Enable Single Regression in RSNRegression

global/scripts/RSNregression.m

@@ -1,5 +1,5 @@
-function RSNregression(InputFile, InputVNFile, GroupMaps, Method, ParamsFile, VAWeightsName, OutputBeta, varargin)
-    optional = myargparse(varargin, {'VolInputFile' 'VolInputVNFile' 'VolCiftiTemplate' 'OldBias' 'OldVolBias' 'GoodBCFile' 'VolGoodBCFile' 'SpectraParams' 'OutputZ' 'OutputVolBeta' 'OutputVolZ' 'SurfString' 'ScaleFactor' 'WRSmoothingSigma'});
+function RSNregression(InputFile, InputVNFile, Method, ParamsFile, OutputBeta, varargin)
+    optional = myargparse(varargin, {'GroupMaps' 'VAWeightsName' 'VolInputFile' 'VolInputVNFile' 'VolCiftiTemplate' 'OldBias' 'OldVolBias' 'GoodBCFile' 'VolGoodBCFile' 'SpectraParams' 'OutputZ' 'OutputVolBeta' 'OutputVolZ' 'SurfString' 'ScaleFactor' 'WRSmoothingSigma'});
 
     %InputFile - text file containing filenames of timeseries to concatenate
     %InputVNFile - text file containing filenames of the variance maps of each input
@@ -135,9 +135,11 @@ function RSNregression(InputFile, InputVNFile, GroupMaps, Method, ParamsFile, VA
         clear vnvolsum;
     end
 
-    GroupMapcii = ciftiopen(GroupMaps, wbcommand);
-    weightscii = ciftiopen(VAWeightsName, wbcommand); %normalized vertex areas, voxels are all 1s
-    AreaWeights = weightscii.cdata;
+    if strcmp(Method,'weighted') || strcmp(Method,'dual')
+        GroupMapcii = ciftiopen(optional.GroupMaps, wbcommand);
+        weightscii = ciftiopen(optional.VAWeightsName, wbcommand); %normalized vertex areas, voxels are all 1s
+        AreaWeights = weightscii.cdata;
+    end
     switch Method
         case 'weighted'
             if strcmp(optional.WRSmoothingSigma, '')
@@ -174,15 +176,21 @@ function RSNregression(InputFile, InputVNFile, GroupMaps, Method, ParamsFile, VA
             [betaICA, NODEts] = weightedDualRegression(normalise(betaICAone), inputConcat, AreaWeights);
         case 'dual'
             [betaICA, NODEts] = weightedDualRegression(GroupMapcii.cdata, inputConcat, AreaWeights);
+        case 'single'
+            SpectraArray = textscan(optional.SpectraParams, '%s', 'Delimiter', {'@'});
+            InputSpectraTS = SpectraArray{1}{1};
+            NODEts=ciftiopen(InputSpectraTS, wbcommand);
+            NODEts=NODEts.cdata';
+            betaICA = ((pinv(normalise(NODEts)) * demean(inputConcat')))';
         otherwise
-            error(['unrecognized method: "' Method '", use "weighted" or "dual"']);
+            error(['unrecognized method: "' Method '", use "weighted," "dual," or "single"']);
     end
 
     NODEtsnorm = normalise(NODEts);
 
     %outputs
     %Save Timeseries and Spectra if Desired
-    if ~strcmp(optional.SpectraParams, '')
+    if ~strcmp(optional.SpectraParams, '') && ~strcmp(Method,'single')
         SpectraArray = textscan(optional.SpectraParams, '%s', 'Delimiter', {'@'});
         nTPsForSpectra = min(str2double(SpectraArray{1}{1}), size(NODEts, 1));
         OutputSpectraTS = SpectraArray{1}{2};

global/scripts/RSNregression.sh

@@ -32,12 +32,13 @@ PARAMETERs are [ ] = optional; < > = user supplied value
 #arguments to opts_Add*: switch, variable to set, name for inside of <> in help text, description, [default value other than empty string if AddOptional], [compatibility flag, ...]
 opts_AddMandatory '--study-folder' 'StudyFolder' 'path' "folder containing all subjects"
 opts_AddMandatory '--subject' 'Subject' 'subject ID' ""
-opts_AddMandatory '--group-maps' 'GroupMaps' 'file' "the group template maps to regress"
+opts_AddOptional  '--group-maps' 'GroupMaps' 'file' "the group template spatial maps for weighted or dual regression"
+opts_AddOptional  '--timeseries' 'Timeseries' 'file' "the timeseries for single regression"
 opts_AddMandatory '--subject-timeseries' 'InputList' 'fmri@fmri@fmri...' "the timeseries fmri names to concatenate"
 opts_AddOptional '--surf-reg-name' 'RegName' 'name' "the registration string corresponding to the input files"
 opts_AddMandatory '--low-res' 'LowResMesh' 'meshnum' "mesh resolution, like '32' for 32k_fs_LR"
 opts_AddMandatory '--proc-string' 'ProcString' 'string' "part of filename describing processing, like '_hp2000_clean'"
-opts_AddMandatory '--method' 'Method' 'regression method' "'weighted' or 'dual' - weighted regression finds locations in the subject that don't match the template well and downweights them; dual is simpler, both methods use vertex area information"
+opts_AddMandatory '--method' 'Method' 'regression method' "'weighted', 'dual', or 'single' - weighted regression finds locations in the subject that don't match the template well and downweights them; dual is simpler, both methods use vertex area information.  single temporal regression requires a prior run of weighted or dual regression and is intended for adding an additional output space"
 opts_AddOptional '--weighted-smoothing-sigma' 'WRSmoothingSigma' 'number' "default 14 for human data - when using --method=weighted, the smoothing sigma, in mm, to apply to the 'alignment quality' weighting map" '14'
 opts_AddOptional '--low-ica-dims' 'LowICADims' 'num@num@num...' "when using --method=weighted, the low ICA dimensionality files to use for determining weighting"
 opts_AddOptional '--low-ica-template-name' 'ICATemplateName' 'filename' "filename template where 'REPLACEDIM' will be replaced by each of the --low-ica-dims values in turn to form the low-dim inputs"
@@ -55,6 +56,7 @@ opts_AddOptional '--matlab-run-mode' 'MatlabMode' '0, 1, or 2' "defaults to $g_m
 0 = compiled MATLAB (not implemented)
 1 = interpreted MATLAB
 2 = Octave" "$g_matlab_default_mode"
+
 opts_ParseArguments "$@"
 
