From 772daf1ef3c336e4bff618c67746a82ea32ecbb6 Mon Sep 17 00:00:00 2001
From: WillForan <willforan@gmail.com>
Date: Thu, 25 Sep 2025 13:37:29 -0400
Subject: [PATCH 1/3] feat(regress): add -custom_regression_prefix

---
 preproc_functions/nuisance_regression   | 151 +++++++++++++++---------
 preproc_functions/parse_args            |  11 +-
 preprocessFunctional                    |   7 +-
 test/fmripp_parseargs.bats              |   9 ++
 test/fmripp_remove_autocorr_and_br.bats |  48 ++++++--
 5 files changed, 156 insertions(+), 70 deletions(-)

diff --git a/preproc_functions/nuisance_regression b/preproc_functions/nuisance_regression
index 2164bcd..85795aa 100644
--- a/preproc_functions/nuisance_regression
+++ b/preproc_functions/nuisance_regression
@@ -46,7 +46,7 @@ motionderiv() {
 COMPUTE_NUISANCE_REGRESSORS_GLOBALS=(nuisance_file nuisance_regressors no_warp \
    postWarp postDespike postSS \
    templateName mprageBet_base ext tr prefix bpLow bpHigh \
-   gsr_in_prefix)
+   gsr_in_prefix custom_regprefix)
 
 # give
 # - a nifti get basis functions to remove autocorrelation
@@ -529,6 +529,50 @@ function compute_nuisance_regressors {
     return 0
 }
 
+# look into regression options and build todo string
+# A b g (r || custom_prefix)
+function regression_todo {
+    local todo=""
+    [ $rmautocorr -eq 1 ] && todo="A"
+    [ $bandpass_filter -eq 1 ] && todo="${todo}b"
+    [ $gsr_in_prefix       -eq 1 ] && todo="${todo}g"
+    [ $nuisance_regression -eq 1 ] && todo="${todo}${custom_regprefix:-r}"
+    echo "$todo"
+}
+function reg_already_done {
+    local todo="${1:?regression operations by prefix}"
+    local reg_prefix=${custom_regprefix:-r}
+
+    [[ -f .nuisance_regression_complete && $todo=$reg_prefix ]] && return 0
+    [[ -f .bandpass_filter_complete && $todo=b ]] && return 0
+    [[ -f .bandpass_filter_complete && .remove_autocorr_complete && $todo=Ab ]] && return 0
+    [[ -f .nuisance_regression_complete && -f .bandpass_filter_complete && $todo=b$reg_prefix ]] && return 0
+    [[ -f .nuisance_regression_complete && -f .remove_autocorr_complete && $todo=A$reg_prefix ]] && return 0
+    [[ -f .nuisance_regression_complete && -f .bandpass_filter_complete && -f .remove_autocorr_complete && $todo=Ab$reg_prefix ]] && return 0
+
+    # not already done
+    return 1
+}
+function reg_todo_to_desc {
+    [[ $# -eq 0 || -z $1 ]] && echo "none" && return
+
+    local todo="${1:?$FUNC_NAME first arg is regression operations by prefix/todo. eg. Abgr }"
+    #bandpass + prewhitening only
+    if [ "$todo" = "Ab" ]; then
+       echo "bandpass+prewhite"
+    #bandpass only
+    elif [[ "$todo" = "b" ]]; then
+       echo "bandpass"
+    # regress only (withour or without 'A'utocorrelation rm'ed (w/reml)
+    elif [[ $todo =~ "A?${custom_regprefix:-r}" ]]; then
+       echo "regressonly"
+    elif [[ "$todo" =~ A?bg?${custom_regprefix:-r} ]]; then
+       echo "bandpass+regress"
+    else
+       echo "none"
+    fi
+}
+
 function nuisance_regression {
 
     #handle nuisance regression and/or bandpass filtering
@@ -547,77 +591,68 @@ function nuisance_regression {
 
     preNRBP="${prefix}${funcFile}${smoothing_suffix}${ext}"
 
