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Makefile.am
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AUTOMAKE_OPTIONS = check-news
## ACLOCAL_AMFLAGS = -I local_m4
MNI_MODELS = mni-models
# mess with the data install directory
bindir = $(prefix)/CIVET-$(VERSION)/
pkgdatadir = $(bindir)/models/
progsdir = $(bindir)/progs/
bin_SCRIPTS = \
src/average_surface_builder_mc.pl \
src/CIVET_Processing_Pipeline \
src/CIVET_QC_Pipeline \
src/Classify.pm \
src/Clean_Scans.pm \
src/Cortex_Mask.pm \
src/Cortical_Measurements.pm \
src/Linear_Transforms.pm \
src/Link_Native.pm \
src/MRI_Image.pm \
src/Non_Linear_Transforms.pm \
src/Processing_Pipeline_Main.pm \
src/Segment.pm \
src/Skull_Masking.pm \
src/Surface_Fit.pm \
src/Surface_Register.pm \
src/VBM.pm \
src/Verify_Image.pm
progs_SCRIPTS = \
progs/asymmetry_cortical_thickness \
progs/asymmetry_position_map \
progs/asymmetry_vbm_map \
progs/best1stepnlreg.pl \
progs/bestlinreg.pl \
progs/bestsurfreg.pl \
progs/brain_mask_qc \
progs/cerebral_volume \
progs/civet_qc \
progs/classify_qc \
progs/clean_native_scan \
progs/cortical_area_stats \
progs/cortical_mask \
progs/cortical_volume_stats \
progs/diff_civet.pl \
progs/extract_wm_hemispheres \
progs/geom_surfreg.pl \
progs/gyrification_index \
progs/lobe_area \
progs/lobe_stats \
progs/make_asp_grid \
progs/mean_curvature \
progs/multispectral_stx_registration \
progs/nuc_inorm_stage \
progs/remove_skull \
progs/surface_fit_classify \
progs/surface_qc \
progs/surf_qc_image \
progs/talto6 \
progs/talto7 \
progs/verify_angles \
progs/verify_atlas \
progs/verify_clasp \
progs/verify_convergence \
progs/verify_gradient \
progs/verify_image \
progs/verify_laplacian \
progs/verify_surfsurf
# installed data
modelsdir = $(bindir)/models/
icbmdir = $(bindir)/models/icbm/
icbmaaldir = $(bindir)/models/icbm/AAL/
icbmdktdir = $(bindir)/models/icbm/DKT/
icbmlobesdir = $(bindir)/models/icbm/lobes/
icbmgyridir = $(bindir)/models/icbm/gyri/
colindir = $(bindir)/models/colin/
colinaaldir = $(bindir)/models/colin/AAL/
colindktdir = $(bindir)/models/colin/DKT/
colinlobesdir = $(bindir)/models/colin/lobes/
colingyridir = $(bindir)/models/colin/gyri/
samirdir = $(bindir)/models/samir/
samiraaldir = $(bindir)/models/samir/AAL/
samirdktdir = $(bindir)/models/samir/DKT/
samirlobesdir = $(bindir)/models/samir/lobes/
samirgyridir = $(bindir)/models/samir/gyri/
ibisv24dir = $(bindir)/models/ibis/
ibisv24aaldir = $(bindir)/models/ibis/AAL/
ibisv24dktdir = $(bindir)/models/ibis/DKT/
ibisv24lobesdir = $(bindir)/models/ibis/lobes/
ibisv24gyridir = $(bindir)/models/ibis/gyri/
models_DATA = \
models/Cerebellum_Ventricles_SubCortical_Mask-VI.mnc \
models/Cerebellum_Ventricles_SubCortical_Mask-2009s.mnc \
models/Cerebellum_Ventricles_SubCortical_Mask-ADNIhi.mnc \
models/Cerebellum_Ventricles_SubCortical_Mask-IBISv24.mnc \
models/Cerebellum_Ventricles_SubCortical_Mask.mnc \
models/flip_right.xfm \
models/hemi_left_mask.mnc \
models/hemi_right_mask.mnc \
models/identity.xfm \
models/midline_mask.mnc \
models/slide_left.xfm \
models/slide_right.xfm
icbm_DATA = \
models/icbm/icbm_avg_mid_sym_mc_left_hires.obj \
models/icbm/icbm_avg_mid_sym_mc_left.obj \
models/icbm/icbm_avg_mid_sym_mc_right_hires.obj \
models/icbm/icbm_avg_mid_sym_mc_right.obj \
models/icbm/icbm_avg_white_sym_mc_left_hires.obj \
models/icbm/icbm_avg_white_sym_mc_left.obj \
