#! /bin/csh -f
# Script file to take a reconstructed dataset and make analyze BRIKs
# Should be placed in and run from FIDAP directory, output goes to analyze directory
# Must be started from iris:/usr/people/mbeaucha
# (Can't run in /data1/EC directory on iris because of "pwd" confusion,
# can't run on hippo because no padstring command)
	# experiment code
        set ec = AN
     	# Change to correct directory
	cd /data2/mike/AN
        # number of total tasks
        set max_tasks = 6
	# number of reps of each task
        set repnumlist = ( 2 2 2 2 2 1 )
        # number of slices
        set max_slices = 23   
        # number of timepoints
        set max_time = 88   
# Make directory to hold results
mkdir analyze
chdir analyze
# Loop over all tasks
set tasknum = 1
while ( $tasknum <= $max_tasks )
  cd ../{$ec}t{$tasknum}
  # analyze utilities append, so must remove any already existing files
  rm {$ec}*hdr {$ec}*img
  set repnum = 1
  while ( $repnum <= $repnumlist[$tasknum] )	
  	set time_pt = 1    
	while ( $time_pt <= $max_time )    
 	    set padtm = `pad_string $time_pt +0 2`
	    set slice_no = 1
  	    while ($slice_no <= $max_slices)
		set padsl = `pad_string $slice_no +0 2`
		# echo excise {$ec}t{$tasknum}r{$repnum}_{$padsl}.{$padtm} {$ec}t{$tasknum}r{$repnum}_{$padtm}.img 0 8192
		excise {$ec}t{$tasknum}r{$repnum}_{$padsl}.{$padtm} {$ec}t{$tasknum}r{$repnum}_{$padtm}.img 0 8192
		@ slice_no++
	    end
           @ time_pt ++
	   set max = `max16bit {$ec}t{$tasknum}r{$repnum}_{$padtm}`
 	   makeheader4 {$ec}t{$tasknum}r{$repnum}_{$padtm}.hdr 64 64 $max_slices 3.75 3.75 5 1 16 $max 0 $max 0 4 
        end
        @ repnum ++
	# move results to analyze directory
	mv {$ec}*hdr {$ec}*img ../analyze/
  end
  @ tasknum ++
end
# Don't want to analyze first three images
cd ../analyze
mkdir EPanat
mv {$ec}t?r?_0[0-3].img EPanat/
mv {$ec}t?r?_0[0-3].hdr EPanat/
# create a universal header for generating a mask (and other operations)
cp {$ec}t1r1_04.hdr anyhdr.hdr