#!/bin/sh

# copyright and script setup

#   feat - main FEAT command-line script
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2002-2008 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
#   Imaging of the Brain), Department of Clinical Neurology, Oxford
#   University, Oxford, UK
#   
#   
#   LICENCE
#   
#   FMRIB Software Library, Release 5.0 (c) 2012, The University of
#   Oxford (the "Software")
#   
#   The Software remains the property of the University of Oxford ("the
#   University").
#   
#   The Software is distributed "AS IS" under this Licence solely for
#   non-commercial use in the hope that it will be useful, but in order
#   that the University as a charitable foundation protects its assets for
#   the benefit of its educational and research purposes, the University
#   makes clear that no condition is made or to be implied, nor is any
#   warranty given or to be implied, as to the accuracy of the Software,
#   or that it will be suitable for any particular purpose or for use
#   under any specific conditions. Furthermore, the University disclaims
#   all responsibility for the use which is made of the Software. It
#   further disclaims any liability for the outcomes arising from using
#   the Software.
#   
#   The Licensee agrees to indemnify the University and hold the
#   University harmless from and against any and all claims, damages and
#   liabilities asserted by third parties (including claims for
#   negligence) which arise directly or indirectly from the use of the
#   Software or the sale of any products based on the Software.
#   
#   No part of the Software may be reproduced, modified, transmitted or
#   transferred in any form or by any means, electronic or mechanical,
#   without the express permission of the University. The permission of
#   the University is not required if the said reproduction, modification,
#   transmission or transference is done without financial return, the
#   conditions of this Licence are imposed upon the receiver of the
#   product, and all original and amended source code is included in any
#   transmitted product. You may be held legally responsible for any
#   copyright infringement that is caused or encouraged by your failure to
#   abide by these terms and conditions.
#   
#   You are not permitted under this Licence to use this Software
#   commercially. Use for which any financial return is received shall be
#   defined as commercial use, and includes (1) integration of all or part
#   of the source code or the Software into a product for sale or license
#   by or on behalf of Licensee to third parties or (2) use of the
#   Software or any derivative of it for research with the final aim of
#   developing software products for sale or license to a third party or
#   (3) use of the Software or any derivative of it for research with the
#   final aim of developing non-software products for sale or license to a
#   third party, or (4) use of the Software to provide any service to an
#   external organisation for which payment is received. If you are
#   interested in using the Software commercially, please contact Isis
#   Innovation Limited ("Isis"), the technology transfer company of the
#   University, to negotiate a licence. Contact details are:
#   innovation@isis.ox.ac.uk quoting reference DE/9564.

# the next line restarts using wish \
exec $FSLTCLSH "$0" "$@"

source $env(FSLDIR)/tcl/fslstart.tcl
proc fullFirstLevelAnalysis { session } { 

global FSLDIR FSLSLASH fmri feat_files fsfroot logout confoundev_files
#setup FEAT output directory
  if { $fmri(level) == 1 && $fmri(inputtype) == 1 } { #working in an existing feat directory
	set FD $feat_files($session)
	cd $FD
	fsl:exec "/bin/rm ?endered_thresh_* cluster_* lmax_* prob_mask_* thresh_* tsplot/* stats/*; rmdir stats tsplot" -n -i
} else { 
#setup new featdir name

   if { $fmri(outputdir) != "" } {
      if { $fmri(multiple) == 1 } {
	set FD [ feat5:strip $fmri(outputdir) ].feat
      } else {
	set FD [ file rootname $feat_files($session) ]_[ file rootname [ file tail $fmri(outputdir) ] ].feat
      }
   } else {
     set FD [ feat5:strip [ remove_ext $feat_files($session) ] ].feat
  }
  set FD [ new_filename $FD ]
  fsl:exec "/bin/mkdir -p $FD" -n
}
cd $FD
set FD [ pwd ]
fsl:exec "mkdir -p logs" -n
set logout ${FD}/logs/feat1

fsl:exec "/bin/cp ${fsfroot}.fsf design.fsf"

set confevs ""
if { [ file exists confoundevs.txt ] } {
    set confevs "confoundevs.txt"
}

set haltForModel 1
if { ! [ info exists fmri(featModelOpts) ] } {
set fmri(featModelOpts) ""
set haltForModel 0
}

set featModelID 0
if { $fmri(analysis) != 0 } {
    set featModelID [ fsl:exec "${FSLDIR}/bin/feat_model design $confevs" $fmri(featModelOpts) -N feat0_model -l logs ]
}
set fsfroot ${FD}/design