-    local todo=
-    [ $rmautocorr -eq 1 ] && todo="${todo}A"
-    [ $bandpass_filter -eq 1 ] && todo="${todo}b"
-    [ $gsr_in_prefix       -eq 1 ] && todo="${todo}g"
-    [ $nuisance_regression -eq 1 ] && todo="${todo}r"
-
+    todo=$(regression_todo)
     # todo is 
     #  only: A b r 
     #  combined: Ab Abr br
     #  'A' alone is not allowed, will throw error -- checked by parseargs or preprocessFunctional
     #  gsr_in_prefix (-gsr) must have gs in $nuisance_regressors, check by parseargs
     
+    #check whether requisite steps are complete
+    reg_already_done "$todo" && return 0
+    
     prefix="${todo}${prefix}"
     postNRBP="${prefix}${funcFile}${smoothing_suffix}${ext}"
 
-    #check whether requisite steps are complete
-    [[ -f .nuisance_regression_complete && $todo=r ]] && return 0
-    [[ -f .bandpass_filter_complete && $todo=b ]] && return 0
-    [[ -f .bandpass_filter_complete && .remove_autocorr_complete && $todo=Ab ]] && return 0
-    [[ -f .nuisance_regression_complete && -f .bandpass_filter_complete && $todo=br ]] && return 0
-    [[ -f .nuisance_regression_complete && -f .remove_autocorr_complete && $todo=Ar ]] && return 0
-    [[ -f .nuisance_regression_complete && -f .bandpass_filter_complete && -f .remove_autocorr_complete && $todo=Abr ]] && return 0
-
     if [[ ! -f "${nuisance_file}" && ( $nuisance_regression == 1 || $nuisance_compute == 1 ) ]]; then
 	compute_nuisance_regressors
     fi
 
