Index: src/csh/estireg3d.csh
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/csh/estireg3d.csh,v
retrieving revision 1.5
retrieving revision 1.6
diff -r1.5 -r1.6
31c31
< echo '#$Id: estireg3d.csh,v 1.5 2003/07/18 21:27:59 welling Exp $'
---
> echo '#$Id: estireg3d.csh,v 1.6 2003/10/01 20:49:13 bakalj Exp $'
39c39
< set dimstr = `mri_printfield -input $1 -field images.dimensions`
---
> set dimstr = `mri_printfield -field images.dimensions $1`
52c52
<   mri_rpn_math -o data/junk -c missing \
---
>   mri_rpn_math -out data/junk -c missing \
64,66c64,66
<   mri_permute -input $1 -headerout ${1}_p -order $perm_order
<   mri_subsample -median -d t -e 1 ${1}_p ${1}_median
<   mri_subsample -iqr -d t -e 1 ${1}_p ${1}_iqr
---
>   mri_permute -order $perm_order $1 ${1}_p 
>   mri_subsample -median -d t -l 1 ${1}_p ${1}_median
>   mri_subsample -iqr -d t -l 1 ${1}_p ${1}_iqr
68,69c68,69
<   mri_remap -file ${1}_median -order vxyzt
<   mri_remap -file ${1}_iqr -order vxyzt
---
>   mri_remap -order vxyzt ${1}_median 
>   mri_remap -order vxyzt ${1}_iqr
Index: src/image_proc/colorize_help.help
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/image_proc/colorize_help.help,v
retrieving revision 1.2
retrieving revision 1.3
diff -r1.2 -r1.3
7c7
<     colorize -color_map color_table infile outfile
---
>     colorize -colormap color_table infile outfile
14c14
<   colorize -color_map color_table_AFNI infile outfile
---
>   colorize -colormap color_table_AFNI infile outfile
16,17c16,17
< *Arguments:color_map
<   color_map Color_Table
---
> *Arguments:colormap
>   colormap Color_Table
19c19
<   Ex. -color_map color_table_AFNI
---
>   Ex. -colormap color_table_AFNI
30,35c30,35
<   [v(0)=RED value, v(1)=GREEN value, v(3)=BLUE value, v(4)=ALPHA value,
<    and v(5) = bound]
<   and dimension c = number of different boundaries.  Colorize will
<   interpolate each RGB value between the bounds.  Values below the
<   first or above the last bound will be mapped to that bound.  Bounds
<   must appear in the file in increasing order! 
---
>   [v(0)=RED value, v(1)=GREEN value, v(3)=BLUE value, v(4)=ALPHA
>   value, and v(5) = bound] and dimension b (can be any letter allowed
>   by dimension lettering scheme) = number of different boundaries.
>   Colorize will interpolate each RGB value between the bounds.  Values
>   below the first or above the last bound will be mapped to that
>   bound.  Bounds must appear in the file in increasing order!
40,46c40,46
<   RED	 GREEN	  BLUE	BOUND
<   255	 255	  0	3
<   255	 255	  0	3.499
<   255	 0	  255	3.5
<   255	 0	  255	3.99
<   0	 255	  255	4.00
<   0	 255	  255	9.99
\ No newline at end of file
---
>   RED	 GREEN	  BLUE	ALPHA  BOUND
>   255	 255	  0	1      3
>   255	 255	  0	1      3.499
>   255	 0	  255	1      3.5
>   255	 0	  255	1      3.99
>   0	 255	  255	1      4.00
>   0	 255	  255	1      9.99
\ No newline at end of file
Index: src/reader/multi_reader.c
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/reader/multi_reader.c,v
retrieving revision 1.19
retrieving revision 1.20
diff -r1.19 -r1.20
50c50
< static char rcsid[] = "$Id: multi_reader.c,v 1.19 2003/07/01 21:35:22 welling Exp $";
---
> static char rcsid[] = "$Id: multi_reader.c,v 1.20 2003/10/02 01:12:12 welling Exp $";
317a318,321
>   }
>   else {
>     /* We don't have the information necessary to distinguish slices */