#setup web pages

if { ! [ file exists .files ] } {
    fsl:exec "mkdir .files;cp ${FSLDIR}/doc/fsl.css .files;ln -s ${FSLDIR}/doc/images .files/images"
}

fsl:echo report.html "<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">

<TABLE BORDER=0><TR>

<TD ALIGN=CENTER WIDTH=\"100%\">

<TABLE BORDER=0>

<tr><td align=center><font size=+3><b>FEAT Report</b></font></tr>

<tr><td valign=center height=\"25\" align=center>$FD<br>
<!--runningstart-->
Started at [ exec date ]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font color=\"red\">STILL RUNNING<blink>.</blink></font>
<!--runningstop-->
</tr>

<tr valign=bottom><td align=center>
<A HREF=\"report_reg.html\" target=\"_top\">Registration</A> &nbsp;-&nbsp;
<A HREF=\"report_prestats.html\" target=\"_top\">Pre-stats</A> &nbsp;-&nbsp;
<A HREF=\"report_stats.html\" target=\"_top\">Stats</A> &nbsp;-&nbsp;
<A HREF=\"report_poststats.html\" target=\"_top\">Post-stats</A> &nbsp;-&nbsp;
<A HREF=\"report_log.html\" target=\"_top\">Log</A>

</tr></table>

<TD ALIGN=RIGHT>
<a href=\"http://www.fmrib.ox.ac.uk/fsl\" target=\"_top\">
<IMG BORDER=0 SRC=\"file:${FSLSLASH}${FSLDIR}/doc//images/fsl-logo-big.jpg\" WIDTH=165></a>
</TD>

</TR></TABLE><hr>
" -o

if { ! [ file exists report_prestats.html ] } {
    fsl:echo report_prestats.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Prestats</h2>...not yet run..." -o
}

if { ! [ file exists report_stats.html ] } {
    fsl:echo report_stats.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Stats</h2>...not yet run..." -o
}

if { ! [ file exists report_poststats.html ] } {
    fsl:echo report_poststats.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Poststats</h2>...not yet run..." -o
}

if { ! [ file exists report_reg.html ] } {
    fsl:echo report_reg.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Registration</h2>...not yet run..." -o
}

fsl:echo logs/feat0 "<HTML><HEAD>
<!--refreshstart-->
<META HTTP-EQUIV=REFRESH CONTENT=5>
<!--refreshstop-->
<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Progress Report / Log</h2>
Started at [ exec date ]<p>
Feat main script<br><pre>" -o

fsl:echo logs/feat9 "</pre><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br></BODY></HTML>"

#working to here

if { $fmri(featwatcher_yn) } {
    FmribWebHelp file: ${FD}/report_log.html
} else {
    fsl:echo "" "To view the FEAT progress and final report, point your web browser at ${FD}/report_log.html"
}

    set jobHalt ""
    if { $haltForModel != 0 } {
       set jobHalt "-h $featModelID"
    }        
    set initID -1
    set prestatsID -1
    set statsID -1
    set poststatsID -1
    set prestatsTime 0
    if { ! [ info exists fmri(totalVoxels) ] || $fmri(totalVoxels) < 0 || $fmri(totalVoxels) == "totalVoxels" } {
	    set fmri(totalVoxels) 10000000
     }

    if { ( $fmri(filtering_yn) ||  $fmri(stats_yn) ) && $fmri(inputtype) == 2 } {
	set initID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session -init" -b 10 -N feat0_init -l logs ]
    }


    if { $fmri(reginitial_highres_yn) || $fmri(reghighres_yn) || $fmri(regstandard_yn) } {
	set prestatsTime [ expr $prestatsTime + 30 + 30 * $fmri(regstandard_nonlinear_yn) ]
    }


