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65041639 · Stephen Smith · 15f9b34d · 65041639 · 15f9b34d
Commit 65041639 authored 20 years ago by Stephen Smith
--- a/melodic.tcl
+++ b/melodic.tcl
@@ -336,8 +336,7 @@ checkbutton $w.ostats -variable fmri(ostats) -text "Output full stats folder" -f
 $w.bhelp bind $w.ostats -msg "
 When switched on, Melodic will save the thresholded IC 
-maps and the probability maps in Analyze (.img/.hdr) 
+maps and the probability maps inside a folder \/stats. 
-format inside a folder \/stats. 
 This will substantially increase the amount of space used, 
 so only switch this on if you intend to use these maps."
@@ -448,7 +447,7 @@ proc melodic2:apply { w dialog } {
 	#{{{ setup filenames
-set INPUT [ file rootname $feat_files($session) ]
+set INPUT [ remove_ext $feat_files($session) ]
 set OUTPUT [ new_filename ${INPUT}.ica ]

--- a/melodicreport
+++ b/melodicreport
-#!/bin/sh
-#   melodicreport - makes the report page for melodic
-#
-#   Christian Beckmann, Stephen Smith and Mark Jenkinson
-#   FMRIB Image Analysis Group
-#
-#   Copyright (C) 1999-2004 University of Oxford
-#
-#   SHCOPYRIGHT
-# the next line restarts using wish \
-exec $FSLDIR/bin/tclsh "$0" "$@"
-if { [ lindex $argv 0 ] == "" } {
-    puts "Usage: melodicreport <melodic_output_directory> \[background_image \]"
-    exit
-}
-set background 0
-if { [ lindex $argv 1 ] != "" } {
-    set background 1
-    set bgimage [ lindex $argv 1 ]
-}
-set S 0.2
-catch {  [ expr $S ] } errrr 
-set FSLDIR $env(FSLDIR)
-set MD [ lindex $argv 0 ]
-catch { exec sh -c "mkdir ${MD}/report" }
-if { ! [ file exists ${MD}/melodic_IC.hdr ] && ! [ file exists ${MD}/melodic_IC.hdr.gz ] } {
-    puts "No MELODIC output melodic_IC - exiting."
-    exit
-}
-if { ! [ file exists ${MD}/melodic_IC.img ] && ! [ file exists ${MD}/melodic_IC.img.gz ] } {
-    puts "No MELODIC output melodic_IC - exiting."
-    exit
-}
-set REPORTFILE ${MD}/report/report.html
-set report [ open $REPORTFILE "w" ]
-fconfigure $report -buffering none
-puts $report "<HTML>
-<TITLE>MELODIC Report</TITLE>
-<BODY BACKGROUND=\"file:${FSLDIR}/doc/images/fsl-bg.jpg\">
-<hr><CENTER>
-<H1>MELODIC Report</H1>
-$REPORTFILE<br>
-[ exec date ]
-</CENTER>
-<hr><H2>Components:</H2><p>"
-set dim  [ exec sh -c "${FSLDIR}/bin/avwval ${MD}/melodic_IC dim4" ]
-set npts [ expr [ exec sh -c "cat ${MD}/melodic_mix | wc -l" ] * 1 ]
-set xscale [ expr $npts * 4 ]
-if { $xscale < 750 } {
-    set xscale 750
-}
-if { $xscale > 3000 } {
-    set xscale 3000
-}
-set xscale [ expr $xscale / 750.0 ]
-for { set i 1 } { $i <= $dim } { incr i 1 } {
-    puts $report "<a href=\"c${i}.html\">$i</a>"
-    exec sh -c "${FSLDIR}/bin/avwroi ${MD}/melodic_IC ${MD}/grot [ expr $i - 1 ] 1"
