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Makefile
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#------------------------------------------------------------------------------
# Author: Piotr Majka, M.Sc.
# E-mail: [email protected]
# Affiliation: Laboratory of Neuroinformatics
# Nencki Institute of Experimental Biology
# 3 Pasteur St, 02-093 Warsaw, Poland
#
# Licencing: GNU General Public License
# http://www.gnu.org/licenses/gpl.html
#
#------------------------------------------------------------------------------
PARSERS_DIR = bin/parsers/
ATLASES_DIR = atlases/
SBA_PARSERS = sba_DB08 sba_PHT00 sba_WHS09 sba_WHS10 sba_LPBA40_on_SRI24 sba_RM_on_F99 sba_FVE91_on_F99
FAST_PARSERS = nl_olek ${SBA_PARSERS} tem
WHS = whs_0.5 whs_0.51 whs_0.5_symm whs_0.6.1 whs_0.6.2
POS = pos_0.1
WHS_RAT = WHS_SD_rat_atlas_v2 WHS_SD_rat_atlas_v101
PARSERS = aba aba2011 ${FAST_PARSERS} ${WHS} ${POS} ${WHS_RAT}
all: clean ${PARSERS} doc
echo "Done"
doc_clean:
rm -rfv doc/api doc/gui/ doc/service
doc: doc_api doc_gui doc_service
echo "Done doc"
doc_api:
mkdir -p doc/api/html
epydoc lib/pymodules/python2.6/bar -v --graph all --no-sourcecode --output doc/api/html
cd doc/sphinx/; make html; python -m doctest source/*.rst
doc_gui:
mkdir -p doc/gui/html
epydoc bin/reconstructor -v --graph all --output doc/gui/html
doc_service:
mkdir -p doc/service/html
epydoc bin/sql -v --graph all --output doc/service/html
parsers: ${PARSERS}
parsers_fast: ${FAST_PARSERS}
echo "Done"
parsers_sba: ${SBA_PARSERS}
echo "Done"
whs_0.5:
mkdir -p ${ATLASES_DIR}whs_0.5/src
mkdir -p ${ATLASES_DIR}whs_0.5/caf
wget --keep-session-cookies --save-cookies ${ATLASES_DIR}whs_0.5/src/cookies.txt --post-data 'username=civmpub&password=civmpub' http://civmvoxport.duhs.duke.edu/voxbase/login.php -O /dev/null
wget --load-cookies ${ATLASES_DIR}whs_0.5/src/cookies.txt http://civmvoxport.duhs.duke.edu/voxbase/downloaddataset.php?stackID=18746 -O ${ATLASES_DIR}whs_0.5/src/canon_labels_r.nii.gz
rm ${ATLASES_DIR}whs_0.5/src/cookies.txt
gunzip -f -d ${ATLASES_DIR}whs_0.5/src/canon_labels_r.nii.gz
python ${PARSERS_DIR}whs_0.5/__init__.py
if [ -e ${ATLASES_DIR}whs_0.5/caf-reference ]; then diff -r ${ATLASES_DIR}whs_0.5/caf ${ATLASES_DIR}whs_0.5/caf-reference > diff_whs_0.5.txt; fi
whs_0.5_symm:
mkdir -p ${ATLASES_DIR}whs_0.5_symm/src
mkdir -p ${ATLASES_DIR}whs_0.5_symm/caf
