rpipe 0.0.1

data/lib/custom_methods/JohnsonMerit220Visit1Stats.rb

@@ -0,0 +1,63 @@
+require 'logfile'
+module JohnsonMerit220Visit1Stats
+
+	DEFAULT_CONDITIONS = [:new_correct_, :new_incorrect_, :old_correct_, :old_incorrect, {:misses => [:new_misses, :old_misses]} ]
+  
+  # runs the complete set of tasks using data in a subject's "proc" directory and a preconfigured template spm job.
+	def run_first_level_stats
+		flash "Highway to the dangerzone..."
+		setup_directory(@statsdir, "STATS")
+		
+		Dir.chdir(@statsdir) do
+			link_files_from_proc_directory(File.join(@procdir, "sw*.nii"), File.join(@procdir, "rp*.txt"))
+			setup_onsets
+			run_stats_spm_job
+		end
+	end
+
+	alias_method :perform, :run_first_level_stats
+	
+	def setup_onsets
+	  setup_conditions
+    create_or_link_onsets_files
+  end
+  
+  def setup_conditions
+    @conditions = @conditions ? @conditions.collect! {|c| c.to_sym if c.respond_to? :to_sym } : DEFAULT_CONDITIONS 
+  end
+  
+  def create_or_link_onsets_files
+    if @onsetsfiles.nil?
+		  if @responses.nil?
+		    raise ScriptError, "Condition vectors cannot be created because neither log response files nor onsets mat files have been specified."
+	    else
+	      @onsetsfiles = create_onsets_files(@responses, conditions)
+      end
+    else
+	    link_onsets_files
+		end
+  end
+  
+  # Finally runs the stats job 
+  def run_stats_spm_job
+    images = Dir.glob(File.join(@statsdir, "sw*#{@subid}*[Tt]ask*.nii"))
+    raise ScriptError, "Can't find any smoothed, warped images in #{@statsdir}" if images.empty?
+    
+    queue = MatlabQueue.new
+	  queue.paths << ['/Applications/spm/spm8/spm8_current',
+	    '/apps/spm/spm8_current',
+      File.join(@libdir, 'custom_methods'), 
+      File.join(@libdir, 'matlab_helpers')    ]
+
+	  queue << "#{@method}('#{@statsdir}/', \
+    { #{images.collect {|im| "'#{File.basename(im)}'"}.join(' ')} }, \
+    { #{@bold_reps.join(' ') } }, \
+    { #{@onsetsfiles.collect { |file| "'#{File.basename(file)}'"}.join(' ') } }, \
+    { #{@regressorsfiles.collect { |file| "'#{File.basename(file)}'"}.join(' ') } }, \
+    '#{@method}_job.m')"
+    
+    # puts queue.to_s
+    queue.run!
+  end
+  
+end