     #bandpass + prewhitening only
-    if [ "$todo" = "Ab" ]; then
-	run_3dremlfit $preNRBP $postNRBP ${subjMask}${ext} #function should pick up this circumstance
-	rel "date > .bandpass_filter_complete"
-    #bandpass only
-    elif [[ "$todo" = "b" ]]; then
-	rel "3dBandpass -input \"$preNRBP\" -mask \"${subjMask}${ext}\" -dt $tr \
-		-prefix \"$postNRBP\" $bpLow $bpHigh"
-
-	rel "date > .bandpass_filter_complete"	
-    # regress only
-    elif [[ "$todo" = "r" || "$todo" = "Ar" ]]; then
-	#default to 3dREMLfit here
-	if [ $arma_nuisance_regression -eq 0 ]; then
-	    rel "3dDetrend -overwrite -verb -polort 2 -vector ${nuisance_file} \
-	    	-prefix \"$postNRBP\" \"$preNRBP\""
-	    #need to mask detrend by brain mask as with 3dBandpass (3dDetrend doesn't support -mask)
-	    rel "fslmaths \"$postNRBP\" -mas \"$subjMask\" \"$postNRBP\""
-	else
-	    #use 3dREMLfit for regression (default)
-	    run_3dremlfit $preNRBP $postNRBP ${subjMask}${ext}	    
-	fi
-	
-	rel "date > .nuisance_regression_complete"
-    # bandpass and regress
-    elif [[ "$todo" =~ A?bg?r ]]; then
-	if [ $arma_nuisance_regression -eq 0 ]; then
-	    rel "3dTproject -overwrite -input \"$preNRBP\" -mask \"${subjMask}${ext}\" -dt $tr \
-	    	-prefix \"$postNRBP\" -polort 2 -ort ${nuisance_file} -passband $bpLow $bpHigh"
-
-	    #Deprecated -- 3dTproject performs true simultaneous approach, not filter all -> bandpass
-            #rel "3dBandpass -overwrite -input \"$preNRBP\" -mask \"${subjMask}${ext}\" -dt $tr \
-	    #     	-prefix \"$postNRBP\" -ort ${nuisance_file} $bpLow $bpHigh"
-	else
-	    #use 3dREMLfit for bandpass + regression (default)
-	    run_3dremlfit $preNRBP $postNRBP ${subjMask}${ext}
-	fi
-
-	rel "date > .bandpass_filter_complete"
-	rel "date > .nuisance_regression_complete"
-    else
-	# we were only computing things
-       rel "(Regressors computed but no bandpass or nuisance regression applied)" c
-    fi
+    case $(reg_todo_to_desc "$todo") in
+       bandpass+prewhite)
+          run_3dremlfit $preNRBP $postNRBP ${subjMask}${ext} #function should pick up this circumstance
+          rel "date > .bandpass_filter_complete"
+          ;;
+       bandpass)
+          rel "3dBandpass -input \"$preNRBP\" -mask \"${subjMask}${ext}\" -dt $tr \
+                 -prefix \"$postNRBP\" $bpLow $bpHigh"
+          rel "date > .bandpass_filter_complete"	
+          ;;
+       regressonly)
+          if [ $arma_nuisance_regression -eq 0 ]; then
+              rel "3dDetrend -overwrite -verb -polort 2 -vector ${nuisance_file} \
+                 -prefix \"$postNRBP\" \"$preNRBP\""
+              #need to mask detrend by brain mask as with 3dBandpass (3dDetrend doesn't support -mask)
+              rel "fslmaths \"$postNRBP\" -mas \"$subjMask\" \"$postNRBP\""
+          else
+              #use 3dREMLfit for regression (default)
+              run_3dremlfit $preNRBP $postNRBP ${subjMask}${ext}	    
+          fi
+          rel "date > .nuisance_regression_complete"
+          ;;
+       bandpass+regress) 
+	   if [ $arma_nuisance_regression -eq 0 ]; then
+	       rel "3dTproject -overwrite -input \"$preNRBP\" -mask \"${subjMask}${ext}\" -dt $tr \
+	       	-prefix \"$postNRBP\" -polort 2 -ort ${nuisance_file} -passband $bpLow $bpHigh"
+
+	       #Deprecated -- 3dTproject performs true simultaneous approach, not filter all -> bandpass
+               #rel "3dBandpass -overwrite -input \"$preNRBP\" -mask \"${subjMask}${ext}\" -dt $tr \
+	       #     	-prefix \"$postNRBP\" -ort ${nuisance_file} $bpLow $bpHigh"
+	   else
+	       #use 3dREMLfit for bandpass + regression (default)
+	       run_3dremlfit $preNRBP $postNRBP ${subjMask}${ext}
+	   fi
+	   rel "date > .bandpass_filter_complete"
+	   rel "date > .nuisance_regression_complete"
+          ;;
+       none) rel "(Regressors computed but no bandpass or nuisance regression applied)" c ;;
+       *)
+          rel "ERROR: don't know what to do with $todo = '$(reg_todo_to_desc "$todo")'" c
+          return 1
+        ;;
+    esac
+       
     
     #explicit return code needed to avoid implicit status of prior command
     return 0
diff --git a/preproc_functions/parse_args b/preproc_functions/parse_args
index 863b252..ee5076c 100644
--- a/preproc_functions/parse_args
+++ b/preproc_functions/parse_args
@@ -14,6 +14,7 @@ function parse_args {
     cleanup_only=0
     compute_warp=0 #used for -compute_warp_only. Specifies to compute warp to template without applying it to preprocessed data.
     constrainToTemplate="y"
+    custom_regprefix="" # added 20250925 - used instead of 'r' for regression prefix
     deoblique_all=0
     despike=0
     despikeThresh="2.5 4.0"
@@ -251,6 +252,9 @@ function parse_args {
 	    sliceTimesFile="$2"
 	    sliceMotion4D=1 #for now, this option is only relevant for sliceMotion4d correction
 	    shift 2
+	elif [ $1 = -custom_regression_prefix ]; then
+	    custom_regprefix="$2"
+	    shift 2
 	elif [ $1 = -constrain_to_template ]; then
 	    if [[ $2 = [NnYy] ]]; then
 		constrainToTemplate="${2}"
@@ -650,6 +654,11 @@ function parse_args {
        exit 1
     fi
 