wget --keep-session-cookies --save-cookies ${ATLASES_DIR}whs_0.5_symm/src/cookies.txt --post-data 'username=civmpub&password=civmpub' http://civmvoxport.duhs.duke.edu/voxbase/login.php -O /dev/null
wget --load-cookies ${ATLASES_DIR}whs_0.5_symm/src/cookies.txt http://civmvoxport.duhs.duke.edu/voxbase/downloaddataset.php?stackID=20494 -O ${ATLASES_DIR}whs_0.5_symm/src/SYMCLabel.nii.gz
rm ${ATLASES_DIR}whs_0.5_symm/src/cookies.txt
gunzip -f -d ${ATLASES_DIR}whs_0.5_symm/src/SYMCLabel.nii.gz
python ${PARSERS_DIR}whs_0.5_symm/__init__.py
if [ -e ${ATLASES_DIR}whs_0.5_symm/caf-reference ]; then diff -r ${ATLASES_DIR}whs_0.5_symm/caf ${ATLASES_DIR}whs_0.5_symm/caf-reference > diff_whs_0.5_symm.txt; fi
whs_0.51:
mkdir -p ${ATLASES_DIR}whs_0.51/src
mkdir -p ${ATLASES_DIR}whs_0.51/caf
wget -O ${ATLASES_DIR}whs_0.51/src/whs051mbatatlas.zip "http://software.incf.org/software/waxholm-space/waxholm-space/LabeledAtlas0.5.1/file_download?file_field=file"
unzip -o ${ATLASES_DIR}whs_0.51/src/whs051mbatatlas.zip -d ${ATLASES_DIR}whs_0.51/src/
rm ${ATLASES_DIR}whs_0.51/src/whs051mbatatlas.zip
python ${PARSERS_DIR}whs_0.51/__init__.py
if [ -e ${ATLASES_DIR}whs_0.51/caf-reference ]; then diff -r ${ATLASES_DIR}whs_0.51/caf ${ATLASES_DIR}whs_0.51/caf-reference > diff_whs_0.51.txt; fi
whs_0.6.1:
mkdir -p ${ATLASES_DIR}whs_0.6.1/src
mkdir -p ${ATLASES_DIR}whs_0.6.1/caf
python ${PARSERS_DIR}whs_0.6.1/__init__.py
if [ -e ${ATLASES_DIR}whs_0.6.1/caf-reference ]; then diff -r ${ATLASES_DIR}whs_0.6.1/caf ${ATLASES_DIR}whs_0.6.1/caf-reference > diff_whs_0.6.1.txt; fi
whs_0.6.2:
mkdir -p ${ATLASES_DIR}whs_0.6.2/src
mkdir -p ${ATLASES_DIR}whs_0.6.2/caf
wget -O ${ATLASES_DIR}whs_0.6.2/src/whs_0.6.2_atlas.zip "http://software.incf.org/software/waxholm-space/waxholm-space/mbat-ready-label-volume-v0.6.2/file_download?file_field=file"
unzip -o ${ATLASES_DIR}whs_0.6.2/src/whs_0.6.2_atlas.zip -d ${ATLASES_DIR}whs_0.6.2/src/
rm ${ATLASES_DIR}whs_0.6.2/src/whs_0.6.2_atlas.zip
python ${PARSERS_DIR}whs_0.6.2/__init__.py
if [ -e ${ATLASES_DIR}whs_0.6.2/caf-reference ]; then diff -r ${ATLASES_DIR}whs_0.6.2/caf ${ATLASES_DIR}whs_0.6.2/caf-reference > diff_whs_0.6.2.txt; fi
nl_olek:
mkdir -p ${ATLASES_DIR}nl_olek/caf
python ${PARSERS_DIR}nl_olek/__init__.py
if [ -e ${ATLASES_DIR}nl_olek/caf-reference ]; then diff -r ${ATLASES_DIR}nl_olek/caf ${ATLASES_DIR}nl_olek/caf-reference > diff_neurolucidaXML.txt; fi
vector-test:
mkdir -p ${ATLASES_DIR}vector-test/caf