data/lib/custom_methods/JohnsonMerit220Visit1Stats_job.m

@@ -0,0 +1,63 @@
+%-----------------------------------------------------------------------
+% Job configuration created by cfg_util (rev $Rev: 3599 $)
+%-----------------------------------------------------------------------
+%% Specification
+matlabbatch{1}.spm.stats.fmri_spec.dir = '<UNDEFINED>';
+matlabbatch{1}.spm.stats.fmri_spec.timing.units = 'scans';
+matlabbatch{1}.spm.stats.fmri_spec.timing.RT = 2;
+matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t = 16;
+matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t0 = 1;
+matlabbatch{1}.spm.stats.fmri_spec.sess(1).scans = '<UNDEFINED>';
+matlabbatch{1}.spm.stats.fmri_spec.sess(1).cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {});
+matlabbatch{1}.spm.stats.fmri_spec.sess(1).multi = '<UNDEFINED>';
+matlabbatch{1}.spm.stats.fmri_spec.sess(1).regress = struct('name', {}, 'val', {});
+matlabbatch{1}.spm.stats.fmri_spec.sess(1).multi_reg = '<UNDEFINED>';
+matlabbatch{1}.spm.stats.fmri_spec.sess(1).hpf = 128;
+matlabbatch{1}.spm.stats.fmri_spec.sess(2).scans = '<UNDEFINED>';
+matlabbatch{1}.spm.stats.fmri_spec.sess(2).cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {});
+matlabbatch{1}.spm.stats.fmri_spec.sess(2).multi = '<UNDEFINED>';
+matlabbatch{1}.spm.stats.fmri_spec.sess(2).regress = struct('name', {}, 'val', {});
+matlabbatch{1}.spm.stats.fmri_spec.sess(2).multi_reg = '<UNDEFINED>';
+matlabbatch{1}.spm.stats.fmri_spec.sess(2).hpf = 128;
+matlabbatch{1}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});
+matlabbatch{1}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];
+matlabbatch{1}.spm.stats.fmri_spec.volt = 1;
+matlabbatch{1}.spm.stats.fmri_spec.global = 'None';
+matlabbatch{1}.spm.stats.fmri_spec.mask = {''};
+matlabbatch{1}.spm.stats.fmri_spec.cvi = 'AR(1)';
+%% Estimation
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep;
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tname = 'Select SPM.mat';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tgt_spec{1}(1).name = 'filter';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tgt_spec{1}(1).value = 'mat';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tgt_spec{1}(2).name = 'strtype';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tgt_spec{1}(2).value = 'e';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).sname = 'fMRI model specification: SPM.mat File';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).src_output = substruct('.','spmmat');
+matlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;
+%% Contrast Creation
+matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep;
+matlabbatch{3}.spm.stats.con.spmmat(1).tname = 'Select SPM.mat';
+matlabbatch{3}.spm.stats.con.spmmat(1).tgt_spec{1}(1).name = 'filter';
+matlabbatch{3}.spm.stats.con.spmmat(1).tgt_spec{1}(1).value = 'mat';
+matlabbatch{3}.spm.stats.con.spmmat(1).tgt_spec{1}(2).name = 'strtype';
+matlabbatch{3}.spm.stats.con.spmmat(1).tgt_spec{1}(2).value = 'e';
+matlabbatch{3}.spm.stats.con.spmmat(1).sname = 'Model estimation: SPM.mat File';
+matlabbatch{3}.spm.stats.con.spmmat(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1});
+matlabbatch{3}.spm.stats.con.spmmat(1).src_output = substruct('.','spmmat');
+matlabbatch{3}.spm.stats.con.consess{1}.fcon.name       = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{1}.fcon.convec{1}  = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{1}.fcon.sessrep    = 'repl';
+matlabbatch{3}.spm.stats.con.consess{2}.tcon.name       = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{2}.tcon.convec     = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{2}.tcon.sessrep    = 'repl';
+matlabbatch{3}.spm.stats.con.consess{3}.tcon.name       = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{3}.tcon.convec     = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{3}.tcon.sessrep    = 'repl';
+matlabbatch{3}.spm.stats.con.delete = 0;
+
+% NOTE! F-contrasts expect cells containing contrast arrays, while
+% T-contrasts expect the arrays themslves (hence the cell reference in
+% F-contrast definition (convec{1} = [];) but not in T-contrast definition
+% (convec = [];)

data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.m

@@ -0,0 +1,26 @@
+function [] = JohnsonTbiLongitudinalSnodPreproc(studypath, images, image_boldreps, job_mfile)
+% [] =  Calls and runs TBI Longitudinal preproc job.
+% merit_preproc('/private/tmp/mrt00015_orig/', ...
+% {'amrt00015_task1.nii' 'amrt00015_task2.nii' 'amrt00015_rest.nii'}, ...
+% {164 164 164}, ...
+% '/private/tmp/mrt00015_orig/mrt00015_preproc_job.m') 
+% 
+
+spm('defaults', 'FMRI');
+
+% List of open inputs
+% Realign: Estimate: Session - cfg_files
+% Realign: Estimate: Session - cfg_files
+% Realign: Estimate: Session - cfg_files
+nrun = 1; % enter the number of runs here
+jobfile = {job_mfile};
+jobs = repmat(jobfile, 1, nrun);
+inputs = cell(3, nrun);
+
+for crun = 1:nrun
+    for index = 1:length(images)
+			inputs{index, crun} = CreateFunctionalVolumeStruct(studypath, images{index}, image_boldreps{index}); % Realign: Estimate: Session - cfg_files
+    end
+end
+
+spm_jobman('serial', jobs, '', inputs{:});