+    if [[ "$nuisance_regression" -eq 0 && -n $custom_regprefix ]]; then
+       echo "Cannot request -custom_regression_prefix without also specifying -nuisance_regression"
+       exit 1
+    fi
+
     # Not legal to use -rm_completefiles without warping
     if [[ -n "$rmgroup_component_1d" && $no_warp -ge 1 ]]; then
        echo "Cannot request -rmgroup_component and not preform a warp!"
@@ -693,7 +702,7 @@ function parse_args {
     #if we have v6.0+, then incorporate fieldmap unwarping into BBR func2struct
     #and use resulting unwarping information for EPI -> unwarp -> struct -> MNI transform.
     #for older versions, need to use EPI-registered fieldmap for unwarping
-    flirtVersion=$( flirt | head -1 | perl -pe 's/^FLIRT version ([0-9\\.]+)$/\1/' )
+    command -v flirt && flirtVersion=$( flirt | head -1 | perl -pe 's/^FLIRT version ([0-9\\.]+)$/\1/' ) || flirtVersion=0
     bbrCapable=$( echo "${flirtVersion} >= 6" | bc )
 
     #The smoothing kernel parameter is expected to be the full width at half
diff --git a/preprocessFunctional b/preprocessFunctional
index aeb5a07..90e234d 100755
--- a/preprocessFunctional
+++ b/preprocessFunctional
@@ -50,6 +50,9 @@ Command line options:
   -custom_slice_times: For use with 4d slice timing + motion correction. 
         A csv file containing the times (in seconds summing to TR) of each slice (bottom to top).
         Example: -custom_slice_times "../SPECCMBSliceTimes.csv"
+  -custom_regression_prefix
+        Use a specified letter or letters instead of 'r' for regression. Also see -gsr
+        Approprate for tracking eg '-custom_regression_prefix M -nuisance_regression motion6' seperatly from default
   -delete_dicom: if converting dicom to nifti, whether delete or archive DICOM files. If not
         passed, user will be prompted for action. Options are:
         -delete_dicom no. (leaves DICOM untouched)
@@ -204,7 +207,7 @@ The major steps in the processing pipeline are, in order:
   10)   ICA-AROMA (optional) - a
   11)   High-pass filtering - f
   12)   Intensity normalization - n
-  13)   Nuisance regression (optional) - r
+  13)   Nuisance regression (optional) - r (also see -custom_regression_prefix)
   13.5) Global signal regression (optional, label optional) - g
   14)   Bandpass filtering (optional) - b
   15)  Auto Correlation removal (optional) - A
@@ -235,6 +238,8 @@ EndOfHelp
 #
 #Changelog:
 #
+# 09/25/2025 (WF)
+#  - add '-custom_regression_prefix' (refactor preproc_functions/nuisance_regression)
 #04/30/2024 (WF)
 #  - added '-ignore_bids' option and handle slicetiming missing errors
 #08/26/2022 (WF)
diff --git a/test/fmripp_parseargs.bats b/test/fmripp_parseargs.bats
index 364a2f8..662fc4f 100755
--- a/test/fmripp_parseargs.bats
+++ b/test/fmripp_parseargs.bats
@@ -177,8 +177,17 @@ teardown() {
  parse_args -4d fake.nii.gz -gsr -nuisance_regression dwm,gs,wm
  [ $gsr_in_prefix -eq 1 ]
  [ $nuisance_regressors = "dwm,gs,wm" ]
+
 }
 
+@test "custom reg" {
+ run parse_args -4d fake.nii.gz -custom_regression_prefix R 
+ [ $status -eq 1 ]
+ [[ $output =~ Cannot.*without ]]
+
+ parse_args -4d fake.nii.gz -custom_regression_prefix Mr  -nuisance_regression 6motion
+ [[ $custom_regprefix = "Mr" ]]
+}
 