models/icbm/icbm_avg_white_sym_mc_mask_left.txt \
models/icbm/icbm_avg_white_sym_mc_mask_right.txt \
models/icbm/icbm_avg_white_sym_mc_right_hires.obj \
models/icbm/icbm_avg_white_sym_mc_right.obj
icbmaal_DATA = \
models/icbm/AAL/AAL_license.txt \
models/icbm/AAL/AAL_README.txt \
models/icbm/AAL/icbm_avg_mid_mc_AAL_left.txt \
models/icbm/AAL/icbm_avg_mid_mc_AAL_right.txt \
models/icbm/AAL/icbm_avg_mid_mc_AAL.txt \
models/icbm/AAL/icbm_avg_mid_mc_AAL_lowres.txt
icbmdkt_DATA = \
models/icbm/DKT/DKTatlas40.labels \
models/icbm/DKT/icbm_avg_mid_mc_dkt40_left.txt \
models/icbm/DKT/icbm_avg_mid_mc_dkt40_right.txt \
models/icbm/DKT/README
icbmgyri_DATA = \
models/icbm/gyri/icbm_avg_mid_sym_mc_gyri_left.txt \
models/icbm/gyri/icbm_avg_mid_sym_mc_gyri_right.txt
icbmlobes_DATA = \
models/icbm/lobes/icbm_avg_mid_sym_mc_atlas_left.txt \
models/icbm/lobes/icbm_avg_mid_sym_mc_atlas_right.txt \
models/icbm/lobes/README
colin_DATA = \
models/colin/colin_mid_mc_left_hires.obj \
models/colin/colin_mid_mc_left.obj \
models/colin/colin_mid_mc_right_hires.obj \
models/colin/colin_mid_mc_right.obj \
models/colin/colin_white_mc_left.obj \
models/colin/colin_white_mc_mask_left.txt \
models/colin/colin_white_mc_mask_right.txt \
models/colin/colin_white_mc_right.obj
colinaal_DATA = \
models/colin/AAL/AAL_atlas_colin_mc_hires_left.txt \
models/colin/AAL/AAL_atlas_colin_mc_hires_right.txt \
models/colin/AAL/AAL_license.txt \
models/colin/AAL/AAL_README.txt
colingyri_DATA = \
models/colin/gyri/surface_gyri_colin_mc_left.txt \
models/colin/gyri/surface_gyri_colin_mc_right.txt
colinlobes_DATA = \
models/colin/lobes/surface_atlas_colin_mc_left.txt \
models/colin/lobes/surface_atlas_colin_mc_right.txt \
models/colin/lobes/README
samir_DATA = \
models/samir/samir_mid_left_hires.obj \
models/samir/samir_mid_left.obj \
models/samir/samir_mid_right_hires.obj \
models/samir/samir_mid_right.obj \
models/samir/samir_white_left.obj \
models/samir/samir_white_mc_mask_left.txt \
models/samir/samir_white_mc_mask_right.txt \
models/samir/samir_white_right.obj
samirgyri_DATA = \
models/samir/gyri/surface_gyri_samir_mc_left.txt \
models/samir/gyri/surface_gyri_samir_mc_right.txt
samirlobes_DATA = \
models/samir/lobes/surface_atlas_samir_mc_left.txt \
models/samir/lobes/surface_atlas_samir_mc_right.txt
# not ready yet for ibis-v24
# models/ibis/ibis-v24_mid_mc_left_hires.obj \
# models/ibis/ibis-v24_mid_mc_left.obj \
# models/ibis/ibis-v24_mid_mc_right_hires.obj \
# models/ibis/ibis-v24_mid_mc_right.obj
ibisv24_DATA = \
models/ibis/ibis-v24_white_sym_left_hires.obj \
models/ibis/ibis-v24_white_sym_left.obj \
models/ibis/ibis-v24_white_sym_mask_left.txt \
models/ibis/ibis-v24_white_sym_mask_right.txt \
models/ibis/ibis-v24_white_sym_right_hires.obj \
models/ibis/ibis-v24_white_sym_right.obj
ibisv24aal_DATA =
ibisv24gyri_DATA =
ibisv24lobes_DATA =
EXTRA_DIST = \
$(bin_SCRIPTS) \
$(progs_SCRIPTS) \
$(models_DATA) \
$(icbm_DATA) \
$(icbmaal_DATA) \
$(icbmdkt_DATA) \
$(icbmgyri_DATA) \
$(icbmlobes_DATA) \
$(colin_DATA) \
$(colinaal_DATA) \
$(colindkt_DATA) \
$(colingyri_DATA) \
$(colinlobes_DATA) \
$(samir_DATA) \
$(samiraal_DATA) \
$(samirdkt_DATA) \
$(samirgyri_DATA) \
$(samirlobes_DATA) \
$(ibisv24_DATA) \
$(ibisv24aal_DATA) \
$(ibisv24gyri_DATA) \
$(ibisv24lobes_DATA) \
epm-header.in
# gunzip rule
%: %.gz
$(gzip) -d -c $< > $@