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Script¬¿ | Contents¬¿ | Notes¬¿ | Replaced ¬¿By |
01_copy_flip_lines.csh¬¿ | #!/bin/csh¬¿ | Pipeline¬¿ | |
#### KATHERINE'S SCRIPTS¬¿ | |||
###RUN IN LISTS DIRECTORY¬¿ | |||
###THIS SCRIPT COPIES ALL L AND R LINES INTO CASE DIRECTORIES. NOTE THAT RIGHT LINES NEED TO BE IN L HEMISPHERIC SPACE!.The R HEM LINES are copied to an original space subdirectory first; the R HEM LINES are then flipped with the output directed to the directory above which is where the L HEM lines are.¬¿ | |||
#foreach x ( `cat medial_anal.list` )¬¿ | |||
#foreach x ( `cat new_medial_anal.list` )¬¿ | medial_anal.list' is a list of subjects in the study¬¿ | ||
foreach x (/cxfs/schizo/family_study/10396_/10396)¬¿ | |||
if (! -e ${x:h}/MED_UCFs) mkdir ${x:h}/MED_UCFs¬¿ | |||
endif¬¿ | |||
if (! -e ${x:h}/MED_UCFs/original_space) mkdir ${x:h}/MED_UCFs/original_space¬¿ | |||
endif¬¿ | |||
foreach y (1 2a 2c 3 4 5 6 7 8 9 10m 15 16 17m 19 21 30 31 32a 32b 32c 33 34 36 37a 37b 38 50m 51m 53m 54m 55m)¬¿ | |||
cp ${x:h}/${y}R.obj ${x:h}/MED_UCFs/original_space/${x:t}_${y}R.obj¬¿ | |||
cp ${x:h}/${y}L.obj ${x:h}/MED_UCFs/${x:t}_${y}L.obj¬¿ | |||
echo "done ${x:h}/${y}"¬¿ | |||
end¬¿ | |||
foreach z (${x:h}/MED_UCFs/original_space/*_*R.obj)¬¿ | |||
set out = `basename ${z}`¬¿ | |||
echo "transforming object ${z}."¬¿ | |||
echo "transforming object ${out}"¬¿ | |||
transform_objects ${z} /nethome/users/narr/invert.xfm ${x:h}/MED_UCFs/${out}¬¿ | Transform_Type = Linear;¬¿ Linear_Transform ¬¿-1 0 0 0 ¬¿0 1 0 0 ¬¿0 0 1 0; | ||
end¬¿ | |||
¬¿ | |||
end¬¿ | |||
02_divide_redig_lines.csh¬¿ | #! /bin/tcsh -f¬¿ | ||
# KATHERINE'S SCRIPTS¬¿ | |||
# Run in lists directory. ¬¿ | |||
#foreach x ( `cat medial_anal.list` )¬¿ | |||
#foreach x ( `cat new_medial_anal.list` )¬¿ | |||
foreach x (/cxfs/schizo/family_study/10396_/10396)¬¿ | |||
¬¿ ¬¿ echo "\nMaking subdirectories\n" | |||
¬¿if ( ! -e ${x:h}/MED_TMP ) mkdir ${x:h}/MED_TMP | |||
¬¿if ( ! -e ${x:h}/MED_RSPs ) mkdir ${x:h}/MED_RSPs | |||
¬¿if ( ! -e ${x:h}/MED_RSPs/DIVIDED ) mkdir ${x:h}/MED_RSPs/DIVIDED | |||
¬¿ | |||
¬¿ ¬¿ foreach y (${x:h}/MED_UCFs/*.obj) | |||
¬¿ | |||
¬¿ ¬¿ ¬¿ ¬¿ echo "Converting ${y} to RSP-ucf" | |||
¬¿set object = `basename ${y}` | |||
¬¿set ucf = ${x:h}/MED_UCFs/${object:r}.ucf | |||
¬¿set tl_ucf = ${x:h}/MED_TMP/3_${object:r}.ucf | |||