    if { $fmri(filtering_yn) } {
	set howlong [ expr int( $fmri(npts) / 10 ) ]
	if { $fmri(regunwarp_yn) } {
	    set howlong [ expr int( $fmri(npts) / 3 ) ]
	}
	if { $fmri(melodic_yn) } {
	    set howlong 300
	}                 
 	if { $fmri(totalVoxels) > 80000000 } {
 	   set howlong [ expr int( $fmri(totalVoxels) / 1000000 ) ]
	}
	set prestatsTime [ expr $prestatsTime + $howlong ]
     }
     if { $fmri(inputtype) == 2 } {
	set prestatsID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session -prestats" -b $prestatsTime -h $initID $jobHalt -N feat2_pre -l logs ]
     }
     set actualEVs $fmri(evs_real)
     if { $fmri(motionevsbeta) != "" } {
	 set actualEVs [ expr $actualEVs + [ exec sh -c "wc -l $fmri(motionevsbeta) | awk '{print \$1}'" ] ]
     }
     if { $fmri(motionevs) == 1 } {
	 set actualEVs [ expr $actualEVs + 6 ] 
     }
     if { $fmri(motionevs) == 2 } {
	 set actualEVs [ expr $actualEVs + 24 ] 
     }
     if { $fmri(confoundevs) && [ file exists $confoundev_files($session) ] } {
	  set actualEVs [ expr $actualEVs + [ exec sh -c "head -1 $confoundev_files($session) | wc -w  | awk '{print \$1}'" ] ]
     }

    if { $fmri(stats_yn) } {
	#This seems to be an fairly accurate estimate, for old-style feat, revisit when contrast film_gls goes on the system
	set howlong [ expr int ( ceil($fmri(totalVoxels)/1e7) * ( $fmri(totalVoxels) *  $fmri(npts)  * $actualEVs / 7e9 ) + 1 ) ]
	set statsID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session -stats" -b $howlong -h $prestatsID -N feat3_film -l logs ]
	set poststatsID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -poststats 0 " -b 119 -h $statsID -N feat4_post -l logs ]
    }
    fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -stop" -b 1 -h $prestatsID -h $statsID -h $poststatsID -N feat5_stop -l logs
} 

if { [ lindex $argv 0 ] == "" } {
    puts "
Usage: feat <design.fsf>
"
    exit 1
    puts "
Usage: feat <design.fsf> \[options\]

If no options are set then the whole design.fsf is processed

Misc options (these need to come before the partial analysis options):
 -I <N>   : run just session <N> of the multiple setups in <design.fsf>
 -D <dir> : use <dir> as the working output directory (instead of what is in <design.fsf>)

Partial analysis options:
 -init                             : run basic first-level initialisation
 -prestats                         : run first-level preprocessing
 -stats                            : run first-level statistics  
 -poststats <higherlevel>          : run post-stats (first or higher-level)
 -gfeatprep                        : run higher-level preparation
 -flame1                           : run higher-level stats part 1 (pre-FLAME)
 -flame2                           : run higher-level stats part 2 (FLAME)
 -flame3                           : run higher-level stats part 3 (post-FLAME)
 -gica                             : run higher-level MELODIC
 -stop                             : clean-up logs files etc.
"
}

set fsfroot [ file rootname [ lindex $argv 0 ] ]
if { [ string range $fsfroot 0 0 ] != "/" } {
    set fsfroot [ pwd ]/$fsfroot
}

set session 0
set done_something 0

feat5:setupdefaults
feat5:load -1 1 ${fsfroot}.fsf


if { [ catch {

for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
    switch -- [ lindex $argv $argindex ] {

	-I {
	    incr argindex 1
	    set session [ lindex $argv $argindex ]
	}

	-D {
	    incr argindex 1
	    set fmri(outputdir) [ lindex $argv $argindex ]
	}

	-init {
	    feat5:proc_init $session
	    set done_something 1
	}

	-prestats {
 	    feat5:proc_prestats $session
 	    set done_something 1
	}

	-stats { 
	    feat5:proc_stats $session 
	    set done_something 1
	}

	-poststats {
	    incr argindex 1
	    set higherLevel [ lindex $argv $argindex ]
 	    feat5:proc_poststats $higherLevel
 	    set done_something 1
	}

