#!/bin/tcsh -f
# make surface spec files from the surface files
#
# usage @SUMA_Make_Spec_SF [options]
#
# options: -sid subject_id : specify subject ID
# -sfpath SureFit_path : specify path to SureFit files
# -debug level : display extra output
#
#----------------------------------------------------------------------
goto L_INIT_VARS
L_INIT_VARS_DONE:
goto L_CHECK_USAGE
L_CHECK_USAGE_DONE:
goto L_PARSE_COMMAND
L_PARSE_COMMAND_DONE:
goto L_VERIFY_PROGRAMS
L_VERIFY_PROGRAMS_DONE:
goto L_SET_SURF_DIRS
L_SET_SURF_DIRS_DONE:
goto L_CHECK_FOR_OVERWRITE
L_CHECK_FOR_OVERWRITE_DONE:
goto L_LOOK_FOR_SURF
L_LOOK_FOR_SURF_DONE:
goto L_LOOK_FOR_TOPO
L_LOOK_FOR_TOPO_DONE:
goto L_LOOK_FOR_VOLPARAMS
L_LOOK_FOR_VOLPARAMS_DONE:
goto L_CREATE_SPEC
L_CREATE_SPEC_DONE:
goto L_TEST_SURF_VOL
L_TEST_SURF_VOL_DONE:
goto L_GOOD_END # finished, woohooo!
####################################################################
# variable initialization
L_INIT_VARS:
set prog_name = $0:t
set endstr = "$prog_name ... finished"
set debug = 0
set surf_attribs = (fiducial \
ellipsoid \
inflated \
)
goto L_INIT_VARS_DONE
####################################################################
# check usage, and possibly print help
L_CHECK_USAGE:
if ( $#argv == 0 ) then
echo "usage: $prog_name [options] -sid SUBJECT_ID"
echo "usage: $prog_name -help"
echo "See Also @SUMA_Make_Spec_Caret"
set endstr = ""
goto L_GOOD_END
endif
goto L_CHECK_USAGE_DONE
####################################################################
# parse the command line
L_PARSE_COMMAND:
# init command line arg values
set sf_dir = "."
set subj_id = ""
set args = $#argv
set count = 1
while ( $count <= $args )
switch ( "$argv[$count]" )
# ----------------------------------------------------------
# usage: -help
case "-h":
case "-help":
goto L_HELP_END # and don't ya' come back, neither
breaksw
# ----------------------------------------------------------
# usage: -sid SUBJECT_ID
case "-sid":
if ( $count >= $args ) then
set endstr = "arg usage: -sid SUBJECT_ID"
goto L_BAD_END
endif
@ count ++
set subj_id = $argv[$count]
breaksw
# ----------------------------------------------------------
# usage: -sfpath SUREFIT_PATH
case "-sfpath":
if ( $count >= $args ) then
set endstr = "arg usage: -sfpath SUREFIT_PATH"
goto L_BAD_END
endif
@ count ++
set sf_dir = $argv[$count]
if ( ! -d $sf_dir ) then
set endstr = "failure: directory not found - '$sf_dir'"
goto L_BAD_END
endif
breaksw
# ----------------------------------------------------------
# usage : -debug DEBUG_LEVEL
case "-debug":
if ( $count >= $args ) then
set endstr = "arg usage: -debug DEBUG_LEVEL"
goto L_BAD_END
endif
@ count ++
set debug = $argv[$count]
if ( "$debug" > 2 ) set debug = 2
if ( "$debug" < 0 ) set debug = 0
breaksw
# ----------------------------------------------------------
# bad argument
default:
set endstr = "invalid option: '$argv[$count]'"
goto L_BAD_END
breaksw
endsw
@ count ++
end
if ( $subj_id == "" ) then
set endstr = "missing required option: -sid"
goto L_BAD_END
endif
if ( $debug ) echo "-- usage okay"
if ( $debug > 1 ) set echo
set spec_files = ({$subj_id}_lh.spec {$subj_id}_rh.spec )
set afni_prefix = ${subj_id}_SurfVol
set afni_dataset = $afni_prefix+orig
# set and go to the base directory
cd $sf_dir
set start_dir = $cwd
if ( $debug ) echo "-- using start_dir '$start_dir'"
goto L_PARSE_COMMAND_DONE
####################################################################
# make sure programs exist
L_VERIFY_PROGRAMS:
set failed_pgms = 0
foreach test_command ( afni suma )
(which $test_command) >& /dev/null
if ( $status ) then
echo "Warning: program not found in path: $test_command"
#these programs are not necessary
#@ failed_pgms ++
endif
end
if ( $failed_pgms ) then
set endstr = "$failed_pgms program(s) not found"
goto L_BAD_END
endif
if ( $debug ) echo "-- all programs found"
goto L_VERIFY_PROGRAMS_DONE
####################################################################
# 1. set surfaces_dir and vol_dir - check cwd and parent
L_SET_SURF_DIRS:
# find SURFACES directory
if ( -d SURFACES) then
set surfaces_dir = ./SURFACES
else if ( $cwd:t == SURFACES ) then
set surfaces_dir = .
