From 63e7aedd26c446f1f62098013e7f818ec63ac6b6 Mon Sep 17 00:00:00 2001
From: WillForan <willforan@gmail.com>
Date: Fri, 19 Jul 2024 17:52:20 -0400
Subject: [PATCH] =?UTF-8?q?=F0=9F=90=9B=20FIX=20no=5Fvol=20uses=20mean=20v?=
 =?UTF-8?q?alue=20not=20voxel=20value=20to=20correct?=
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---
 t/tat2.bats | 22 +++++++++++++++-------
 tat2        | 16 +++++++++-------
 2 files changed, 24 insertions(+), 14 deletions(-)

diff --git a/t/tat2.bats b/t/tat2.bats
index 5c54e44..9ad2e7a 100644
--- a/t/tat2.bats
+++ b/t/tat2.bats
@@ -454,13 +454,6 @@ x_cmp_y(){
   [[ $output == "(x/m)*1" ]]
 }
 
-@test gen_calc_nonorm {
-  # TODO: THIS IS WRONG?
-  source tat2
-  parse_args -no_vol
-  run args_to_3dcalc_expr
-  [[ $output == "(x/m)*x*1" ]]
-}
 @test gen_calc_zscore {
   # TODO: this should error?
   source tat2
@@ -482,3 +475,18 @@ x_cmp_y(){
   run args_to_3dcalc_expr
   [[ $output == "-1*log(x/m)*1" ]]
 }
+
+@test gen_calc_no_vol_noscale {
+  source tat2
+  parse_args -no_vol -no_voxscale
+  run args_to_3dcalc_expr
+  [[ $output == "(x/m)*m*1" ]]
+}
+@test gen_calc_no_vol {
+  source tat2
+  parse_args -no_vol
+  numvox="NVOX"
+  run args_to_3dcalc_expr
+  [[ $output == "(x/m)*m*$SCALE/NVOX" ]]
+}
+
diff --git a/tat2 b/tat2
index a164f4c..4e469cb 100755
--- a/tat2
+++ b/tat2
@@ -30,7 +30,7 @@ declare -a GLOBFILES
 
 filedesc_whichvol=""
 
-TAT2_VER="20240719-calc_ln"
+TAT2_VER="20240719-calc_ln+BUGFIX-no_vol"
 # 20201116
 #  back to mean default
 # add
@@ -58,9 +58,9 @@ USAGE
 SYNOPSIS
   calculates time averaged T2* like:
      1) 3dROIstats > volnorm.1D
-        # tune with -{median,mean,zscor}_vol, and -mask, -mkmask, or -mask_rel
+        # tune with -{median,mean,no}_vol, and -mask, -mkmask, or -mask_rel
      2) 3dcalc -x input_1  -m volnorm_1.1D -expr "(x/m)*SCALE/numvox #rep. f.ea. input
-        # tune with -no_voxscale, -scale
+        # tune with -no_voxscale, -scale, -calc_zscore, -calc_ln
         # numvox derived from mask (but output not masked)
      3) 3dTstat allnormed_concated.nii.gz
         # tune with -{median,mean}_time
@@ -106,7 +106,7 @@ OPTIONS (in order of relevance)
   -median_vol or -mean_vol or -no_vol
         set value used to scale across volume (each TR, 3dROIstats)
         vol norm default: '$volnorm_opt'
-        (history: median [20210302],  mean [20201116], median [20201016]. no_vol added 20210921)
+        (history: median [20210302],  mean [20201116], median [20201016]. no_vol added 20210921 but *x instead of *m. fixed 20240719)
 
   -calc_zscore or -calc_log
     for 3dcalc per volume voxelwise normalization:
@@ -323,9 +323,11 @@ args_to_3dcalc_expr(){
    [ $vox_scale -eq 0 ] && calc_scale="1"
 
    # 20210921 - BL measure effect of volume normalization
-   [ $volnorm_opt == "none" ] && calc_scale="x*1"
-   # TODO BUG? should calc_scale = m*1 ?
-   # TODO BUG? should '$vox_scale -ne 0' => calc_scale "x*$SCALE/$numvox"
+   # 20240719 - BUGFIX
+   #     1. had 'x*1' but want to undo x/m. is now (x/m)*m
+   #     2. did not respect scaling
+   #        now can do: x/m*m * scale/nvox (but thats a bad idea?)
+   [ $volnorm_opt == "none" ] && calc_scale="m*$calc_scale" 
 
 
    # normalize each voxel by the volume average or median