¬¿set RS_ucf = ${x:h}/MED_TMP/RS3_${object:r}.ucf | |||
¬¿set RSP_ucf = ${x:h}/MED_RSPs/RSP3_${object:r}.ucf | |||
¬¿if ( ! -e ${ucf} ) then | |||
¬¿ ¬¿ ¬¿/nethome/users/drex/bin/obj_line_to_ucf ${y} ${ucf} | Do we need to use UCF?¬¿ | ||
¬¿endif | |||
¬¿if ( ! -e ${tl_ucf} ) then | |||
¬¿ ¬¿ ¬¿/nethome/users/drex/scripts/1_to_3_level_ucf ${ucf} ${tl_ucf} | Create a ¿Äúsurface¿Äù from a contour¬¿ | ||
¬¿endif | |||
¬¿if ( ! -e ${RS_ucf} ) then | |||
¬¿ ¬¿ ¬¿/nethome/users/drex/scripts/3D_redigarb ${tl_ucf} ${RS_ucf} | Smooths the contours¬¿ | ||
¬¿endif | |||
¬¿if ( ! -e ${RSP_ucf} ) then | |||
¬¿ ¬¿ ¬¿/nethome/users/drex/scripts/3D_reslicer ${RS_ucf} ${RSP_ucf} | ¿ÄúAdd more levels to the ¿Äúsurface¿Äù¬¿ | ||
¬¿endif | |||
¬¿ ¬¿ end | |||
¬¿cp ${x:h}/MED_RSPs/RSP3_*_5?.ucf ${x:h}/MED_RSPs/DIVIDED | |||
¬¿cp ${x:h}/MED_RSPs/RSP3_*_21?.ucf ${x:h}/MED_RSPs/DIVIDED | |||
¬¿cp ${x:h}/MED_RSPs/RSP3_*_1?.ucf ${x:h}/MED_RSPs/DIVIDED | |||
¬¿ | |||
¬¿set split_dir = ${x:h}/MED_RSPs/DIVIDED/ | |||
¬¿cd $split_dir | |||
¬¿ren 's/RSP3_//g' .ucf | |||
¬¿echo "renaming done" | |||
¬¿ ¬¿ ¬¿ ¬¿foreach line (.ucf) | |||
¬¿ ¬¿ ¬¿ ¬¿echo "dividing lines" | |||
¬¿ set ucf = ${line:r} | |||
¬¿ if ( ! -e ${ucf}a.ucf ) then | |||
¬¿ /nethome/users/thompson/SEG/SGI/divide_mesh_in_2 1 2 3 4 5 6 ${ucf}.ucf > ${ucf}a.ucf | |||
¬¿ endif | |||
¬¿ if ( ! -e ${ucf}b.ucf ) then | |||
¬¿ /nethome/users/thompson/SEG/SGI/divide_mesh_in_2 2 2 3 4 5 6 ${ucf}.ucf > ${ucf}b.ucf | |||
¬¿ endif | |||
¬¿ ¬¿ ¬¿ ¬¿end | |||
¬¿ ren 's/La/aL/g' La* | Renames files¬¿ | ||
¬¿ ren 's/Ra/aR/g' *Ra* | ¿Äú¬¿ | ||
¬¿ ren 's/Lb/bL/g' *Lb* | ¿Äú¬¿ | ||
¬¿ ren 's/Rb/bR/g' *Rb* | ¿Äú¬¿ | ||
¬¿ foreach ucf2 (*a.ucf b.ucf) | |||
¬¿ set ucf3 = 3_${ucf2} | |||
¬¿ set RS_ucf = RS3_${ucf2} | |||
¬¿ set RSP_ucf = RSP3_${ucf2} | |||
¬¿ echo "making three levels" | |||
¬¿ if ( ! -e ${ucf3} ) then | |||
¬¿ /nethome/users/drex/scripts/1_to_3_level_ucf ${ucf2} ${ucf3} | Redundant?¬¿ | ||
¬¿ endif | |||
¬¿ echo "making RSPs" | |||
¬¿ if ( ! -e ${RS_ucf} ) then | |||
¬¿ ¬¿ ¬¿ /nethome/users/drex/scripts/3D_redigarb ${ucf3} ${RS_ucf} | Redundant?¬¿ | ||
¬¿ endif | |||
¬¿ if ( ! -e ${RSP_ucf} ) then | |||
¬¿ /nethome/users/drex/scripts/3D_reslicer ${RS_ucf} ${x:h}/MED_RSPs/${RSP_ucf} | Redundant?¬¿ | ||
¬¿ endif | |||
¬¿ ¬¿ ¬¿ ¬¿ ¬¿ ¬¿ ¬¿ ¬¿ ¬¿ ¬¿ end | |||
¬¿ | |||
cd /cxfs/schizo/family_study/lists¬¿ | |||