else if ( -d ../SURFACES ) then
set surfaces_dir = ../SURFACES
else
# this is a general failure case, even if we find one
set surfaces_dirs = ( `find . -maxdepth 4 -type d -name SURFACES -print` )
if ( $#surfaces_dirs == 0 ) then
echo "failure: cannot find directory 'SURFACES' under '$sf_dir'"
echo "(subject to a maximum search depth of 4 subdirectories)"
set endstr = ""
else if ( $#surfaces_dirs == 1 ) then
echo "SURFACES directory found at '$surfaces_dirs[1]'"
set endstr = "consider running program from '$surfaces_dirs[1]:h'"
else
echo "multiple SURFACES directories found:"
set count = 1
while ( $count <= $#surfaces_dirs )
echo " $surfaces_dirs[$count]"
@ count ++
end
set endstr = ( "consider running program from one of the" \
"SURFACES directories" )
endif
goto L_BAD_END
endif
# verify SURFACES dir permissions
if ( ! -w $surfaces_dir ) then
set endstr = "failure: no write permissions for directory '$surfaces_dir'"
goto L_BAD_END
endif
if ( $debug ) echo "-- using SURFACES directory '$surfaces_dir'..."
# vol_dir is the parent directory of SURFACES
set vol_dir = $surfaces_dir/../
# verify orig dir permissions
if ( ! -w $vol_dir ) then
set endstr = "failure: no write permissions for directory '$vol_dir'"
goto L_BAD_END
endif
if ( $debug ) echo "-- using volume directory '$vol_dir'..."
#set suma_dir to be surfaces_dir
set suma_dir = $surfaces_dir
goto L_SET_SURF_DIRS_DONE
####################################################################
# verify non-existence of spec files and AFNI files
L_CHECK_FOR_OVERWRITE:
set test_failures = 0
foreach test_file ( $suma_dir/$spec_files[1] \
$suma_dir/$spec_files[2] \
)
if ( -f $test_file ) then
if ( $test_failures == 0 ) then
echo "failure: will not overwrite files: "
set test_failures = 1
endif
echo " '$test_file'"
endif
end
if ( $test_failures ) then
set endstr = "please remove these files if you want to rerun the script."
goto L_BAD_END
endif
goto L_CHECK_FOR_OVERWRITE_DONE
####################################################################
# find surface files
L_LOOK_FOR_SURF:
cd $surfaces_dir
set list_lh = "X" # init to something useless - allows nice empty check
set list_rh = "X"
foreach Side ( 'L' 'R' )
#get all the surfaces and ask user to identify one to use
set CHOOSE_LIST = `ls -t *.$Side.*segment*fiducial*.coord`
echo "Choose final fiducial surface (1st one is most likely since it was created last):"
#vvvvvvvvvvvvvvvvvvvv chooser block
#This cannot be used inside a loop with a goto statement.