python ${PARSERS_DIR}vector-test/__init__.py
if [ -e ${ATLASES_DIR}vector-test/caf-reference ]; then diff -r ${ATLASES_DIR}vector-test/caf ${ATLASES_DIR}vector-test/caf-reference > diff_vector-test.txt; fi
sba_DB08:
mkdir -p ${ATLASES_DIR}sba_DB08/src
mkdir -p ${ATLASES_DIR}sba_DB08/caf
python ${PARSERS_DIR}sba_DB08/__init__.py
if [ -e ${ATLASES_DIR}sba_DB08/caf-reference ]; then diff -r ${ATLASES_DIR}sba_DB08/caf ${ATLASES_DIR}sba_DB08/caf-reference > diff_sba_DB08.txt; fi
sba_PHT00:
mkdir -p ${ATLASES_DIR}sba_PHT00/src
mkdir -p ${ATLASES_DIR}sba_PHT00/caf
python ${PARSERS_DIR}sba_PHT00/__init__.py
if [ -e ${ATLASES_DIR}sba_PHT00/caf-reference ]; then diff -r ${ATLASES_DIR}sba_PHT00/caf ${ATLASES_DIR}sba_PHT00/caf-reference > diff_sba_PHT00.txt; fi
sba_WHS09:
mkdir -p ${ATLASES_DIR}sba_WHS09/src
mkdir -p ${ATLASES_DIR}sba_WHS09/caf
python ${PARSERS_DIR}sba_WHS09/__init__.py
if [ -e ${ATLASES_DIR}sba_WHS09/caf-reference ]; then diff -r ${ATLASES_DIR}sba_WHS09/caf ${ATLASES_DIR}sba_WHS09/caf-reference > diff_sba_WHS09.txt; fi
sba_WHS10:
mkdir -p ${ATLASES_DIR}sba_WHS10/src
mkdir -p ${ATLASES_DIR}sba_WHS10/caf
python ${PARSERS_DIR}sba_WHS10/__init__.py
if [ -e ${ATLASES_DIR}sba_WHS10/caf-reference ]; then diff -r ${ATLASES_DIR}sba_WHS10/caf ${ATLASES_DIR}sba_WHS10/caf-reference > diff_sba_WHS10.txt; fi
sba_LPBA40_on_SRI24:
mkdir -p ${ATLASES_DIR}sba_LPBA40_on_SRI24/src
mkdir -p ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf
python ${PARSERS_DIR}sba_LPBA40_on_SRI24/__init__.py
if [ -e ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf-reference ]; then diff -r ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf-reference > diff_sba_LPBA40_on_SRI24.txt; fi
sba_RM_on_F99:
mkdir -p ${ATLASES_DIR}sba_RM_on_F99/src
mkdir -p ${ATLASES_DIR}sba_RM_on_F99/caf
python ${PARSERS_DIR}sba_RM_on_F99/__init__.py
if [ -e ${ATLASES_DIR}sba_RM_on_F99/caf-reference ]; then diff -r ${ATLASES_DIR}sba_RM_on_F99/caf ${ATLASES_DIR}sba_RM_on_F99/caf-reference > diff_sba_RM_on_F99.txt; fi
sba_FVE91_on_F99:
mkdir -p ${ATLASES_DIR}sba_FVE91_on_F99/src
mkdir -p ${ATLASES_DIR}sba_FVE91_on_F99/caf
python ${PARSERS_DIR}sba_FVE91_on_F99/__init__.py
if [ -e ${ATLASES_DIR}sba_FVE91_on_F99/caf-reference ]; then diff -r ${ATLASES_DIR}sba_FVE91_on_F99/caf ${ATLASES_DIR}sba_FVE91_on_F99/caf-reference > diff_sba_FVE91_on_F99.txt; fi
sba_B05_on_Conte69:
mkdir -p ${ATLASES_DIR}sba_B05_on_Conte69/src
mkdir -p ${ATLASES_DIR}sba_B05_on_Conte69/caf