 @test "-rmgroup_component" {
  parse_args -4d fake.nii.gz -rmgroup_component test.1d -tr 1
diff --git a/test/fmripp_remove_autocorr_and_br.bats b/test/fmripp_remove_autocorr_and_br.bats
index 2115604..8bd5c45 100755
--- a/test/fmripp_remove_autocorr_and_br.bats
+++ b/test/fmripp_remove_autocorr_and_br.bats
@@ -4,7 +4,6 @@
 # test remove_autocorr_and_br #
 ###############################
 
-testdir=batsautocorr
 
 mknii() {
  name=$1; shift
@@ -13,13 +12,13 @@ mknii() {
 
 # go into a special temp dir
 setup() {
- cd $BATS_TEST_DIRNAME
- source ../preproc_functions/helper_functions
- source ../preproc_functions/parse_args
- source ../preproc_functions/nuisance_regression
+ THISTESTDIR=$(mktemp -d $BATS_TMPDIR/autocor-XXX)
+ cd ${THISTESTDIR}
+ MRI_STDDIR=$THISTESTDIR # to stop helper_functions from complaining about missing MNI
+ source $BATS_TEST_DIRNAME/../preproc_functions/helper_functions
+ source $BATS_TEST_DIRNAME/../preproc_functions/parse_args
+ source $BATS_TEST_DIRNAME/../preproc_functions/nuisance_regression # regression_todo reg_todo_to_desc nuisance_regression
 
- mkdir $testdir
- cd $testdir
  # for where to save log file
  funcdir=$(pwd) 
 
@@ -34,14 +33,12 @@ setup() {
 
  # COMPUTE_NUISANCE_REGRESSORS_GLOBALS=(nuisance_file nuisance_regressors no_warp postWarp postDespike postSS templateName mprageBet_base ext tr prefix)
  # compute_nuisance_regressors 
- 
-
 }
 
 # remove tempdir and contents
 teardown() {
  cd ..
- rm -r $testdir
+ test -d "${THISTESTDIR}" && rm -r ${THISTESTDIR} || echo "WARNING: no tempdir $THISTESTDIR ?" >&2
  return 0
 }
 
@@ -150,3 +147,34 @@ teardown() {
   #cp -r . ../batsautocorr_sav
 
 }
+
+@test "regression todo: bp+reg" {
+ parse_args -4d fake.nii.gz -4d test.nii.gz -rmautocorr -bandpass_filter 0.009 .08 -log "" -nuisance_regression 6motion,csf,wm,dcsf,dwm
+ todo=$(regression_todo)
+ echo "$todo" >&2
+ [[ $todo = Abr ]]
+ [[ $(reg_todo_to_desc $todo) == bandpass+regress ]]
+}
+@test "regression todo: bp+reg (custom)" {
+ parse_args -4d fake.nii.gz -custom_regression_prefix R  -4d test.nii.gz -rmautocorr -bandpass_filter 0.009 .08 -log ""  -nuisance_regression 6motion
+ todo=$(regression_todo)
+ echo "$todo" >&2
+ [[ $todo = AbR ]]
+ [[ $(reg_todo_to_desc $todo) == bandpass+regress ]]
+}
+
+@test "regression todo: bp" {
+ parse_args -4d fake.nii.gz -4d test.nii.gz -bandpass_filter 0.009 .08 -log ""
+ todo=$(regression_todo)
+ echo "$todo" >&2
+ [[ $todo = b ]]
+ [[ $(reg_todo_to_desc $todo) == bandpass ]]
+}
+
+@test "regression todo: none" {
+ parse_args -4d fake.nii.gz -4d test.nii.gz -log ""
+ todo=$(regression_todo)
+ echo "$todo" >&2
+ [[ $todo = "" ]]
+ [[ $(reg_todo_to_desc $todo) == none ]]
+}