set CHOOSE_LIST_cnt = 1
foreach CHOOSE_LIST_item ( $CHOOSE_LIST )
echo "$CHOOSE_LIST_cnt- $CHOOSE_LIST_item"
@ CHOOSE_LIST_cnt ++
end
set CHOOSE_LIST_select = 0
while ($CHOOSE_LIST_select > $#CHOOSE_LIST || $CHOOSE_LIST_select < 1)
echo "Enter number of Choice:"
set CHOOSE_LIST_select = $<
end
set CHOSEN_ITEM = $CHOOSE_LIST[$CHOOSE_LIST_select]
set CHOSEN_ITEM_INDEX = $CHOOSE_LIST_select
#^^^^^^^^^^^^^^^^^^ chooser block
set NoExt = $CHOSEN_ITEM:r #remove the .coord extension
set NodeNumb = $NoExt:e #extract the number before .coord
foreach attrib ( $surf_attribs )
set candidate = `ls *.$Side.*segment*$attrib*$NodeNumb*.coord`
if ($#candidate != 1) then
echo 'candidate surfaces= '
echo $candidate
set endstr = "found 0 or more than one candidate surfaces matching '*."$Side'.*segment*'$attrib'*'$NodeNumb'*.coord'
goto L_BAD_END
else
if ($Side == 'L') then
set list_lh = ( $list_lh $candidate )
else
set list_rh = ( $list_rh $candidate )
endif
endif
end
end
set list_lh = ( $list_lh[2-] ) # now remove the leading "X"
set list_rh = ( $list_rh[2-] )
if ( $#list_lh == 0 && $#list_rh == 0 ) then
set endstr = "found no LH or RH surface files under '$surfaces_dir'"
goto L_BAD_END
endif
if ( $#list_lh > 0 ) then
echo "-- found $#list_lh LH surfaces"
if ( $debug ) echo " --" $list_lh
endif
if ( $#list_rh > 0 ) then
echo "-- found $#list_rh RH surfaces"
if ( $debug ) echo " --" $list_rh
endif
cd $start_dir
goto L_LOOK_FOR_SURF_DONE
####################################################################
# choose an item from a list files
L_CHOOSE_LIST:
#pass a list in CHOOSE_LIST and a return label in CHOOSE_LIST_RET variables
#expect CHOSEN_ITEM and CHOSEN_ITEM_INDEX (first item is 1)
set CHOOSE_LIST_cnt = 1
foreach CHOOSE_LIST_item ( $CHOOSE_LIST )
echo "$CHOOSE_LIST_cnt- $CHOOSE_LIST_item"
@ CHOOSE_LIST_cnt ++
end
set CHOOSE_LIST_select = 0
while ($CHOOSE_LIST_select > $#CHOOSE_LIST || $CHOOSE_LIST_select < 1)
echo "Enter number of Choice:"
set CHOOSE_LIST_select = $<
end
set CHOSEN_ITEM = $CHOOSE_LIST[$CHOOSE_LIST_select]
set CHOSEN_ITEM_INDEX = $CHOOSE_LIST_select
goto $CHOOSE_LIST_RET
####################################################################
# find topo files
L_LOOK_FOR_TOPO:
cd $surfaces_dir
foreach Side (L R)
set list_topo = "X" # init to something useless - allows nice empty check
if ($Side == 'L') then
set list = ( $list_lh )
else
set list = ( $list_rh )
endif
#for each item in list, try to guess the appropriate .topo file
foreach coord ( $list )
#remove .coord
set NoExt = $coord:r
set NodeNumb = $NoExt:e
set candidate = `ls *.$Side.*segment*$NodeNumb.topo`
if ($#candidate == 0) then
set endstr = "found no topo for $coord."
goto L_BAD_END
else
if ($#candidate > 1) then
echo "Choose topo file to go with $list file:"
set CHOOSE_LIST = ( $candidate )
#vvvvvvvvvvvvvvvvvvvv chooser block
set CHOOSE_LIST_cnt = 1
foreach CHOOSE_LIST_item ( $CHOOSE_LIST )
echo "$CHOOSE_LIST_cnt- $CHOOSE_LIST_item"
@ CHOOSE_LIST_cnt ++
end
set CHOOSE_LIST_select = 0
while ($CHOOSE_LIST_select > $#CHOOSE_LIST || $CHOOSE_LIST_select < 1)
echo "Enter number of Choice:"
set CHOOSE_LIST_select = $<
end
set CHOSEN_ITEM = $CHOOSE_LIST[$CHOOSE_LIST_select]
set CHOSEN_ITEM_INDEX = $CHOOSE_LIST_select
#^^^^^^^^^^^^^^^^^^ chooser block
set candidate = $CHOSEN_ITEM
endif
endif
set list_topo = ( $list_topo $candidate )
end
if ($Side == 'L') then
set list_topo_lh = ( $list_topo[2-] ) #Remove the X
#echo "Topo List side $Side :"
#echo "$list_topo_lh"
else
set list_topo_rh = ( $list_topo[2-] )
#echo "Topo List side $Side :"
#echo "$list_topo_lh"
endif
end
cd $start_dir
goto L_LOOK_FOR_TOPO_DONE
####################################################################
# Get the vol param file (and the afni brick used in creating surface)
L_LOOK_FOR_VOLPARAMS:
cd $vol_dir
foreach Side (L R)
set candidate = `ls -t *.$Side.*.params`