wget -O ${ATLASES_DIR}sba_B05_on_Conte69/src/Human_Conte69_L_brodmann_paint_to_volume.nii.gz "http://sba.incf.org/B05_on_Conte69/source/Human_Conte69_L_brodmann_paint_to_volume.nii.gz"
wget -O ${ATLASES_DIR}sba_B05_on_Conte69/src/index2acr_Human_Conte69_L_brodmann_paint_to_volume.json "http://sba.incf.org/B05_on_Conte69/source/index2acr_Human_Conte69_L_brodmann_paint_to_volume.json"
python ${PARSERS_DIR}sba_B05_on_Conte69/__init__.py
python ${PARSERS_DIR}sba_B05_on_Conte69/__init__volume.py
if [ -e ${ATLASES_DIR}sba_B05_on_Conte69/caf-reference ]; then diff -r ${ATLASES_DIR}B05_on_Conte69/caf ${ATLASES_DIR}sba_B05_on_Conte69/caf-reference > diff_sba_B05_on_Conte69.txt; fi
aba:
mkdir -p ${ATLASES_DIR}aba/src
mkdir -p ${ATLASES_DIR}aba/caf
python ${PARSERS_DIR}aba/preprocess_volume.py
python ${PARSERS_DIR}aba/__init__.py
if [ -e ${ATLASES_DIR}aba/caf-reference ]; then diff -r ${ATLASES_DIR}aba/caf ${ATLASES_DIR}aba/caf-reference > diff_aba.txt; fi
aba2011:
mkdir -p ${ATLASES_DIR}aba2011/src
mkdir -p ${ATLASES_DIR}aba2011/caf
python ${PARSERS_DIR}aba2011/__init__.py
if [ -e ${ATLASES_DIR}aba2011/caf-reference ]; then diff -r ${ATLASES_DIR}aba2011/caf ${ATLASES_DIR}2011/caf-reference > diff_aba2011.txt; fi
tem:
mkdir -p ${ATLASES_DIR}tem/src
mkdir -p ${ATLASES_DIR}tem/caf
python ${PARSERS_DIR}tem/preprocess_data.py
python ${PARSERS_DIR}tem/__init__.py
if [ -e ${ATLASES_DIR}tem/caf-reference ]; then diff -r ${ATLASES_DIR}tem/caf ${ATLASES_DIR}tem/caf-reference > diff_tem.txt; fi
mbisc_11:
mkdir -p ${ATLASES_DIR}mbisc_11/src
mkdir -p ${ATLASES_DIR}mbisc_11/caf
#python ${PARSERS_DIR}/mbisc_11/preprocessSVG.py ${ATLASES_DIR}mbisc_11/src/src_atlas.svg "${ATLASES_DIR}mbisc_11/src/%03d_v1.svg"
python ${PARSERS_DIR}/mbisc_11/__init__.py
if [ -e ${ATLASES_DIR}mbisc_11/caf-reference ]; then diff -r ${ATLASES_DIR}mbisc_11/caf ${ATLASES_DIR}mbisc_11/caf-reference > diff_mbisc_11.txt; fi
pos_0.1:
mkdir -p ${ATLASES_DIR}pos_0.1/src
mkdir -p ${ATLASES_DIR}pos_0.1/caf
wget http://doc.3dbar.org/possum/01/segmentation_in_srs.nii.gz -O ${ATLASES_DIR}/pos_0.1/src/segmentation_in_uct_space.nii.gz
wget http://doc.3dbar.org/possum/01/labels.txt -O ${ATLASES_DIR}/pos_0.1/src/label_descriptions.txt
python ${PARSERS_DIR}/pos_0.1/preprocess_data.py ${ATLASES_DIR}pos_0.1/src/label_descriptions.txt ${ATLASES_DIR}pos_0.1/src/fullnames.txt ${ATLASES_DIR}pos_0.1/src/parents.txt