	-gfeatprep { 
	    feat5:proc_gfeatprep
 	    set done_something 1
	}

	-flame1 { 
	    feat5:proc_flame1 $session
	    set done_something 1
	}

	-flame2 { 
	    feat5:proc_flame2
 	    set done_something 1
	}

	-flame3 { 
 	    feat5:proc_flame3
 	    set done_something 1
	}

	-gica { 
	    feat5:proc_gica
	    set done_something 1
	}

	-stop { 
 	    feat5:proc_stop
 	    set done_something 1
	}
    }
}

} errMsg ] } {  

	puts "[lindex $argv $argindex]" 
        puts "$errMsg"
	feat5:proc_stop 
	return -code error "$errMsg"
}


# if we haven't processed a single-task job, this must be a full analysis:
if { $done_something == 0 } {

    if { ! $fmri(inmelodic) } {
       if { $fmri(level) == 1 } {
	  for { set session 1 } { $session <= $fmri(multiple) } { incr session 1 } {
	      fullFirstLevelAnalysis $session
	  }
      } else {


if { $fmri(outputdir) != "" } {
    set FD [ feat5:strip $fmri(outputdir) ].gfeat
} else {
    set FD [ feat5:strip [ remove_ext $feat_files(1) ] ].gfeat
}

if { ! [ info exists fmri(overwrite_yn) ] || $fmri(overwrite_yn) == 0 } {
    set FD [ new_filename $FD ]
}
fsl:exec "mkdir -p ${FD}/logs" -n

cd $FD
set FD [ pwd ]
set GFD $FD
set logout ${FD}/logs/feat1

fsl:exec "/bin/cp ${fsfroot}.fsf design.fsf"
fsl:exec "${FSLDIR}/bin/feat_model design"

set fsfroot ${FD}/design

#
# setup toplevel .gfeat web pages

if { ! [ file exists .files ] } {
    fsl:exec "mkdir .files;cp ${FSLDIR}/doc/fsl.css .files;ln -s ${FSLDIR}/doc/images .files/images"
}

fsl:echo report.html "<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">

<TABLE BORDER=0><TR>

<TD ALIGN=CENTER WIDTH=\"100%\">

<TABLE BORDER=0>

<tr><td align=center><font size=+3><b>Higher-Level FEAT Report</b></font></tr>

<tr><td valign=center height=\"25\" align=center>$FD<br>
<!--runningstart-->
Started at [ exec date ]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font color=\"red\">STILL RUNNING<blink>.</blink></font>
<!--runningstop-->
</tr>

<tr valign=bottom><td align=center>
<A HREF=\"report_firstlevel.html\" target=\"_top\">Inputs</A> &nbsp;-&nbsp;" -o
if { ! [ file exists $feat_files(1)/design.lev ] } {
    fsl:echo report.html "<A HREF=\"report_reg.html\" target=\"_top\">Registration summary</A> &nbsp;-&nbsp;"
}
fsl:echo report.html "<A HREF=\"report_stats.html\" target=\"_top\">Results</A> &nbsp;-&nbsp;
<A HREF=\"report_log.html\" target=\"_top\">Log</A>

</tr></table>

<TD ALIGN=RIGHT>
<a href=\"http://www.fmrib.ox.ac.uk/fsl\" target=\"_top\">
<IMG BORDER=0 SRC=\"file:${FSLSLASH}${FSLDIR}/doc//images/fsl-logo-big.jpg\" WIDTH=165></a>
</TD>