end¬¿ | |||
echo ".Done."¬¿ | |||
exit 0¬¿ | |||
03_copy_rediged_lines.csh¬¿ | #! /bin/tcsh -f¬¿ | ||
# copies redigitized files to subdirectories for averaging.¬¿ | |||
#foreach x ( `cat medial_anal.list` )¬¿ | |||
#foreach x ( `cat new_medial_anal.list` )¬¿ | |||
foreach x (/cxfs/schizo/family_study/10396_/10396)¬¿ | |||
set FOLDER = /cxfs/schizo/family_study/MEDIAL_ANAL/all¬¿ | |||
¬¿if (! -e ${FOLDER}) mkdir ${FOLDER} | |||
¬¿if (! -e ${FOLDER}/RSPs) mkdir ${FOLDER}/RSPs | |||
cp ${x:h}/MED_RSPs/*.* ${FOLDER}/RSPs/¬¿ | |||
echo "${x:h}"¬¿ | |||
end¬¿ | |||
echo ".Done."¬¿ | |||
exit 0¬¿ | |||
04_avg_lines.csh¬¿ | #! /bin/tcsh -f¬¿ | ||
# analyze.csh <directory> will compute the variance maps and average location (e.g. analyze.csh all)¬¿ | |||
# for all sulci for all subjects in the directory.¬¿ | |||
if ( $#argv < 1 ) then¬¿ | |||
¬¿ ¬¿ echo "USAGE: analyze.csh [-clean] <director(y,ies)>" | |||
¬¿ ¬¿ echo " ¬¿Will compute the variance maps and the average sulcal line positions" | |||
¬¿ ¬¿ echo " ¬¿for each sulcus in the directory." | |||
¬¿ ¬¿ exit 1 | |||
endif¬¿ | |||
set clean = FALSE¬¿ | |||
while ($#argv)¬¿ | |||
¬¿ ¬¿ if ( $1 = "-clean" ) then | |||
¬¿set clean = TRUE | |||
¬¿shift | |||
¬¿continue | |||
¬¿ ¬¿ endif | |||
¬¿ ¬¿ set FOLDER = $1 | |||
¬¿ ¬¿ if ( ! -d ${FOLDER} ) then | |||
¬¿echo "ERROR: ${FOLDER} is not a valid directory." | |||
¬¿shift | |||
¬¿continue | |||
¬¿ ¬¿ endif | |||
¬¿ ¬¿ echo "Working on directory ${FOLDER}." | |||
¬¿ ¬¿ echo "\nMaking subdirectories\n" | |||
¬¿ ¬¿ | |||
¬¿ ¬¿ if ( ! -e ${FOLDER}/AVG ) mkdir ${FOLDER}/AVG | |||
¬¿ ¬¿ if ( ! -e ${FOLDER}/VAR ) mkdir ${FOLDER}/VAR | |||
¬¿ ¬¿ if ( ! -e ${FOLDER}/TMP ) mkdir ${FOLDER}/TMP | |||
¬¿ ¬¿ cd ${FOLDER} | |||
¬¿ ¬¿ ¬¿foreach line ( 1L 1aL 1bL 2aL 2cL 3L 4L 5L 5aL 5bL 6L 7L 8L 9L 10mL 15L 16L 17mL 19L 21L 21aL 21bL 30L 31L 32aL 32bL 32cL 33L 34L 36L 37aL 37bL 38L 10mL 17mL 50mL 51mL 53mL 54mL 55mL 1R 1aR 1bR 2aR 2cR 3R 4R 5R 5aR 5bR 6R 7R 8R 9R 10mR 15R 16R 17mR 19R 21R 21aR 21bR 30R 31R 32aR 32bR 32cR 33R 34R 36R 37aR 37bR 38R 10mR 17mR 50mR 51mR 53mR 54mR 55mR) | |||
¬¿ ¬¿ ¬¿set wc_lines = `((ls RSPs/RSP3_*_${line}.ucf > TMP/$$.tmp) >&! /dev/null); wc TMP/$$.tmp` | |||
¬¿ ¬¿ ¬¿/bin/rm -f TMP/$$.tmp | |||
¬¿ ¬¿ ¬¿@ num_lines = $wc_lines[1] | |||
¬¿ ¬¿ ¬¿if ( ${num_lines} > 0 ) then | |||