From ffe0d67e95f6023faf875eebdc7f0fcd578c8dc1 Mon Sep 17 00:00:00 2001
From: WillForan <willforan@gmail.com>
Date: Thu, 25 Sep 2025 14:06:19 -0400
Subject: [PATCH 2/3] feat(regression): must specify file if custom; custom
 complete flag file

---
 preproc_functions/nuisance_regression   | 21 +++++++++++----------
 preproc_functions/parse_args            |  4 ++++
 preprocessFunctional                    |  2 +-
 test/fmripp_parseargs.bats              |  8 ++++++--
 test/fmripp_remove_autocorr_and_br.bats | 17 ++++++++++++++++-
 5 files changed, 38 insertions(+), 14 deletions(-)

diff --git a/preproc_functions/nuisance_regression b/preproc_functions/nuisance_regression
index 85795aa..048700a 100644
--- a/preproc_functions/nuisance_regression
+++ b/preproc_functions/nuisance_regression
@@ -122,7 +122,7 @@ function run_3dremlfit(){
 
 function compute_nuisance_regressors {
     # 20170421WF: skipping might be a problem if we change what regressors we want
-    if [ -r .nuisance_compute_complete ]; then
+    if [ -r .nuisance_compute_complete${custom_regprefix:-} ]; then
        rel "already computed nuisance regression" c
        return 0
     fi
@@ -522,9 +522,9 @@ function compute_nuisance_regressors {
     fi    
     
     # TODO: do multiple passes to build nuisancecols so we can check that would should be redoing?
-    rel "echo '${nuisancecols[*]}' > .regressors_in_use"
+    rel "echo '${nuisancecols[*]}' > .regressors_in_use${custom_regprefix:-}"
 
-    rel "date > .nuisance_compute_complete"
+    rel "date > .nuisance_compute_complete${custom_regprefix:-}"
 
     return 0
 }
@@ -540,15 +540,16 @@ function regression_todo {
     echo "$todo"
 }
 function reg_already_done {
-    local todo="${1:?regression operations by prefix}"
+    local todo="${1:?$FUNC_NAME needs regression operations by prefix, eg Abr}"
     local reg_prefix=${custom_regprefix:-r}
+    local complete_file=.nuisance_regression${custom_regprefix:-}_complete # default .nuisance_regression_complete
 
-    [[ -f .nuisance_regression_complete && $todo=$reg_prefix ]] && return 0
+    [[ -f $complete_file && $todo=$reg_prefix ]] && return 0
     [[ -f .bandpass_filter_complete && $todo=b ]] && return 0
     [[ -f .bandpass_filter_complete && .remove_autocorr_complete && $todo=Ab ]] && return 0
-    [[ -f .nuisance_regression_complete && -f .bandpass_filter_complete && $todo=b$reg_prefix ]] && return 0
-    [[ -f .nuisance_regression_complete && -f .remove_autocorr_complete && $todo=A$reg_prefix ]] && return 0
-    [[ -f .nuisance_regression_complete && -f .bandpass_filter_complete && -f .remove_autocorr_complete && $todo=Ab$reg_prefix ]] && return 0
+    [[ -f $complete_file && -f .bandpass_filter_complete && $todo=b$reg_prefix ]] && return 0
+    [[ -f $complete_file && -f .remove_autocorr_complete && $todo=A$reg_prefix ]] && return 0
+    [[ -f $complete_file && -f .bandpass_filter_complete && -f .remove_autocorr_complete && $todo=Ab$reg_prefix ]] && return 0
 