</TR></TABLE><hr>
"

fsl:echo report_firstlevel.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Inputs to higher-level analysis</h2>(lower-level FEAT reports)<p>" -o
for { set i 1 } { $i <= $fmri(multiple) } { incr i 1 } {
    set thelink $feat_files($i)/report.html
    if { $fmri(inputtype) == 2 } {
	set thelink [ file dirname [ file dirname $feat_files($i) ] ]/report.html
    }
    fsl:echo report_firstlevel.html "${i} <A HREF=\"${thelink}\">${thelink}</A><br>
"
}
fsl:echo report_firstlevel.html "</BODY></HTML>"

fsl:echo report_reg.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Summary of first-level registrations and masks</h2>" -o

fsl:echo report_stats.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>" -o

fsl:echo logs/feat0 "<HTML><HEAD>
<!--refreshstart-->
<META HTTP-EQUIV=REFRESH CONTENT=5>
<!--refreshstop-->
<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Progress Report / Log</h2>
Started at [ exec date ]<p>
Feat main script<br><pre>" -o

fsl:echo logs/feat9 "</pre><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br></BODY></HTML>"

if { $fmri(featwatcher_yn) } {
    FmribWebHelp file: ${FD}/report_log.html
} else {
    fsl:echo "" "To view the FEAT progress and final report, point your web browser at ${FD}/report_log.html"
}

#
# setup some variables??

if { $fmri(inputtype) == 1 } {

    # "FEAT directories" option
    set STANDARD [ feat5:find_std $feat_files(1) standard ]
    fsl:echo report_stats.html "<h2>Higher-level FEAT results</h2>(one for each lower-level contrast)<p>"
    set ff_one $feat_files(1)
    for { set nci 1 } { $nci <=  $fmri(ncopeinputs) } { incr nci 1 } {   
	if { $fmri(copeinput.$nci) } {
	    set contrastname($nci) "[ feat5:getconname $ff_one $nci ]"
	    set feat_files($nci) ${FD}/cope$nci
	    set conname ""
	    if { $contrastname($nci) != "" } {
		set conname "($contrastname($nci))"
	    }
	    fsl:echo report_stats.html "<a href=\"cope${nci}.feat/report_poststats.html\">Lower-level contrast $nci $conname</a><br>"
	} else {
	    set feat_files($nci) -1
	}
    }
    set fmri(multiple) $fmri(ncopeinputs)

} elseif { $fmri(inputtype) == 2 } {

    # "3D cope input" option
    set STANDARD [ feat5:find_std [ file dirname [ file dirname $feat_files(1) ] ] standard ]
    set contrastname(1) ""
    set fmri(multiple) 1
    set feat_files(1) ${FD}/cope1
    fsl:echo report_stats.html "<hr><a href=\"cope1.feat/report_poststats.html\">Higher-level FEAT results</a><br>"

}

#
# finish toplevel stats report page

if { [ file exists design.mat ] } {
    fsl:echo report_stats.html "<hr><p><b>Design matrix</b><br><a href=\"design.mat\"><IMG BORDER=0 SRC=\"design.png\"></a>"
}
fsl:echo report_stats.html "</BODY></HTML>"

#

set preID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -gfeatprep" -b 60 -N feat2_pre -l logs ]
set allID ""

for { set session 1 } { $session <= $fmri(multiple) } { incr session 1 } {
    if { $feat_files($session) != -1 } {
	# setup FEAT directory

set FD $feat_files($session)
set FD ${FD}.feat
fsl:exec "/bin/mkdir -p ${FD}/logs" -n
cd $FD
set logout ${FD}/logs/feat1
fsl:exec "/bin/cp ../design.* ." -n
set fsfroot ${FD}/design

fsl:echo design.lev "$contrastname($session)"

#setup dummy .flame file to keep the batch submission happy
if { [ exec sh -c "grep NumPoints design.mat | awk '{ print \$2 }'" ] < 30 && $fmri(mixed_yn) != 1 && $fmri(robust_yn) == 0 } {
    fsl:echo .flame "dummy"
} else {
    set DIMZ [ exec sh -c "$FSLDIR/bin/fslval $STANDARD dim3" ]
    for { set slice 0 } { $slice < $DIMZ } { incr slice 1 } {
	fsl:echo .flame "dummy"
    }
}

#
	# setup web pages

set conname ""
if { $contrastname($session) != "" } {
    set conname "($contrastname($session))"
}

fsl:exec "ln -s ../.files .files"

fsl:echo report.html "<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">

<TABLE BORDER=0><TR>

<TD ALIGN=CENTER WIDTH=\"100%\">

<TABLE BORDER=0>

<tr><td align=center><font size=+3><b>Results for lower-level contrast $session $conname</b></font></tr>

