOLATION_ALGORITHM>"
+# interpolation spacing (in mm)
+mask_interpolation_spacing=<MASK_INTERPOLATION_SPACING>
+
+# registration method (blut, elastix)
+method="<METHOD>"
+
+# registration parameters (depend on registration method - see descriptions)
+#
+
+# b-spline spacing (blut, elastix)
+bspline_spacing=<BSPLINE_SPACING>
+
+# multi-resolution levels
+nb_levels=<NB_LEVELS>
+
+# number of histogram bins (blut, elastix)
+nb_hist_bins=<NB_HIST_BINS>
+
+# number of points (samples) to calculate metric
+# (blut: percentage of image size; elastix: absolute number)
+nb_samples=<NBSAMPLES>
+
+# algorithm used to sample points for the metric
+# (elastix: see docs)
+sampling_algo="<SAMPLING_ALGO>"
+
+# number of iterations (blut, elastix)
+nb_iter=<NB_ITER>
+
+# tolerance (stop condition for the metric) (blut)
+tolerance=<TOLERANCE>
+
+# metric used in the registration
+# (blut: see clitkBLUTDIR; elastix: see docs)
+metric="<METRIC>"
+
+# interpolation type
+# (blut: see clitkBLUTDIR; elastix: see docs)
+interpolator="<INTERPOLATOR>"
+
+# optmizer
+# (blut: see clitkBLUTDIR; elastix: see docs)
+optimizer="<OPTIMIZER>"