Custom regprefix

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
@@ -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
@@ -522,13 +522,58 @@ 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
 }
 
+# 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="${1:?$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 $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 $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
+}
+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 +592,68 @@ 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${custom_regprefix:-}_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${custom_regprefix:-}_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

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 +654,15 @@ 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
+    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" && $no_warp -ge 1 ]]; then
        echo "Cannot request -rmgroup_component and not preform a warp!"
@@ -693,7 +706,7 @@ function parse_args {
     #if we have v6.0+, then incorporate fieldmap unwarping into BBR func2struct
     #and use resulting unwarping information for EPI -> unwarp -> struct -> MNI transform.
     #for older versions, need to use EPI-registered fieldmap for unwarping
-    flirtVersion=$( 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

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 -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)
@@ -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)

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"

test/fmripp_parseargs.bats

@@ -177,8 +177,21 @@ 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.*nuisance_reg ]]
+
+ 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" ]]
+}
 
 @test "-rmgroup_component" {
  parse_args -4d fake.nii.gz -rmgroup_component test.1d -tr 1