>     return 0;
Index: src/reader/pghmri_reader.c
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/reader/pghmri_reader.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -r1.7 -r1.8
53c53
< static char rcsid[] = "$Id: pghmri_reader.c,v 1.7 2003/06/26 22:12:42 welling Exp $";
---
> static char rcsid[] = "$Id: pghmri_reader.c,v 1.8 2003/10/02 01:12:12 welling Exp $";
289a290,293
>     if (!kvLookup(info,"rowflip"))
>       kvDefInt(info,"rowflip",0);
>     if (!kvLookup(info,"rowflip_pattern"))
>       kvDefString(info,"rowflip_pattern","none");
Index: src/reader/pghtoafni.c
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/reader/pghtoafni.c,v
retrieving revision 1.5
retrieving revision 1.6
diff -r1.5 -r1.6
55c55
< static char rcsid[] = "$Id: pghtoafni.c,v 1.5 2003/07/02 23:22:40 welling Exp $";
---
> static char rcsid[] = "$Id: pghtoafni.c,v 1.6 2003/10/02 01:12:12 welling Exp $";
513,514c513,517
< 	&& (kvGetDouble(info,"voxel_z")==1.0))
<       return 2; /* "+tlrc" */
---
> 	&& (kvGetDouble(info,"voxel_z")==1.0)) {
>       if (kvLookup(info,"afni.WARP_DATA.0"))
> 	return 2; /* "+tlrc" */
>       else return 0; /* "+orig" */
>     }
Index: src/scripthelp/scripthelp_help.help
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/scripthelp/scripthelp_help.help,v
retrieving revision 1.15
retrieving revision 1.16
diff -r1.15 -r1.16
15a16,32
> *dataset_matches_env.py:Usage
> 
>   This script checks to make sure that the Fiasco environment
>   variables match the internal values of a datafile.  Generally
>   the environment variables come from the .default.csh and .local.csh
>   files, while the dataset's values come from the input file(s) 
>   originally read by smartreader.
> 
>   dataset_matches_env.py [-v] [-d] [-c chunk] MriFile
> 
>    -v requests verbose output
>    -d requests debugging output
>    -c chunk checks the values in the given chunk (default "images")
>    MriFile is the Pgh MRI file to check.
> 
>   If a mismatch is found, the script exits with a non-zero exit code.
> 
Index: Makefile.common
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/Makefile.common,v
retrieving revision 1.41
retrieving revision 1.42
diff -r1.41 -r1.42
43,44c43,44
< 	Makefile.SGIMP64 Makefile.LINUX Makefile.SGI6 config.mk configure \
< 	splus/Makefile.splus
---
> 	Makefile.SGIMP64 Makefile.LINUX Makefile.SGI6 Makefile.DARWIN \
> 	config.mk configure splus/Makefile.splus
Index: Makefile.DARWIN
============================================
--- /dev/null	2002-08-30 19:31:37.000000000 -0400
+++ Makefile.DARWIN	2003-09-25 13:38:41.000000000 -0400
@@ -0,0 +1,18 @@
+#
+# LINUX-specific Makefile for FMRI software
+#
+#
+
+CC     = cc
+ARCH_CFLAGS = -D_BSD_SOURCE -D_XOPEN_SOURCE=500 \
+	-DFORTRAN_ADD_UNDERSCORE -DUSE_PNG -I$(FMRI)/include/$(ARCH) \
+	-Wimplicit -g -O3
+LD     = cc
+ARCH_LFLAGS = 
+ARCH_LIBS   = -lpng 
+AR     = ar
+ARCH_ARFLAGS= -r
+RANLIB = ranlib 
+NEWER = $(FMRI)/src/csh/test_newer.csh
+
+include Makefile.common
Index: src/csh/epi.reader.csh
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/csh/epi.reader.csh,v
retrieving revision 1.19
retrieving revision 1.20
diff -r1.19 -r1.20
30c30
< echo '$Id: epi.reader.csh,v 1.19 2003/09/24 22:55:47 welling Exp $'
---
> echo '$Id: epi.reader.csh,v 1.20 2003/10/02 01:14:48 welling Exp $'
79a80,86
> endif
> 
> # If there is no v dimension, add a trivial one.