python ${PARSERS_DIR}/pos_0.1/__init__.py
#if [ -e ${ATLASES_DIR}pos_0.1/caf-reference ]; then diff -r ${ATLASES_DIR}pos_0.1/caf ${ATLASES_DIR}pos_0.1/caf-reference > diff_pos_0.1.txt; fi
CBWJ13_P80:
wget --keep-session-cookies --save-cookies ${ATLASES_DIR}/CBWJ13_P80/src/cookies.txt --post-data 'username=civmpub&password=civmpub' http://civmvoxport.duhs.duke.edu/voxbase/login.php -O /dev/null
wget --load-cookies ${ATLASES_DIR}/CBWJ13_P80/src/cookies.txt http://civmvoxport.duhs.duke.edu/voxbase/downloaddataset.php?stackID=22940 -O ${ATLASES_DIR}/CBWJ13_P80/src/pnd80_average_labels.nii
rm ${ATLASES_DIR}/CBWJ13_P80/src/cookies.txt
mkdir -p ${ATLASES_DIR}/CBWJ13_P80/src
mkdir -p ${ATLASES_DIR}/CBWJ13_P80/caf
python ${PARSERS_DIR}/CBWJ13_P80/__init__.py
if [ -e ${ATLASES_DIR}/CBWJ13_P80/caf-reference ]; then diff -r ${ATLASES_DIR}/CBWJ13_P80/caf ${ATLASES_DIR}/CBWJ13_P80/caf-reference > diff_CBWJ13_P80.txt; fi
WHS_SD_rat_atlas_v2:
mkdir -p ${ATLASES_DIR}/WHS_SD_rat_atlas_v2/src
wget http://software.incf.org/software/waxholm-space-atlas-of-the-sprague-dawley-rat-brain/waxholm-space-atlas-of-the-sprague-dawley-rat-brain-package/quick-pack/mbat-ready-sprague-dawley-atlas-v2-bundle/at_download/file -O ${ATLASES_DIR}/WHS_SD_rat_atlas_v2/src/MBAT_WHS_SD_rat_atlas_v2_pack.zip
unzip -o ${ATLASES_DIR}WHS_SD_rat_atlas_v2/src/MBAT_WHS_SD_rat_atlas_v2_pack.zip -d ${ATLASES_DIR}WHS_SD_rat_atlas_v2/src/
mkdir -p ${ATLASES_DIR}/WHS_SD_rat_atlas_v2/caf
python ${PARSERS_DIR}/WHS_SD_rat_atlas_v2/__init__.py
if [ -e ${ATLASES_DIR}/WHS_SD_rat_atlas_v2/caf-reference ]; then diff -r ${ATLASES_DIR}/WHS_SD_rat_atlas_v2/caf ${ATLASES_DIR}/WHS_SD_rat_atlas_v2/caf-reference > diff_WHS_SD_rat_atlas_v2.txt; fi
WHS_SD_rat_atlas_v101:
mkdir -p ${ATLASES_DIR}/WHS_SD_rat_atlas_v101/src
wget http://software.incf.org/software/waxholm-space-atlas-of-the-sprague-dawley-rat-brain/waxholm-space-atlas-of-the-sprague-dawley-rat-brain-package/v1.01/mbat-ready-sprague-dawley-atlas-v1.01/at_download/file -O ${ATLASES_DIR}/WHS_SD_rat_atlas_v101/src/MBAT_WHS_SD_rat_atlas_v101_pack.zip
unzip -o ${ATLASES_DIR}WHS_SD_rat_atlas_v101/src/MBAT_WHS_SD_rat_atlas_v101_pack.zip -d ${ATLASES_DIR}WHS_SD_rat_atlas_v101/src/
mkdir -p ${ATLASES_DIR}/WHS_SD_rat_atlas_v101/caf
python ${PARSERS_DIR}/WHS_SD_rat_atlas_v101/__init__.py
if [ -e ${ATLASES_DIR}/WHS_SD_rat_atlas_v101/caf-reference ]; then diff -r ${ATLASES_DIR}/WHS_SD_rat_atlas_v101/caf ${ATLASES_DIR}/WHS_SD_rat_atlas_v101/caf-reference > diff_WHS_SD_rat_atlas_v101.txt; fi