<tr><td valign=center height=\"25\" align=center>$FD<br>
<!--runningstart-->
Started at [ exec date ]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font color=\"red\">STILL RUNNING<blink>.</blink></font>
<!--runningstop-->
</tr>

<tr valign=bottom><td align=center>
<A HREF=\"../report_stats.html\" target=\"_top\">Up to main page</A> &nbsp;-&nbsp;
<A HREF=\"report_stats.html\" target=\"_top\">Stats</A> &nbsp;-&nbsp;
<A HREF=\"report_poststats.html\" target=\"_top\">Post-stats</A> &nbsp;-&nbsp;
<A HREF=\"report_log.html\" target=\"_top\">Log</A>

</tr></table>

<TD ALIGN=RIGHT>
<a href=\"http://www.fmrib.ox.ac.uk/fsl\" target=\"_top\">
<IMG BORDER=0 SRC=\"file:${FSLSLASH}${FSLDIR}/doc//images/fsl-logo-big.jpg\" WIDTH=165></a>
</TD>

</TR></TABLE><hr>
" -o

if { ! [ file exists report_stats.html ] } {
    fsl:echo report_stats.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Stats</h2>...not yet run..." -o
}

if { ! [ file exists report_poststats.html ] } {
    fsl:echo report_poststats.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Poststats</h2>...not yet run..." -o
}

fsl:echo logs/feat0 "<HTML><HEAD>
<!--refreshstart-->
<META HTTP-EQUIV=REFRESH CONTENT=5>
<!--refreshstop-->
<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Progress Report / Log</h2>
Started at [ exec date ]<p>
<pre>" -o

fsl:echo logs/feat9 "</pre><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br></BODY></HTML>"

set logout ${GFD}/logs/feat1

        set howlong 60
        if { $fmri(robust_yn) } { set howlong [ expr int( $fmri(npts) * $fmri(evs_real) / 10 ) ] }
	set ID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session -flame1" -b 60 -N feat3a_flame -h $preID -l logs ]
	set ID [ fsl:exec "./.flame" -b $howlong -N feat3b_flame -h $ID -l logs -f ]
	set ID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -flame3" -b 60 -N feat3c_flame -h $ID -l logs ]
	set ID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -poststats 1" -b 60 -N feat4_post -h $ID -l logs ]
	set allID "$allID -h [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -stop" -b 1 -h $ID -N feat5_stop -l logs ]"
	cd ..
    }
}

fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $GFD -stop" -b 1 $allID -N feat5_stop -l logs

	}
    } else {
	#MELODIC

if { $fmri(icaopt) > 1 } {

if { $fmri(outputdir) != "" } {
    set GFD [ feat5:strip $fmri(outputdir) ].gica
} else {
    set GFD [ feat5:strip [ remove_ext $feat_files(1) ] ].gica
}

set GFD [ new_filename $GFD ]
fsl:exec "mkdir -p ${GFD}/logs" -n
cd $GFD
set GFD [ pwd ]

set logout ${GFD}/logs/feat1

fsl:exec "/bin/cp ${fsfroot}.fsf design.fsf"


if { ! [ file exists .files ] } {
    fsl:exec "mkdir .files;cp ${FSLDIR}/doc/fsl.css .files;ln -s ${FSLDIR}/doc/images .files/images"
}

fsl:echo report.html "<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">

<TABLE BORDER=0><TR>

<TD ALIGN=CENTER WIDTH=\"100%\">

<TABLE BORDER=0>

<tr><td align=center><font size=+3><b>Higher-Level MELODIC Report</b></font></tr>

<tr><td valign=center height=\"25\" align=center>$GFD<br>
<!--runningstart-->
Started at [ exec date ]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font color=\"red\">STILL RUNNING<blink>.</blink></font>
<!--runningstop-->
</tr>

<tr valign=bottom><td align=center>
<A HREF=\"report_firstlevel.html\" target=\"_top\">Inputs</A> &nbsp;-&nbsp;
<A HREF=\"report_reg.html\" target=\"_top\">Registration summary</A> &nbsp;-&nbsp;
<A HREF=\"groupmelodic.ica/report/00index.html\" target=\"_top\">MELODIC output</A> &nbsp;-&nbsp;
<A HREF=\"report_log.html\" target=\"_top\">Log</A>