> if ( $dimstr !~ v* ) then
>   set dimstr_new = v${dimstr}
>   set dimstr = $dimstr_new
>   mri_remap -order $dimstr ${rdr_read_fname}
Index: src/csh/spline_detrend.csh
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/csh/spline_detrend.csh,v
retrieving revision 1.12
retrieving revision 1.13
diff -r1.12 -r1.13
31c31
< echo '#$Id: spline_detrend.csh,v 1.12 2003/01/31 21:21:01 welling Exp $'
---
> echo '#$Id: spline_detrend.csh,v 1.13 2003/10/04 22:00:57 bakalj Exp $'
34,35c34,35
< if (`mri_printfield -i $1 -f ${F_DETREND_CHUNK}.dimensions` == "xyzt") then
< 	mri_remap -file $1 -chunk ${F_DETREND_CHUNK} -order vxyzt
---
> if (`mri_printfield -field ${F_DETREND_CHUNK}.dimensions $1` == "xyzt") then
> 	mri_remap -chunk ${F_DETREND_CHUNK} -order vxyzt $1
37,38c37
< mri_permute -memlimit 32000000 -input $1.mri -headerout ${1}_p.mri \
<           -dataout .dat -chunk ${F_DETREND_CHUNK} -order vtxyz
---
> mri_permute -memlimit 32000000 -chunk ${F_DETREND_CHUNK} -order vtxyz $1 ${1}_p
76,81c75,80
< set images_ext_x = `mri_printfield -input ${1}_s -field images.extent.x`
< set images_ext_y = `mri_printfield -input ${1}_s -field images.extent.y`
< set images_ext_z = `mri_printfield -input ${1}_s -field images.extent.z`
< set images_ext_v = `mri_printfield -input ${1}_s -field images.extent.v`
< set images_ext_t = `mri_printfield -input ${1}_s -field images.extent.t`
< set images_dims  = `mri_printfield -input ${1}_s -field images.dimensions`
---
> set images_ext_x = `mri_printfield -field images.extent.x ${1}_s`
> set images_ext_y = `mri_printfield -field images.extent.y ${1}_s`
> set images_ext_z = `mri_printfield -field images.extent.z ${1}_s`
> set images_ext_v = `mri_printfield -field images.extent.v ${1}_s`
> set images_ext_t = `mri_printfield -field images.extent.t ${1}_s`
> set images_dims  = `mri_printfield -field images.dimensions ${1}_s`
102c101
< mri_copy_chunk -chunk missing -input $1 -output ${3}_d
---
> mri_copy_chunk -chunk missing $1 ${3}_d
111,113c110,112
< mri_subsample -d t -e 1 -mean $1 ${3}_m
< mri_remap -file ${3}_m -order vxyzt
< mri_interp -c -d t -e $images_ext_t ${3}_m ${3}_l
---
> mri_subsample -d t -l 1 -mean $1 ${3}_m
> mri_remap -order vxyzt ${3}_m
> mri_interp -con -d t -len $images_ext_t ${3}_m ${3}_l
115c114
< mri_permute -memlimit 32000000 -input ${3}_l -headerout ${3}_M -order vtxyz
---
> mri_permute -memlimit 32000000 -order vtxyz ${3}_l ${3}_M 
117c116
< mri_rpn_math -o $3 '$1,$2,+' ${3}_f ${3}_M
---
> mri_rpn_math -out $3 '$1,$2,+' ${3}_f ${3}_M
123,124c122
< mri_permute -memlimit 32000000 -input $3.mri -headerout $2.mri \
<           -dataout .dat -chunk ${F_DETREND_CHUNK} -order vxyzt
---
> mri_permute -memlimit 32000000 -chunk ${F_DETREND_CHUNK} -order vxyzt $3 $2
Index: src/csh/spiral.defaults.csh
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/csh/spiral.defaults.csh,v
retrieving revision 1.35
retrieving revision 1.36
diff -r1.35 -r1.36
30c30
< echo '$Id: spiral.defaults.csh,v 1.35 2003/08/07 21:13:19 welling Exp $'
---
> echo '$Id: spiral.defaults.csh,v 1.36 2003/10/04 21:44:43 bakalj Exp $'
64a65
> #
78d78
< #
103d102
< #
111a111
> #
137a138,149
> # phase_b0_homo_correct.csh
> #
> # phase_b0 header file
> setenv F_PHB0HOMO_OUTPUT phase_b0
> # unsmoothed estimates