-    catch { exec sh -c "${FSLDIR}/bin/avwstats ${MD}/grot -R" } minmax
-    set absmin [ expr abs ( [ lindex $minmax 0 ] ) ]
-    set absmax [ expr abs ( [ lindex $minmax 1 ] ) ]
-    if { $absmin > $absmax } {
-	    set absmax $absmin
-    }
-    set absmax [ expr $absmax * 0.75 ]
-    if { $background == 0 } {
-	exec sh -c "${FSLDIR}/bin/slicer ${MD}/grot -l ${FSLDIR}/etc/luts/render3.lut -s 2 -i -$absmax $absmax -A 950 ${MD}/grot.ppm"
-    } else {
-	set llimit [ expr $absmax / 6.0 ]
-	exec sh -c "${FSLDIR}/bin/avwmaths ${MD}/grot -mul -1 ${MD}/grotinv"
-	exec sh -c "${FSLDIR}/bin/overlay 1 0 $bgimage -a ${MD}/grot $llimit $absmax ${MD}/grotinv $llimit $absmax ${MD}/grotoverlay"
-	exec sh -c "${FSLDIR}/bin/slicer ${MD}/grotoverlay -s 2 -A 950 ${MD}/grot.ppm"
-    }
-    exec sh -c "${FSLDIR}/bin/convert ${MD}/grot.ppm ${MD}/report/s$i.gif"
-    exec sh -c "cat ${MD}/melodic_mix | awk '{ print \$$i }' > ${MD}/report/t${i}.txt"
-    exec sh -c "echo \"set term pbm color ; set size $xscale,0.25 ; set title 'Timecourse (TRs)' ; plot '${MD}/report/t${i}.txt' title '' with lines\" | ${FSLDIR}/bin/gnuplot > ${MD}/grot.ppm"
-    exec sh -c "${FSLDIR}/bin/convert ${MD}/grot.ppm ${MD}/report/t$i.gif"
-    exec sh -c "cat ${MD}/melodic_FTmix | awk '{ print NR \" \" \$$i }' > ${MD}/report/f${i}.txt"
-    exec sh -c "echo \"set term pbm color ; set size $xscale,0.25 ; set title 'FT of Timecourse (cycles)  frequency(Hz)=cycles/($npts*TR)  period(s)=($npts*TR)/cycles' ; plot '${MD}/report/f${i}.txt' title '' with lines\" | ${FSLDIR}/bin/gnuplot > ${MD}/grot.ppm"
-    exec sh -c "${FSLDIR}/bin/convert ${MD}/grot.ppm ${MD}/report/f$i.gif"
-    set creport [ open ${MD}/report/c${i}.html "w" ]
-    puts $creport "<HTML>
-    <TITLE>MELODIC Component $i</TITLE>
-    <BODY BACKGROUND=\"file:${FSLDIR}/doc/images/fsl-bg.jpg\">
-    <hr><CENTER><H1>MELODIC Component $i</H1>
-    "
-    if { $i > 1 } {
-	puts $creport "<a href=\"c[ expr $i - 1 ].html\">previous</a> - "
-    }
-    puts $creport "<a href=\"report.html\">index</a>"
-    if { $i < $dim } {
-	puts $creport " - <a href=\"c[ expr $i + 1 ].html\">next</a>"
-    }
-    puts $creport "
-    <hr><p>
-    <IMG BORDER=0 SRC=\"s$i.gif\"><p>
-    <a href=\"t$i.txt\"><IMG BORDER=0 SRC=\"t$i.gif\"></a><p>
-    <a href=\"f$i.txt\"><IMG BORDER=0 SRC=\"f$i.gif\"></a><p>
-    <hr></CENTER></BODY></HTML>
-    "
-    close $creport
-}
-exec sh -c "/bin/rm -f ${MD}/grot*"
-puts $report "<HR><FONT SIZE=1>This page produced automatically by MELODIC - a part of <A HREF=\"http://www.fmrib.ox.ac.uk/fsl\">FSL - FMRIB's Software Library</A>.</FONT>
-</BODY></HTML>
-"
-close $report
-puts "Finished melodicreport at [ exec date ]
-To view the MELODIC report point your web browser at
-$REPORTFILE
-"
-exit