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Enable Single Regression in RSNRegression #170

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Apr 2, 2020
Merged

Enable Single Regression in RSNRegression #170

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705d7b0
Enable Single Regression in RSNRegression
glasserm Apr 2, 2020
fbcaaf1
Address Tim Concerns
glasserm Apr 2, 2020
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22 changes: 15 additions & 7 deletions global/scripts/RSNregression.m
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Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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, '')
Expand Down Expand Up @@ -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};
Expand Down
39 changes: 30 additions & 9 deletions global/scripts/RSNregression.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand All @@ -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))
Expand Down Expand Up @@ -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'"
;;
Expand All @@ -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=""
Expand All @@ -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'"
Expand Down Expand Up @@ -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)
Expand Down