> setenv F_PHB0HOMO_RWPARMS phase_b0_raw.par
> # smoothed estimates
> setenv F_PHB0HOMO_PARMS phase_b0.par
> # smoother bandwidth
> setenv F_PHB0HOMO_BAND 3.0
> #
> #
408c420
< #
\ No newline at end of file
---
> #
Index: src/csh/phase_lock.csh
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/csh/phase_lock.csh,v
retrieving revision 1.7
retrieving revision 1.8
diff -r1.7 -r1.8
31c31
< echo '#$Id: phase_lock.csh,v 1.7 2003/02/07 22:21:59 welling Exp $'
---
> echo '#$Id: phase_lock.csh,v 1.8 2003/10/04 22:02:40 bakalj Exp $'
39,43c39,43
< set vdim = `mri_printfield -input $1 -field images.extent.v`
< set xdim = `mri_printfield -input $1 -field images.extent.x`
< set ydim = `mri_printfield -input $1 -field images.extent.y`
< set zdim = `mri_printfield -input $1 -field images.extent.z`
< set tdim = `mri_printfield -input $1 -field images.extent.t`
---
> set vdim = `mri_printfield -field images.extent.v $1`
> set xdim = `mri_printfield -field images.extent.x $1`
> set ydim = `mri_printfield -field images.extent.y $1`
> set zdim = `mri_printfield -field images.extent.z $1`
> set tdim = `mri_printfield -field images.extent.t $1`
59,63c59,62
< mri_permute -input $1 -headerout $tmpdir/in_p -order vztxy
< mri_remap -file $tmpdir/in_p -order vztp \
<     -extents 2:${zdim}:${tdim}:${pdim}
< mri_complex_to_scalar -m $tmpdir/in_p $tmpdir/raw_mags
< mri_complex_to_scalar -u $tmpdir/in_p $tmpdir/raw_phases
---
> mri_permute -order vztxy $1 $tmpdir/in_p 
> mri_remap -order vztp -length 2:${zdim}:${tdim}:${pdim} $tmpdir/in_p 
> mri_complex_to_scalar -mag $tmpdir/in_p $tmpdir/raw_mags
> mri_complex_to_scalar -phu $tmpdir/in_p $tmpdir/raw_phases
69c68
<   mri_rpn_math -o $tmpdir/product '$1,$2,*' \
---
>   mri_rpn_math -out $tmpdir/product '$1,$2,*' \
71,77c70,74
<   mri_permute -input $tmpdir/product -headerout $tmpdir/product_p \
<       -order vpzt
<   mri_permute -input $tmpdir/raw_mags -headerout $tmpdir/raw_mags_p \
<       -order vpzt
<   mri_subsample -d p -e 1 -sum  $tmpdir/product_p $tmpdir/prod_sum 
<   mri_subsample -d p -e 1 -sum  $tmpdir/raw_mags_p $tmpdir/mag_sum 
<   mri_rpn_math -o $tmpdir/rephase_raw '$1,$2,/' \
---
>   mri_permute -order vpzt $tmpdir/product $tmpdir/product_p 
>   mri_permute -order vpzt $tmpdir/raw_mags $tmpdir/raw_mags_p 
>   mri_subsample -d p -l 1 -sum  $tmpdir/product_p $tmpdir/prod_sum 
>   mri_subsample -d p -l 1 -sum  $tmpdir/raw_mags_p $tmpdir/mag_sum 
>   mri_rpn_math -out $tmpdir/rephase_raw '$1,$2,/' \
79c76
<   mri_remap -file $tmpdir/rephase_raw -order vztp
---
>   mri_remap -order vztp $tmpdir/rephase_raw 
94c91
< mri_rpn_math -o $tmpdir/result_p_r '$1,$2,$3,-,cos,*' \
---
> mri_rpn_math -out $tmpdir/result_p_r '$1,$2,$3,-,cos,*' \
96c93
< mri_rpn_math -o $tmpdir/result_p_i '$1,$2,$3,-,sin,*' \
---
> mri_rpn_math -out $tmpdir/result_p_i '$1,$2,$3,-,sin,*' \
100,101c97,98
< mri_remap -file $tmpdir/result_p_r -order ztpv
< mri_remap -file $tmpdir/result_p_i -order ztpv
---
> mri_remap -order ztpv $tmpdir/result_p_r 
> mri_remap -order ztpv $tmpdir/result_p_i
106c103
< mri_permute -input $tmpdir/result_p_p -headerout $tmpdir/result_p -order vztp
---
> mri_permute -order vztp $tmpdir/result_p_p $tmpdir/result_p 
108,110c105,106
< mri_permute -input $tmpdir/result_p -headerout $2 -order vpzt