</tr></table>

<TD ALIGN=RIGHT>
<a href=\"http://www.fmrib.ox.ac.uk/fsl\" target=\"_top\">
<IMG BORDER=0 SRC=\"file:${FSLSLASH}${FSLDIR}/doc//images/fsl-logo-big.jpg\" WIDTH=165></a>
</TD>

</TR></TABLE><hr>
"

fsl:echo report_firstlevel.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Inputs to higher-level analysis</h2>(lower-level processing)<p>" -o

fsl:echo report_reg.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Summary of first-level registrations and masks</h2>" -o

fsl:exec "mkdir -p groupmelodic.ica/report" -n
fsl:echo groupmelodic.ica/report/00index.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"../../report.html\"></OBJECT>
...not yet run..." -o

fsl:echo logs/feat0 "<HTML><HEAD>
<!--refreshstart-->
<META HTTP-EQUIV=REFRESH CONTENT=5>
<!--refreshstop-->
<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Progress Report / Log</h2>
Started at [ exec date ]<p>
Feat main script<br><pre>" -o

fsl:echo logs/feat9 "</pre><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br></BODY></HTML>"

if { $fmri(featwatcher_yn) } {
    FmribWebHelp file: ${GFD}/report_log.html
} else {
    fsl:echo "" "To view the FEAT progres and final report, point your web browser at ${GFD}/report_log.html"
}

#
}
set ALLID ""

for { set session 1 } { $session <= $fmri(multiple) } { incr session 1 } {

    # setup output directory

if { $fmri(outputdir) != "" } {
    if { $fmri(multiple) == 1 } {
	set FD [ feat5:strip $fmri(outputdir) ].ica
    } else {
	set FD [ file rootname $feat_files($session) ]_[ file rootname [ file tail $fmri(outputdir) ] ].ica
    }
} else {
    set FD [ feat5:strip [ remove_ext $feat_files($session) ] ].ica
}

set FD [ new_filename $FD ]
fsl:exec "/bin/mkdir -p ${FD}/logs" -n

cd $FD
set FD [ pwd ]
set logout ${FD}/logs/feat1

fsl:exec "/bin/cp ${fsfroot}.fsf design.fsf"

set fsfroot ${FD}/design

if { $fmri(icaopt) > 1 } {
    fsl:echo ${GFD}/.filelist ${FD}/reg_standard/filtered_func_data
    fsl:echo ${GFD}/design.fsf "set feat_files($session) \"$FD\""
}

#
    # setup web pages

if { ! [ file exists .files ] } {
    fsl:exec "mkdir .files;cp ${FSLDIR}/doc/fsl.css .files;ln -s ${FSLDIR}/doc/images .files/images"
}

fsl:echo report.html "<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">

<TABLE BORDER=0><TR>

<TD ALIGN=CENTER WIDTH=\"100%\">

<TABLE BORDER=0>

<tr><td align=center><font size=+3><b>MELODIC Report</b></font></tr>

<tr><td valign=center height=\"25\" align=center>$FD<br>
<!--runningstart-->
Started at [ exec date ]
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <font color=\"red\">STILL RUNNING<blink>.</blink></font>
<!--runningstop-->
</tr>

<tr valign=bottom><td align=center>
<A HREF=\"report_prestats.html\" target=\"_top\">Pre-stats</A> &nbsp;-&nbsp;
<A HREF=\"report_reg.html\" target=\"_top\">Registration</A> &nbsp;-&nbsp;" -o

if { $fmri(icaopt) == 1 } {
    fsl:echo report.html "<A HREF=\"filtered_func_data.ica/report/00index.html\" target=\"_top\">ICA</A> &nbsp;-&nbsp;"
}

fsl:echo report.html "<A HREF=\"report_log.html\" target=\"_top\">Log</A>

</tr></table>

<TD ALIGN=RIGHT>
<a href=\"http://www.fmrib.ox.ac.uk/fsl\" target=\"_top\">
<IMG BORDER=0 SRC=\"file:${FSLSLASH}${FSLDIR}/doc//images/fsl-logo-big.jpg\" WIDTH=165></a>
</TD>