data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc.rb

@@ -0,0 +1,41 @@
+require 'matlab_helpers/matlab_queue'
+module JohnsonTbiLongitudinalSnodPreproc
+	
+	# Runs the preprocessing job, including spm job customization, run spm job, and handling motion issues.
+	# This function assumes a destination directory is set up; it will overwrite preexisting data.	Careful!
+	def preproc_visit
+		flash "Spatial Preprocessing Subject: #{@subid}"
+		setup_directory(@procdir, "PREPROC")
+		
+		Dir.chdir(@procdir) do
+			link_files_into_proc
+      run_preproc_mfile
+			deal_with_motion
+		end
+	end
+	
+	alias_method :perform, :preproc_visit
+	
+	private
+	
+	def run_preproc_mfile
+	  images = @scan_labels ? @scan_labels.collect! { |label| Dir.glob("a*#{label}*.nii").to_s } : Dir.glob(File.join(@origdir, "a*#{@subid}*.nii"))
+	  
+	  raise ScriptError, "Can't find any slice-time corrected images in #{@origdir}" if images.empty?
+	  queue = MatlabQueue.new
+	  queue.paths << ['/Applications/spm/spm8/spm8_current', 
+	    '/apps/spm/spm8_current',
+      File.join(@libdir, 'custom_methods'), 
+      File.join(@libdir, 'matlab_helpers')
+    ]
+
+	  queue << "JohnsonTbiLongitudinalSnodPreproc('#{@procdir}/', \
+    { #{images.collect {|im| "'#{File.basename(im)}'"}.join(' ')} },  \
+    { #{@bold_reps.join(' ') } }, \
+    'JohnsonTbiLongitudinalSnodPreproc_job.m')"
+    
+    puts queue.to_s
+    queue.run!
+  end
+  
+end

data/lib/custom_methods/JohnsonTbiLongitudinalSnodPreproc_job.m

@@ -0,0 +1,69 @@
+%-----------------------------------------------------------------------------
+% Unfortunately, there is no easy way to pass in the number of images to this
+% template job, short of writing a function to build one on the fly. Number of
+% sessions is hardcoded.
+nsessions = 6;
+%-----------------------------------------------------------------------------
+
+%-----------------------------------------------------------------------
+% Job configuration created by cfg_util (rev $Rev: 3599 $)
+%-----------------------------------------------------------------------
+for i = 1:nsessions
+	matlabbatch{1}.spm.spatial.realign.estimate.data{i} = '<UNDEFINED>';
+end
+matlabbatch{1}.spm.spatial.realign.estimate.eoptions.quality = 0.9;
+matlabbatch{1}.spm.spatial.realign.estimate.eoptions.sep = 4;
+matlabbatch{1}.spm.spatial.realign.estimate.eoptions.fwhm = 5;
+matlabbatch{1}.spm.spatial.realign.estimate.eoptions.rtm = 1;
+matlabbatch{1}.spm.spatial.realign.estimate.eoptions.interp = 2;
+matlabbatch{1}.spm.spatial.realign.estimate.eoptions.wrap = [0 0 0];
+matlabbatch{1}.spm.spatial.realign.estimate.eoptions.weight = {''};
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.source(1) = cfg_dep;
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.source(1).tname = 'Source Image';
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.source(1).tgt_spec{1}(1).name = 'filter';
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.source(1).tgt_spec{1}(1).value = 'image';
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.source(1).tgt_spec{1}(2).name = 'strtype';
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.source(1).tgt_spec{1}(2).value = 'e';
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.source(1).sname = 'Realign: Estimate: Realigned Images (Sess 1)';
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.source(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.source(1).src_output = substruct('.','sess', '()',{1}, '.','cfiles');
+matlabbatch{2}.spm.spatial.normalise.estwrite.subj.wtsrc = '';
+for i = 1:nsessions
+	matlabbatch{2}.spm.spatial.normalise.estwrite.subj.resample(i) = cfg_dep;
+	matlabbatch{2}.spm.spatial.normalise.estwrite.subj.resample(i).tname = 'Images to Write';
+	matlabbatch{2}.spm.spatial.normalise.estwrite.subj.resample(i).tgt_spec{1}(1).name = 'filter';
+	matlabbatch{2}.spm.spatial.normalise.estwrite.subj.resample(i).tgt_spec{1}(1).value = 'image';
+	matlabbatch{2}.spm.spatial.normalise.estwrite.subj.resample(i).tgt_spec{1}(2).name = 'strtype';
+	matlabbatch{2}.spm.spatial.normalise.estwrite.subj.resample(i).tgt_spec{1}(2).value = 'e';
+	matlabbatch{2}.spm.spatial.normalise.estwrite.subj.resample(i).sname = ['Realign: Estimate: Realigned Images (Sess' i ')'];
+	matlabbatch{2}.spm.spatial.normalise.estwrite.subj.resample(i).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
+	matlabbatch{2}.spm.spatial.normalise.estwrite.subj.resample(i).src_output = substruct('.','sess', '()',{i}, '.','cfiles');
+end
+matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.template = {[spm('Dir') '/templates/EPI.nii,1']};
+matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.weight = '';
+matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.smosrc = 8;
+matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.smoref = 0;
+matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.regtype = 'mni';
+matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.cutoff = 25;
+matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.nits = 16;
+matlabbatch{2}.spm.spatial.normalise.estwrite.eoptions.reg = 1;
+matlabbatch{2}.spm.spatial.normalise.estwrite.roptions.preserve = 0;
+matlabbatch{2}.spm.spatial.normalise.estwrite.roptions.bb = [-78 -112 -50
+                                                             78 76 85];
+matlabbatch{2}.spm.spatial.normalise.estwrite.roptions.vox = [2 2 2];
+matlabbatch{2}.spm.spatial.normalise.estwrite.roptions.interp = 1;
+matlabbatch{2}.spm.spatial.normalise.estwrite.roptions.wrap = [0 0 0];
+matlabbatch{2}.spm.spatial.normalise.estwrite.roptions.prefix = 'w';
+matlabbatch{3}.spm.spatial.smooth.data(1) = cfg_dep;
+matlabbatch{3}.spm.spatial.smooth.data(1).tname = 'Images to Smooth';
+matlabbatch{3}.spm.spatial.smooth.data(1).tgt_spec{1}(1).name = 'filter';
+matlabbatch{3}.spm.spatial.smooth.data(1).tgt_spec{1}(1).value = 'image';
+matlabbatch{3}.spm.spatial.smooth.data(1).tgt_spec{1}(2).name = 'strtype';
+matlabbatch{3}.spm.spatial.smooth.data(1).tgt_spec{1}(2).value = 'e';
+matlabbatch{3}.spm.spatial.smooth.data(1).sname = 'Normalise: Estimate & Write: Normalised Images (Subj 1)';
+matlabbatch{3}.spm.spatial.smooth.data(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
+matlabbatch{3}.spm.spatial.smooth.data(1).src_output = substruct('()',{1}, '.','files');
+matlabbatch{3}.spm.spatial.smooth.fwhm = [8 8 8];
+matlabbatch{3}.spm.spatial.smooth.dtype = 0;
+matlabbatch{3}.spm.spatial.smooth.im = 0;
+matlabbatch{3}.spm.spatial.smooth.prefix = 's';