     # not already done
     return 1
@@ -629,7 +630,7 @@ function nuisance_regression {
               #use 3dREMLfit for regression (default)
               run_3dremlfit $preNRBP $postNRBP ${subjMask}${ext}	    
           fi
-          rel "date > .nuisance_regression_complete"
+          rel "date > .nuisance_regression${custom_regprefix:-}_complete"
           ;;
        bandpass+regress) 
 	   if [ $arma_nuisance_regression -eq 0 ]; then
@@ -644,7 +645,7 @@ function nuisance_regression {
 	       run_3dremlfit $preNRBP $postNRBP ${subjMask}${ext}
 	   fi
 	   rel "date > .bandpass_filter_complete"
-	   rel "date > .nuisance_regression_complete"
+	   rel "date > .nuisance_regression${custom_regprefix:-}_complete"
           ;;
        none) rel "(Regressors computed but no bandpass or nuisance regression applied)" c ;;
        *)
diff --git a/preproc_functions/parse_args b/preproc_functions/parse_args
index ee5076c..805a74e 100644
--- a/preproc_functions/parse_args
+++ b/preproc_functions/parse_args
@@ -658,6 +658,10 @@ function parse_args {
        echo "Cannot request -custom_regression_prefix without also specifying -nuisance_regression"
        exit 1
     fi
+    if [[ -n $custom_regprefix && "$nuisance_file" == .nuisance_regressors ]]; then
+       echo "Cannot request -custom_regression_prefix without also changing default -nuisance_file"
+       exit 1
+    fi
 
     # Not legal to use -rm_completefiles without warping
     if [[ -n "$rmgroup_component_1d" && $no_warp -ge 1 ]]; then
diff --git a/preprocessFunctional b/preprocessFunctional
index 90e234d..d5abf56 100755
--- a/preprocessFunctional
+++ b/preprocessFunctional
@@ -52,7 +52,7 @@ Command line options:
         Example: -custom_slice_times "../SPECCMBSliceTimes.csv"
   -custom_regression_prefix
         Use a specified letter or letters instead of 'r' for regression. Also see -gsr
-        Approprate for tracking eg '-custom_regression_prefix M -nuisance_regression motion6' seperatly from default
+        Approprate for tracking eg '-custom_regression_prefix M -nuisance_regression motion6 -nuisance_file motion_reg.txt' seperatly from default
   -delete_dicom: if converting dicom to nifti, whether delete or archive DICOM files. If not
         passed, user will be prompted for action. Options are:
         -delete_dicom no. (leaves DICOM untouched)
diff --git a/test/fmripp_parseargs.bats b/test/fmripp_parseargs.bats
index 662fc4f..4aef55d 100755
--- a/test/fmripp_parseargs.bats
+++ b/test/fmripp_parseargs.bats
@@ -183,9 +183,13 @@ teardown() {
 @test "custom reg" {
  run parse_args -4d fake.nii.gz -custom_regression_prefix R 
  [ $status -eq 1 ]
- [[ $output =~ Cannot.*without ]]
+ [[ $output =~ Cannot.*without.*nuisance_reg ]]
 
- parse_args -4d fake.nii.gz -custom_regression_prefix Mr  -nuisance_regression 6motion
+ run parse_args -4d fake.nii.gz -custom_regression_prefix R  -nuisance_regression 6motion
+ [ $status -eq 1 ]
+ [[ $output =~ Cannot.*without.*nuisance_file ]]
+
+ parse_args -4d fake.nii.gz -custom_regression_prefix Mr  -nuisance_regression 6motion -nuisance_file reg_motion.txt
  [[ $custom_regprefix = "Mr" ]]
 }
 