¬¿ echo "Computing average and variance maps for ${num_lines} files of ${line} in ${FOLDER}." | |||
¬¿ set var = VAR/var_map${num_lines}_${line}.ucf | |||
¬¿ set svar = VAR/SHORTvar_map${num_lines}_${line}.ucf | |||
¬¿ set avg = AVG/avg_map${num_lines}_${line}.ucf | |||
¬¿ if ( ! -e ${var} ) then | |||
¬¿ ¬¿ ¬¿ /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/surfNstat4D RSPs/RSP3_*_${line}.ucf > ${var} | ShapeStatistics¬¿ | ||
¬¿ endif | |||
¬¿ if ( ! -e ${avg} ) then | |||
¬¿ ¬¿ ¬¿ /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/surfNstat3D RSPs/RSP3_*_${line}.ucf > ${avg} | ShapeAverage¬¿ | ||
¬¿ endif | |||
¬¿ if ( ! -e ${svar} ) then | |||
¬¿ ¬¿ ¬¿ /nethome/users/drex/scripts/ucf_to_short ${var} ${svar} >& /dev/null | Removes all but first level in a UCF¬¿ | ||
¬¿ endif | |||
¬¿ if ( ! -e ${svar:r}.dx ) then | |||
¬¿ ¬¿ ¬¿ ucdx ${svar} >& /dev/null | |||
¬¿ endif | |||
¬¿ ¬¿ ¬¿endif | |||
¬¿end | |||
¬¿ ¬¿ cd .. | |||
¬¿ ¬¿ echo ".Done." | |||
¬¿ ¬¿shift | |||
exit 0¬¿ | |||
05_copy_flip_surf.csh¬¿ | #!/bin/csh¬¿ | ||
###RUN IN LISTS DIRECTORY¬¿ | |||
#foreach x ( `cat medial_anal.list` )¬¿ | |||
#foreach x ( `cat new_medial_anal.list` )¬¿ | |||
foreach x ( /cxfs/schizo/family_study/10396_/10396 )¬¿ | |||
if (! -e ${x:h}/Left_CORT) mkdir ${x:h}/Left_CORT¬¿ | |||
endif¬¿ | |||
if (! -e ${x:h}/Right_CORT) mkdir ${x:h}/Right_CORT¬¿ | |||
endif¬¿ | |||
echo "${x:h}/${x:t}_n3_305_6p_*_R.obj"¬¿ | |||
set out = `basename ${x:h}/${x:t}_n3_305_6p_*_R.obj`¬¿ | |||
echo "transforming object ${out}"¬¿ | |||
transform_objects ${x:h}/${x:t}_n3_305_6p_*_R.obj /nethome/users/narr/invert.xfm ${x:h}/Right_CORT/${out}¬¿ | See first script¬¿ | ||
echo "${x:h}/${x:t}_n3_305_6p_*_L.obj"¬¿ | |||
cp ${x:h}/${x:t}_n3_305_6p_*_L.obj ${x:h}/Left_CORT¬¿ | |||
echo "${x:h}/${x:t}_n3_305_6p_*_L.obj"¬¿ | |||
end¬¿ | |||
06_copy_shortRSPs.csh¬¿ | #!/bin/csh¬¿ | ||
###RUN IN LISTS DIRECTORY¬¿ | |||
#foreach x ( `cat medial_anal.list` )¬¿ | |||
#foreach x ( `cat new_medial_anal.list` )¬¿ | |||
foreach x (/cxfs/schizo/family_study/10396_/10396)¬¿ | |||
set RSPS = ${x:h}/MED_RSPs¬¿ | |||
set LSURF = ${x:h}/Left_CORT¬¿ | |||
set RSURF = ${x:h}/Right_CORT¬¿ | |||
foreach ucf (${RSPS}/*L.ucf)¬¿ | |||
¬¿ ¬¿ /nethome/users/drex/scripts/ucf_to_short ${ucf} ${LSURF}/SHORT${ucf:t} | |||
end¬¿ | |||
foreach ucf (${RSPS}/*R.ucf)¬¿ | |||