clean: clean_diff doc_clean
rm -rfv ${ATLASES_DIR}sba_DB08/caf ${ATLASES_DIR}sba_DB08/src
rm -rfv ${ATLASES_DIR}sba_PHT00/caf ${ATLASES_DIR}sba_PHT00/src
rm -rfv ${ATLASES_DIR}sba_WHS09/caf ${ATLASES_DIR}sba_WHS09/caf/src
rm -rfv ${ATLASES_DIR}sba_WHS10/caf ${ATLASES_DIR}sba_WHS10/src
rm -rfv ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf ${ATLASES_DIR}sba_LPBA40_on_SRI24/src
rm -rfv ${ATLASES_DIR}sba_RM_on_F99/caf ${ATLASES_DIR}sba_RM_on_F99/src
rm -rfv ${ATLASES_DIR}sba_FVE91_on_F99/caf ${ATLASES_DIR}sba_FVE91_on_F99/src
rm -rfv ${ATLASES_DIR}sba_B05_on_Conte69/caf ${ATLASES_DIR}sba_B05_on_Conte69/src
rm -rfv ${ATLASES_DIR}whs_0.51/caf
rm -rfv ${ATLASES_DIR}whs_0.6.1/caf
rm -rfv ${ATLASES_DIR}whs_0.6.2/caf
rm -rfv ${ATLASES_DIR}whs_0.5/caf
rm -rfv ${ATLASES_DIR}whs_0.5_symm/caf
rm -rfv ${ATLASES_DIR}vector-test/caf
rm -rfv ${ATLASES_DIR}nl_olek/caf
rm -rfv ${ATLASES_DIR}aba/caf ${ATLASES_DIR}aba/src
rm -rfv ${ATLASES_DIR}aba2011/caf ${ATLASES_DIR}aba2011/src
rm -rfv ${ATLASES_DIR}tem/caf ${ATLASES_DIR}tem/src
rm -rfv ${ATLASES_DIR}mbisc_11/caf ${ATLASES_DIR}mbisc_11/src
rm -rfv ${ATLASES_DIR}pos_0.1/caf ${ATLASES_DIR}pos_0.1/src
rm -rfv ${ATLASES_DIR}CBWJ13_P80/caf ${ATLASES_DIR}CBWJ13_P80/src
rm -rfv ${ATLASES_DIR}WHS_SD_rat_atlas_v2/caf ${ATLASES_DIR}/WHS_SD_rat_atlas_v2/src
rm -rfv ${ATLASES_DIR}WHS_SD_rat_atlas_v101/caf ${ATLASES_DIR}/WHS_SD_rat_atlas_v101/src
reference_datasets:
rm -rf ${ATLASES_DIR}whs_0.5/caf-reference; cp -r ${ATLASES_DIR}whs_0.5/caf ${ATLASES_DIR}whs_0.5/caf-reference
rm -rf ${ATLASES_DIR}whs_0.5_symm/caf-reference; cp -r ${ATLASES_DIR}whs_0.5_symm/caf ${ATLASES_DIR}whs_0.5_symm/caf-reference
rm -rf ${ATLASES_DIR}whs_0.51/caf-reference; cp -r ${ATLASES_DIR}whs_0.51/caf ${ATLASES_DIR}whs_0.51/caf-reference
rm -rf ${ATLASES_DIR}whs_0.6.1/caf-reference; cp -r ${ATLASES_DIR}whs_0.6.1/caf ${ATLASES_DIR}whs_0.6.1/caf-reference
rm -rf ${ATLASES_DIR}whs_0.6.2/caf-reference; cp -r ${ATLASES_DIR}whs_0.6.2/caf ${ATLASES_DIR}whs_0.6.2/caf-reference
rm -rf ${ATLASES_DIR}nl_olek/caf-reference; cp -r ${ATLASES_DIR}nl_olek/caf ${ATLASES_DIR}nl_olek/caf-reference
rm -rf ${ATLASES_DIR}vector-test/caf-reference; cp -r ${ATLASES_DIR}vector-test/caf ${ATLASES_DIR}vector-test/caf-reference
rm -rf ${ATLASES_DIR}sba_DB08/caf-reference; cp -r ${ATLASES_DIR}sba_DB08/caf ${ATLASES_DIR}sba_DB08/caf-reference