diff --git a/test/fmripp_remove_autocorr_and_br.bats b/test/fmripp_remove_autocorr_and_br.bats
index 8bd5c45..7692225 100755
--- a/test/fmripp_remove_autocorr_and_br.bats
+++ b/test/fmripp_remove_autocorr_and_br.bats
@@ -156,7 +156,7 @@ teardown() {
  [[ $(reg_todo_to_desc $todo) == bandpass+regress ]]
 }
 @test "regression todo: bp+reg (custom)" {
- parse_args -4d fake.nii.gz -custom_regression_prefix R  -4d test.nii.gz -rmautocorr -bandpass_filter 0.009 .08 -log ""  -nuisance_regression 6motion
+ parse_args -4d fake.nii.gz -custom_regression_prefix R  -4d test.nii.gz -rmautocorr -bandpass_filter 0.009 .08 -log ""  -nuisance_regression 6motion -nuisance_file reg_motion.txt
  todo=$(regression_todo)
  echo "$todo" >&2
  [[ $todo = AbR ]]
@@ -178,3 +178,18 @@ teardown() {
  [[ $todo = "" ]]
  [[ $(reg_todo_to_desc $todo) == none ]]
 }
+
+@test "regression test complete" {
+ parse_args -4d fake.nii.gz  -4d test.nii.gz -bandpass_filter 0.009 .08 -log ""  -nuisance_regression 6motion -nuisance_file reg_motion.txt
+ touch .nuisance_regression_complete .bandpass_filter_complete
+ reg_already_done $(regression_todo)
+}
+
+@test "regression test complete (custom)" {
+ parse_args -4d fake.nii.gz -custom_regression_prefix R  -4d test.nii.gz -bandpass_filter 0.009 .08 -log ""  -nuisance_regression 6motion -nuisance_file reg_motion.txt
+ touch .nuisance_regression_complete .bandpass_filter_complete
+ # not done b/c missing 'R' version of complete
+ ! reg_already_done $todo
+ touch .nuisance_regressionR_complete
+ reg_already_done $todo
+}

From 06d7784111a87ee89f096f125bbc51f62faaf826 Mon Sep 17 00:00:00 2001
From: WillForan <willforan@gmail.com>
Date: Thu, 25 Sep 2025 18:05:43 -0400
Subject: [PATCH 3/3] test: skip missing pcorr and missing py2

---
 test/ROI_TempCorr.R.bats | 3 +++
 test/slicemotion4d.bats  | 1 +
 2 files changed, 4 insertions(+)

diff --git a/test/ROI_TempCorr.R.bats b/test/ROI_TempCorr.R.bats
index c9ae6d0..234f45e 100755
--- a/test/ROI_TempCorr.R.bats
+++ b/test/ROI_TempCorr.R.bats
@@ -129,10 +129,13 @@ teardown() {
 
 ## Semi
 @test "semi cor" {
+
+  Rscript -e "installed.packages()['ppcor','Version']" || skip "R missing ppcor"
   ROI_TempCorr.R -ts $shortrestfile -brainmask  $mask -rois $roi -njobs 1 -pcorr_method semi:pearson
   last_rowcol corr_rois_pearson_semipartial.txt "33 102"
 }
 @test "semi+partial+full cor" {
+  Rscript -e "installed.packages()['ppcor','Version']" || skip "R missing ppcor"
   ROI_TempCorr.R -ts $shortrestfile -brainmask  $mask -rois $roi -njobs 1 -pcorr_method semi:pearson,pearson -corr_method pearson
   last_rowcol corr_rois_pearson.txt "33 33"
   last_rowcol corr_rois_pearson_semipartial.txt "33 102"
diff --git a/test/slicemotion4d.bats b/test/slicemotion4d.bats
index af29bb6..e987332 100755
--- a/test/slicemotion4d.bats
+++ b/test/slicemotion4d.bats
@@ -41,6 +41,7 @@ teardown() {
 # only run if we dont have matlab and do have octave
 @test "py2 and py3 have same results" {
  [ ! -r ../../sliceMotion4d_py2 ] && skip
+ [[ "$(python --version 2>&1)" =~ Python\ 2 ]] || skip "python is not py2"
  ../../sliceMotion4d -i example.nii.gz --siemens --slice_times interleaved --prefix mt_ -t 1.5
  ../../sliceMotion4d_py2 -i example.nii.gz --siemens --slice_times interleaved --prefix mt2_ -t 1.5
  results=$(3dBrickStat -non-zero -mean -slow "3dcalc( -a mt_example.nii.gz -b mt2_example.nii.gz -expr a-b )")