¬¿ ¬¿/nethome/users/drex/scripts/ucf_to_short ${ucf} ${RSURF}/SHORT${ucf:t} | |||
end¬¿ | |||
end¬¿ | |||
07_Local_dual_med_flat_catchL.csh¬¿ | #! /bin/csh ¬¿ | Flatten curves in the Left [L] hemisphere¬¿ | |
#NOTE: Need 3 things in CORT directory...1)colored brain object 2)SHORTened RSP3 files for specific case and 3) Divided Lines (1, 5, 21; a & b) ¬¿ | |||
#When done, view with seg and load up by typing: seg -line 3 DUALflat.uvl FLAT_SHORTRSP3*.ucf OR seg -line 3 DUALflat.uvl DUALFLAT_SHORTRSP3*.ucf¬¿ | |||
#You will have two flattened images in DUALflat.uvl¬¿ | |||
#When loading FLAT*.ucf, use LsurrR?_BIGCord to view flattened lines¬¿ | |||
#When loading DUALFLAT*.ucf, use RsurrL?_BIGCord to view flattened lines¬¿ | |||
#foreach x ( `cat medial_anal.list`)¬¿ | |||
#foreach x ( `cat new_medial_anal.list`)¬¿ | |||
foreach x (/cxfs/schizo/family_study/10396_/10396)¬¿ | |||
set STUDY = ${x:h}¬¿ | |||
echo ${STUDY}¬¿ | |||
cd ${STUDY}/Left_CORT¬¿ | |||
¬¿ ¬¿ echo " ¬¿Copying files..." | |||
¬¿ ¬¿ cp /data/ad/d/thompson/Z_DAVES_STUFF_FROM_TMPNET/6NEW_CORTICAL_MESH_CODE/pauls_AD64K_to_FULLvertex_list . | |||
¬¿ ¬¿ cp /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/FLATTENING/rec131072_other_octants . | |||
¬¿ ¬¿ cp /nethome/users/drex/models/64*list . | |||
¬¿ ¬¿ cp /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/FLATTENING/COLORS_rec131072_other_octants . | |||
¬¿ ¬¿ cp /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/FLATTENING/big64K_stream . | |||
¬¿ ¬¿ cp /data/ad/mass3/users/PAULS_SURFACE_CODE/SGI/FLATTENING/real_64K_curve_find . | |||
¬¿ ¬¿ cp /nethome/users/thompson/HEM_FLAT/BIGflat.uvl . | |||
##################################################################¬¿ | |||
¬¿ ¬¿ echo " ¬¿Running perl..." | |||
¬¿ ¬¿ ./pauls_AD64K_to_FULLvertex_list < {$STUDY}/Lef*CORT/*obj > FULLvertex.list | This writes the obj vertex coordinates to a file ¿ÄúFULLvertex.list¿Äù¬¿ | ||
¬¿ ¬¿ echo " ¬¿Getting colors from object..." | |||
¬¿ ¬¿ ## NOTE: ¬¿must use gnu version of tail as SGI sucks and decided in their | |||
¬¿ ¬¿ ## ¬¿ ¬¿ ¬¿ ¬¿infinite wisdom to cut you off at 256K (since that is all their | |||
¬¿ ¬¿ ## ¬¿ ¬¿ ¬¿ ¬¿"faster" buffered mode of tail can handle) -- drex 4/18/00 | |||
¬¿ ¬¿ head -n 196618 ${STUDY}/Lef*CORT/*obj | /usr/gnu/bin/tail -n 65538 | /usr/gnu/bin/tail -c +3 > 64K_colors.txt | Writes the vertex colors to ¿Äú64K_colors.txt¿Äù¬¿ | ||