 if ((pipedirguessed))
@@ -160,6 +162,13 @@ case "$Method" in
     (dual)
         MethodStr="DR"
         ;;
+    (single)
+        if [ -e ${Timeseries} ] ; then
+            MethodStr="SR"
+        else 
+            log_Err_Abort "single method requires a prior run of weighted or dual"
+        fi
+        ;;
     (*)
         log_Err_Abort "unknown method string: '$Method'"
         ;;
@@ -183,10 +192,13 @@ then
     fi
 fi
 SpectraParams=""
-if ((nTPsForSpectra > 0))
+if [[ nTPsForSpectra -gt 0 ]] && [[ ! ${Method} == "single" ]]
 then
     #these files are temporary anyway
     SpectraParams="$nTPsForSpectra@$DownSampleMNIFolder/${Subject}.${OutString}_${MethodStr}${RegString}_ts.${LowResMesh}k_fs_LR.txt@$DownSampleMNIFolder/${Subject}.${OutString}_${MethodStr}${RegString}_spectra.${LowResMesh}k_fs_LR.txt"
+elif [[ ${Method} == "single" ]]
+then
+    SpectraParams="${Timeseries}"
 fi
 #the msmall script should do this for itself instead
 #OutputNorm=""
@@ -198,18 +210,27 @@ fi
 
 #fix the _va_norm file being surface-only
 #extract the all-voxels ROI file and use it in -from-template
-tempfile="$(mktemp --tmpdir XXXXXX.roi.nii.gz)"
-tempfiles_add "$tempfile" "$tempfile.junk.nii.gz" "$tempfile.91k.dscalar.nii"
-wb_command -cifti-separate "$GroupMaps" COLUMN -volume-all "$tempfile.junk.nii.gz" -roi "$tempfile" -crop
-wb_command -cifti-create-dense-from-template "$GroupMaps" "$tempfile.91k.dscalar.nii" -cifti "$VANormOnlySurf" -volume-all "$tempfile" -from-cropped
+if [[ ! ${Method} == "single" ]]
+then
+    tempfile="$(mktemp --tmpdir XXXXXX.roi.nii.gz)"
+    tempfiles_add "$tempfile" "$tempfile.junk.nii.gz" "$tempfile.91k.dscalar.nii"
+    wb_command -cifti-separate "$GroupMaps" COLUMN -volume-all "$tempfile.junk.nii.gz" -roi "$tempfile" -crop
+    wb_command -cifti-create-dense-from-template "$GroupMaps" "$tempfile.91k.dscalar.nii" -cifti "$VANormOnlySurf" -volume-all "$tempfile" -from-cropped
+fi
 
 case "$MatlabMode" in
     (0)
         log_Err_Abort "FIXME: compiled matlab support not yet implemented"
         ;;
     (1 | 2)
         #SurfString and WRSmoothingSigma are optional to the matlab function (needed only for weighted), but we will always have it, so always providing it is simpler here
-        matlab_args="'$tempname.input.txt', '$tempname.inputvn.txt', '$GroupMaps', '$Method', '$tempname.params.txt', '$tempfile.91k.dscalar.nii', '$OutBeta', 'SurfString', '$SurfString', 'WRSmoothingSigma', '$WRSmoothingSigma'"
+        matlab_args="'$tempname.input.txt', '$tempname.inputvn.txt', '$Method', '$tempname.params.txt', '$OutBeta', 'SurfString', '$SurfString', 'WRSmoothingSigma', '$WRSmoothingSigma'"
+
+        if [[ ! ${Method} == "single" ]]
+        then
+        matlab_args+=", 'GroupMaps', '$GroupMaps'"
+        matlab_args+=", 'VAWeightsName', '$tempfile.91k.dscalar.nii'"
+        fi
         if ((DoZ))
         then
             matlab_args+=", 'OutputZ', '$OutputZ'"
@@ -247,7 +268,7 @@ case "$MatlabMode" in
         ;;
 esac
 
-if [[ "$SpectraParams" != "" ]]
+if [[ "$SpectraParams" != "" ]] && [[ ! ${Method} == "single" ]]
 then
     wb_command -file-information "$GroupMaps" -only-map-names > "$tempname.mapnames.txt"
     TR=$(wb_command -file-information "$SpectraTRFile" -only-step-interval)