if ($#candidate == 0) then
set endstr = "found no vol params found for $Side side"
goto L_BAD_END
else
if ($#candidate > 1) then
echo "Choose .params file used in SureFit to create the surfaces:"
set CHOOSE_LIST = ( $candidate )
#vvvvvvvvvvvvvvvvvvvv chooser block
set CHOOSE_LIST_cnt = 1
foreach CHOOSE_LIST_item ( $CHOOSE_LIST )
echo "$CHOOSE_LIST_cnt- $CHOOSE_LIST_item"
@ CHOOSE_LIST_cnt ++
end
set CHOOSE_LIST_select = 0
while ($CHOOSE_LIST_select > $#CHOOSE_LIST || $CHOOSE_LIST_select < 1)
echo "Enter number of Choice:"
set CHOOSE_LIST_select = $<
end
set CHOSEN_ITEM = $CHOOSE_LIST[$CHOOSE_LIST_select]
set CHOSEN_ITEM_INDEX = $CHOOSE_LIST_select
#^^^^^^^^^^^^^^^^^^ chooser block
set candidate = $CHOSEN_ITEM
endif
endif
if ($Side == 'L') then
set Vol_Param_lh = $candidate
else
set Vol_Param_rh = $candidate
endif
end
# try for afni data set used in creating surface
set candidate = `ls -t *.HEAD`
echo $#candidate $candidate
if ($#candidate == 0) then
set endstr = "found no afni data sets used in creating surfaces"
goto L_BAD_END
else
if ($#candidate > 1) then
echo "Choose AFNI data set used in SureFit to create the surfaces:"
set CHOOSE_LIST = ( $candidate )
#vvvvvvvvvvvvvvvvvvvv chooser block
set CHOOSE_LIST_cnt = 1
foreach CHOOSE_LIST_item ( $CHOOSE_LIST )
echo "$CHOOSE_LIST_cnt- $CHOOSE_LIST_item"
@ CHOOSE_LIST_cnt ++
end
set CHOOSE_LIST_select = 0
while ($CHOOSE_LIST_select > $#CHOOSE_LIST || $CHOOSE_LIST_select < 1)
echo "Enter number of Choice:"
set CHOOSE_LIST_select = $<
end
set CHOSEN_ITEM = $CHOOSE_LIST[$CHOOSE_LIST_select]
set CHOSEN_ITEM_INDEX = $CHOOSE_LIST_select
#^^^^^^^^^^^^^^^^^^ chooser block
set candidate = $CHOSEN_ITEM
endif
endif
set afni_dataset = $candidate
cd $start_dir
goto L_LOOK_FOR_VOLPARAMS_DONE
####################################################################
# actually create the spec file
L_CREATE_SPEC:
cd $suma_dir
foreach hand ( lh rh )
if ( $hand == lh ) then
set list_cur = ( $list_lh ) # get a current list copy
set list_topo_cur = ( $list_topo_lh )
set Vol_Param = $Vol_Param_lh
else
set list_cur = ( $list_rh )
set list_topo_cur = ( $list_topo_rh )
set Vol_Param = $Vol_Param_rh
endif
set spec_file = {$subj_id}_$hand.spec
if ( $debug ) echo "++ creating spec file '$spec_file'..."
(echo "# delimits comments" > $spec_file) >& /dev/null
if ( $status ) then
set endstr = ( "failure: no permissions to create spec file" \
"'$suma_dir/$spec_file'" )
goto L_BAD_END
endif
# note user, date, machine, pwd, command line
echo "" >> $spec_file
echo "# Creation information:" >> $spec_file
echo "# user : $user" >> $spec_file
echo "# date : `date`" >> $spec_file
echo "# machine : `uname -n`" >> $spec_file
echo "# pwd : $cwd" >> $spec_file
echo "# command : $prog_name $argv" >> $spec_file
echo "" >> $spec_file
# define the group
echo "# define the group" >> $spec_file
echo " Group = $subj_id" >> $spec_file
echo "" >> $spec_file
# define the states
echo "# define various States" >> $spec_file
foreach attrib ( $surf_attribs )
echo " StateDef = $attrib" >> $spec_file
end
echo "" >> $spec_file
set cnt = 1
foreach surf ( $list_cur )
set NoExt = $surf:r #remove .coord
set NodeNumb = $NoExt:e #store NodeNumb
set NoExt = $NoExt:r #remove NodeNumb
set s_state = $NoExt:e #store state
set s_head = $NoExt:r #store surface header, no state
# check for SAME mapping ref
if ( "$s_state" == "fiducial" ) then
set map_ref = SAME
else
set map_ref = $s_head.fiducial.$NodeNumb.coord
endif
# EmbedDimension is 2 for .flat surfaces, else 3
#this is not set for SureFit yet. Must figure out nomenclature
if ( $surf =~ *.flat* ) then
set embed_ref = 2
else
set embed_ref = 3
endif
echo "NewSurface" >> $spec_file
echo " SurfaceFormat = ASCII" >> $spec_file
echo " SurfaceType = SureFit" >> $spec_file
echo " SureFitCoord = $surf" >> $spec_file
echo " SureFitTopo = $list_topo_cur[$cnt]" >> $spec_file