¬¿ ¬¿ echo " ¬¿Unscrambling tiles to octant .ucfs..." | |||
¬¿ ¬¿ foreach PIECE ( 1 2 3 4 5 6 7 8 ) | |||
¬¿ ¬¿ ¬¿ ¬¿ echo " ¬¿ $PIECE" | |||
¬¿./rec131072_other_octants 0 2 3 4 5 6 FULLvertex.list 64K_tri0_${PIECE}oct.list disord.uif ord.uif > ${PIECE}oct_3D.ucf | Creates a ¿Äúdiamond ucf¿Äù from the vertex list and face list for a given octant¬¿ | ||
¬¿ ¬¿ end | |||
¬¿ ¬¿ echo " ¬¿Starting texture descrambling to texture octant .ucfs..." | |||
¬¿ ¬¿ foreach PIECE ( 1 2 3 4 5 6 7 8 ) | |||
¬¿echo " ¬¿ $PIECE" | |||
¬¿./COLORS_rec131072_other_octants 0 2 3 4 5 6 FULLvertex.list 64K_tri0_${PIECE}oct.list disord.uif ord.uif > C${PIECE}oct_3D.ucf | Creates a ¿Äúdiamond ucf¿Äù from the vertex color list and face list for a given octant¬¿ | ||
¬¿ ¬¿ end | |||
######¬¿ | |||
¬¿ ¬¿ echo " ¬¿Making Right Hem. position map..." | |||
¬¿ ¬¿ ./big64K_stream 1 2 3 4 5 6 1oct_3D.ucf 2oct_3D.ucf 3oct_3D.ucf 4oct_3D.ucf 1oct_3D.ucf 1oct_3D.ucf 1oct_3D.ucf > 1st_oct_set.ucf | Copies the ucf coordinates to the ¿ÄúL¿Äù flatmaps¬¿ | ||
¬¿ ¬¿ cp ord.uif ordR.uif |
Probably created by big64k_stream¬¿ | ||
¬¿ ¬¿ cp DECord.uif DECordR?.uif | Probably created by big64k_stream¬¿ | ||
L corresponds to octants 1-4¬¿ | |||
######¬¿ | |||
¬¿ ¬¿ echo " ¬¿Making Left Hem. position map..." | |||
¬¿ ¬¿ ./big64K_stream 1 2 3 4 5 6 6oct_3D.ucf 5oct_3D.ucf 8oct_3D.ucf ¬¿7oct_3D.ucf 1oct_3D.ucf 1oct_3D.ucf 1oct_3D.ucf > 2nd_oct_set.ucf | Copies the ucf coordinates to the ¿ÄúR¿Äù flatmaps¬¿ | ||
¬¿ ¬¿ cp ord.uif ordL.uif | Probably created by big64k_stream¬¿ | ||
¬¿ ¬¿ cp DECord.uif DECordL?.uif | Probably created by big64k_stream¬¿ | ||
R corresponds to octants 5-8¬¿ | |||
######¬¿ | |||
¬¿ ¬¿ echo " ¬¿Making Right Hem. texture map..." | |||
¬¿ ¬¿ ./big64K_stream 1 2 3 4 5 6 C1oct_3D.ucf C2oct_3D.ucf C3oct_3D.ucf C4oct_3D.ucf C1oct_3D.ucf C1oct_3D.ucf C1oct_3D.ucf > C1st_oct_set.ucf | Copies the color ucf coordinates to the ¿ÄúR¿Äù flatmaps¬¿ | ||
¬¿ ¬¿ cp ord.uif CordR?.uif | Probably created by big64k_stream¬¿ | ||
¬¿ ¬¿ # caution,a DEC file is meaningless and actually makes things worse for a texture map. | |||
¬¿ ¬¿ cp DECord.uif DECCordR?.uif | Probably created by big64k_stream¬¿ | ||
######¬¿ | |||
¬¿ ¬¿ echo " ¬¿Making Left Hem. texture map..." | |||
¬¿ ¬¿ ./big64K_stream 1 2 3 4 5 6 C6oct_3D.ucf C5oct_3D.ucf C8oct_3D.ucf ¬¿C7oct_3D.ucf |