rm -rf ${ATLASES_DIR}sba_PHT00/caf-reference; cp -r ${ATLASES_DIR}sba_PHT00/caf ${ATLASES_DIR}sba_PHT00/caf-reference
rm -rf ${ATLASES_DIR}sba_WHS09/caf-reference; cp -r ${ATLASES_DIR}sba_WHS09/caf ${ATLASES_DIR}sba_WHS09/caf-reference
rm -rf ${ATLASES_DIR}sba_WHS10/caf-reference; cp -r ${ATLASES_DIR}sba_WHS10/caf ${ATLASES_DIR}sba_WHS10/caf-reference
rm -rf ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf-reference; cp -r ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf ${ATLASES_DIR}sba_LPBA40_on_SRI24/caf-reference
rm -rf ${ATLASES_DIR}sba_RM_on_F99/caf-reference; cp -r ${ATLASES_DIR}sba_RM_on_F99/caf ${ATLASES_DIR}sba_RM_on_F99/caf-reference
rm -rf ${ATLASES_DIR}sba_FVE91_on_F99/caf-reference; cp -r ${ATLASES_DIR}sba_FVE91_on_F99/caf ${ATLASES_DIR}sba_FVE91_on_F99/caf-reference
rm -rf ${ATLASES_DIR}sba_B05_on_Conte69/caf-reference; cp -r ${ATLASES_DIR}sba_B05_on_Conte69/caf ${ATLASES_DIR}sba_B05_on_Conte69/caf-reference
rm -rf ${ATLASES_DIR}aba/caf-reference; cp -r ${ATLASES_DIR}aba/caf ${ATLASES_DIR}aba/caf-reference
rm -rf ${ATLASES_DIR}aba2011/caf-reference; cp -r ${ATLASES_DIR}aba2011/caf ${ATLASES_DIR}aba2011/caf-reference
rm -rf ${ATLASES_DIR}tem/caf-reference; cp -r ${ATLASES_DIR}tem/caf ${ATLASES_DIR}tem/caf-reference
rm -rf ${ATLASES_DIR}mbisc_11/caf-reference; cp -r ${ATLASES_DIR}mbisc_11/caf ${ATLASES_DIR}mbisc_11/caf-reference
rm -rf ${ATLASES_DIR}pos_0.1/caf-reference; cp -r ${ATLASES_DIR}pos_0.1/caf ${ATLASES_DIR}pos_0.1/caf-reference
rm -rf ${ATLASES_DIR}CBWJ13_P80/caf-reference; cp -r ${ATLASES_DIR}CBWJ13_P80/caf ${ATLASES_DIR}CBWJ13_P80/caf-reference
rm -rf ${ATLASES_DIR}WHS_SD_rat_atlas_v2/caf-reference; cp -r ${ATLASES_DIR}WHS_SD_rat_atlas_v2/caf ${ATLASES_DIR}WHS_SD_rat_atlas_v2/caf-reference
rm -rf ${ATLASES_DIR}WHS_SD_rat_atlas_v101/caf-reference; cp -r ${ATLASES_DIR}WHS_SD_rat_atlas_v101/caf ${ATLASES_DIR}WHS_SD_rat_atlas_v101/caf-reference
clean_diff:
rm -rfv diff_neurolucidaXML.txt diff_vector-test.txt\
diff_whs_0.51.txt diff_whs_0.5.txt diff_sba_PHT00.txt diff_sba_DB08.txt\
diff_sba_WHS09.txt diff_sba_WHS10.txt diff_sba_LPBA40_on_SRI24.txt\
diff_sba_RM_on_F99.txt diff_aba.txt diff_tem.txt diff_whs_0.6.1.txt diff_whs_0.6.2.txt\
diff_sba_FVE91_on_F99.txt diff_aba2011.txt diff_sba_B05_on_Conte69.txt \
diff_mbisc_11.txt diff_pos_0.1.txt diff_CBWJ13_P80.txt diff_WHS_SD_rat_atlas_v2.txt \
diff_WHS_SD_rat_atlas_v101.txt