</TR></TABLE><hr>
"

if { ! [ file exists report_prestats.html ] } {
    fsl:echo report_prestats.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Prestats</h2>...not yet run..." -o
}

if { ! [ file exists report_reg.html ] } {
    fsl:echo report_reg.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Registration</h2>...not yet run..." -o
}

if { $fmri(icaopt) == 1 } {
    fsl:exec "mkdir -p filtered_func_data.ica/report" -n
    fsl:echo filtered_func_data.ica/report/00index.html "<HTML><HEAD><link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"../../report.html\"></OBJECT>
...not yet run..." -o
}

fsl:echo logs/feat0 "<HTML><HEAD>
<!--refreshstart-->
<META HTTP-EQUIV=REFRESH CONTENT=5>
<!--refreshstop-->
<link REL=\"stylesheet\" TYPE=\"text/css\" href=\".files/fsl.css\">
<TITLE>FSL</TITLE></HEAD><BODY><OBJECT data=\"report.html\"></OBJECT>
<h2>Progress Report / Log</h2>
Started at [ exec date ]<p>
Main script<br><pre>" -o

fsl:echo logs/feat9 "</pre><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br></BODY></HTML>"

if { $fmri(icaopt) == 1 } {
    if { $fmri(featwatcher_yn) } {
	FmribWebHelp file: ${FD}/report_log.html
    } else {
	fsl:echo "" "To view the MELODIC progress and final report, point your web browser at ${FD}/report_log.html"
    }
}

if { $fmri(icaopt) > 1 } {
    set logout ${GFD}/logs/feat1
}

#
    set ID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session -init" -b 10 -N feat1a_init -l logs ]


    set howlong [ expr int( $fmri(npts) / 10 ) ] 
    if 	{ ( $fmri(regstandard_nonlinear_yn) || $fmri(regunwarp_yn) ) && $howlong < 250 } {
       set howlong 250	   
    }



    set ID [ fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -I $session -prestats" -b $howlong -h $ID -N feat2_pre -l logs ]
    set ALLID "$ALLID -h $ID"


    if { $fmri(icaopt) == 1 } {
	# setup melodic command

#set logout ${FD}/logs/feat4
fsl:echo ${FD}/logs/feat4 "</pre><hr>Stats<br><pre>"

set thecommand "${FSLDIR}/bin/melodic -i filtered_func_data -o filtered_func_data.ica -v --nobet --bgthreshold=$fmri(thresh) --tr=$fmri(tr) --report --guireport=../../report.html"

set howlong 30
if { $fmri(dim_yn) == 1 } {
    set thecommand "$thecommand -d 0"
    if { $fmri(npts) > 300 } {
	set howlong 180
    }
} else {
    set thecommand "$thecommand -d $fmri(dim)"
    if { $fmri(dim) > 100 } {
	set howlong 180
    }
}

if { $fmri(varnorm) == 0 } {
    set thecommand "$thecommand --vn"
}

if { $fmri(thresh_yn) == 0 } {
    set thecommand "$thecommand --no_mm"
} else {
    set thecommand "$thecommand --mmthresh=\"$fmri(mmthresh)\""
}

if { $fmri(ostats) == 1 } {
    set thecommand "$thecommand --Ostats"
}

if { [ file exists $fmri(ts_model_mat) ] && [ file exists $fmri(ts_model_con) ] } {
    set thecommand "$thecommand --Tdes=$fmri(ts_model_mat) --Tcon=$fmri(ts_model_con)"
}

#
	set ID [ fsl:exec "$thecommand" -b $howlong -h $ID -N feat4_ica -l logs ]
    }
    fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -stop" -b 1 -h $ID -N feat5_stop -l logs
}

if { $fmri(icaopt) > 1 } {
    cd $GFD
    set ID [ fsl:exec "${FSLDIR}/bin/feat ${GFD}/design.fsf -D $GFD -gica" -b 180 $ALLID -N feat4_gica -l logs ]
    fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $GFD -stop" -b 1 -h $ID -N feat5_stop -l logs
}

#
    }
}