< mri_remap -file $2 -order vxyzt \
<     -extents 2:${xdim}:${ydim}:${zdim}:${tdim}
---
> mri_permute -order vpzt $tmpdir/result_p $2
> mri_remap -order vxyzt -length 2:${xdim}:${ydim}:${zdim}:${tdim} $2
117c113
< mri_rpn_math -o $tmpdir/junk '0,$t,$z,$1,1,if_print_3' \
---
> mri_rpn_math -out $tmpdir/junk '0,$t,$z,$1,1,if_print_3' \
122c118
< mri_rpn_math -o $tmpdir/junk '0,$t,$z,$1,1,if_print_3' \
---
> mri_rpn_math -out $tmpdir/junk '0,$t,$z,$1,1,if_print_3' \
Index: src/csh/mri_to_ps.csh
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/csh/mri_to_ps.csh,v
retrieving revision 1.12
retrieving revision 1.13
diff -r1.12 -r1.13
30c30
< echo '#$Id: mri_to_ps.csh,v 1.12 2003/05/09 18:08:52 welling Exp $'
---
> echo '#$Id: mri_to_ps.csh,v 1.13 2003/10/04 22:03:05 bakalj Exp $'
72,74c72,74
< set zdim = `mri_printfield -input $1 -field images.extent.z -nofail`
< set tdim = `mri_printfield -input $1 -field images.extent.t -nofail`
< set type = `mri_printfield -input $1 -field images.datatype -nofail`
---
> set zdim = `mri_printfield -field images.extent.z -nofail $1`
> set tdim = `mri_printfield -field images.extent.t -nofail $1`
> set type = `mri_printfield -field images.datatype -nofail $1`
Index: src/csh/merge_stats.csh
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/csh/merge_stats.csh,v
retrieving revision 1.7
retrieving revision 1.8
diff -r1.7 -r1.8
69c69
< 	    -input $statfile -headerout ${dirname}/stat_aligned/${statfile:t} 
---
> 	    -input $statfile -headerout ${dirname}/stat_aligned/${statfile:t} \
Index: src/csh/epi.reconcile.csh
===================================================================
RCS file: /home/TINGENEK/welling/cvsroot/Fiasco/src/csh/epi.reconcile.csh,v
retrieving revision 1.3
retrieving revision 1.4
diff -r1.3 -r1.4
31c31,32
< echo '# $Id: epi.reconcile.csh,v 1.3 2002/01/08 00:50:16 welling Exp $'
---
> echo '# $Id: epi.reconcile.csh,v 1.4 2003/10/04 23:02:51 bakalj Exp $'
> echo '# This script has been replaced by dataset_matches_env.py'
33,71c34
< #Get dimensions
< set vextent = \
< `mri_printfield -input data/$F_READER_OUTPUT -field images.extent.v -nofail`
< set textent = \
< `mri_printfield -input data/$F_READER_OUTPUT -field images.extent.t -nofail`
< set zextent = \
< `mri_printfield -input data/$F_READER_OUTPUT -field images.extent.z -nofail`
< set xextent = \
< `mri_printfield -input data/$F_READER_OUTPUT -field images.extent.x -nofail`
< set yextent = \
< `mri_printfield -input data/$F_READER_OUTPUT -field images.extent.y -nofail`
< 
< # Set slice and image numbers
< setenv F_NSLICE $zextent
< setenv F_NIMAGE $textent
< 
< # Are clip dims compatible with image dims?
< @ xctr = $xextent / 2
< @ yctr = $yextent / 2
< if ($F_CLIP1_XCENTER != $xctr) then
<   echo "%%%%% Error! First clip not centered in X %%%%%"
<   exit -1
< endif
< if ($F_CLIP1_YCENTER != $yctr) then
<   echo "%%%%% Error! First clip not centered in Y %%%%%"
<   exit -1
< endif
< if ($F_CLIP1_WIDTH > $xextent) then
<   echo "%%%%% Error! First clip region too wide %%%%%"
<   exit -1
< endif
< if ($F_CLIP1_HEIGHT > $yextent) then
<   echo "%%%%% Error! First clip region too high %%%%%"
<   exit -1
< endif
< 
< # Set some titling information
< setenv F_PS_TITLE1 "$F_DESCRIPTION"
< setenv F_PS_TITLE2 "$F_NSLICE Slices"
---
> exit -1