echo " SureFitVolParam = ../$Vol_Param" >> $spec_file
echo " LocalDomainParent = $map_ref" >> $spec_file
echo " SurfaceState = $s_state" >> $spec_file
echo " EmbedDimension = $embed_ref" >> $spec_file
echo "" >> $spec_file
@ cnt ++
end
echo "++ created spec file'$suma_dir/$spec_file'"
end # foreach hand
cd $start_dir
goto L_CREATE_SPEC_DONE
####################################################################
# echo details for the user to launch suma and afni, in order to
# check the alignment
L_TEST_SURF_VOL:
echo ""
echo "------------------------------------------------------------------"
echo "Please verify that the datasets are aligned properly in both"
echo "afni and suma. You may do this by running the following commands:"
echo ""
echo " cd $suma_dir"
echo " afni -niml &"
echo " suma -spec $spec_file -sv $afni_dataset"
goto L_TEST_SURF_VOL_DONE
####################################################################
# display help and exit
L_HELP_END:
echo ""
echo "$prog_name - prepare for surface viewing in SUMA"
echo ""
echo "Use @SUMA_Make_Spec_Caret for caret surfaces"
echo ""
echo " This script goes through the following steps:"
echo " - determine the location of surfaces and "
echo " then AFNI volume data sets used to create them."
echo " - creation of left and right hemisphere SUMA spec files"
echo ""
echo " - all created files are stored in SURFACES directory"
echo ""
echo " Usage: $prog_name [options] -sid SUBJECT_ID"
echo ""
echo " examples:"
echo ""
echo " $prog_name -sid subject1"
echo " $prog_name -help"
echo " $prog_name -sfpath subject1/surface_stuff -sid subject1"
echo ""
echo " options:"
echo ""
echo " -help : show this help information"
echo ""
echo " -debug LEVEL : print debug information along the way"
echo " e.g. -debug 1"
echo " the default level is 0, max is 2"
echo ""
echo " -sfpath PATH : path to directory containing 'SURFACES'"
echo " and AFNI volume used in creating the surfaces."
echo " e.g. -sfpath subject1/surface_models"
echo " the default PATH value is './', the current directory"
echo ""
echo " This is generally the location of the 'SURFACES' directory,"
echo " though having PATH end in SURFACES is OK. "
echo ""
echo " Note: when this option is provided, all file/path"
echo " messages will be with respect to this directory."
echo ""
echo ""
echo " -sid SUBJECT_ID : required subject ID for file naming"
echo ""
echo ""
echo " notes:"
echo ""
echo " 0. More help may be found at http://afni.nimh.nih.gov/ssc/ziad/SUMA/SUMA_doc.htm"
echo " 1. Surface file names should look like the standard names used by SureFit:"
echo " rw_1mmLPI.L.full.segment_vent_corr.fiducial.58064.coord"
echo " Otherwise the script cannot detect them. You will need to decide which"
echo " surface is the most recent (the best) and the script helps you by listing"
echo " the available surfaces with the most recent one first."
echo " This sorting ususally works except when the time stamps on the surface files"
echo " are messed up. In such a case you just need to know which one to use."
echo " Once the fiducial surface is chosen, it's complimentary surfaces are selected"
echo " using the node number in the file name."
echo " 3. You can tailor the script to your needs. Just make sure you rename it or risk"
echo " having your modifications overwritten with the next SUMA version you install."
echo ""
echo " R. Reynolds (rickr@codon.nih.gov), Z. Saad (ziad@nih.gov)"
echo ""
exit
####################################################################
# failure!
L_BAD_END:
echo ""
if ( "$endstr" != "" ) echo "$endstr"
echo program failure: exiting...
echo ""
exit
####################################################################
# finished!
L_GOOD_END:
if ( $debug > 1 ) unset echo
echo ""
if ( "$endstr" != "" ) then
echo "$endstr"
echo ""
endif
exit # just to be consistent
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