data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats.m

@@ -0,0 +1,76 @@
+function [] = JohnsonTbiLongitudinalSnodStats(statsdir, images, image_boldreps, conditions, regressors, job_mfile) 
+	
+% List of open inputs
+% fMRI model specification: Directory - cfg_entry
+% 6 Scans Each with: 
+% fMRI model specification: Scans
+% fMRI model specification: Multiple Conditions File - cfg_entry
+% fMRI model specification: Multiple Regressors File - cfg_entry
+
+spm('defaults', 'FMRI');
+
+% statsdir = '/private/tmp/mrt00015_stats/'
+% images = { 'swamrt00015_task1.nii' 'swamrt00015_task2.nii' }
+% image_boldreps = {164 164}
+% regressors =  { 'mrt00015_faces3_recognitionA.mat' 'mrt00015_faces3_recognitionB.mat' }
+% job_mfile = '/private/tmp/mrt00015_stats/Merit220Stats_job.m'
+
+nrun = 1; % enter the number of runs here
+% jobfile = {'/private/tmp/mrt00015_proc/Merit220_Stats_job.m'};
+jobfile = {job_mfile};
+jobs = repmat(jobfile, 1, nrun);
+inputs = cell(length(images) + 1, nrun);
+
+% Load the first conditions file to get the length of the names.
+eval(['load ' conditions{1}]);
+
+switch numel(names)
+    case 2 % New, Old
+        fcontrast_vector = [1 0
+        										0 1];
+        tcontrast_1_vector = [-1 1];
+        tcontrast_2_vector = [1 -1];
+    % case 4 % New_correct, New_incorrect, Old_correct, Old_incorrect
+    %     fcontrast_vector = [1 0 0 0 
+    %                         0 1 0 0 
+    %                         0 0 1 0 
+    %                         0 0 0 1 ];
+    %     tcontrast_1_vector = [-1 0  1 0];
+    %     tcontrast_2_vector = [ 1 0 -1 0];
+    % case 5 % New_correct, New_incorrect, Old_correct, Old_incorrect, Misses
+    %     fcontrast_vector = [1 0 0 0
+    %                         0 1 0 0 
+    %                         0 0 1 0 
+    %                         0 0 0 1 ];
+    %     tcontrast_1_vector = [-1 0  1 0];
+    %     tcontrast_2_vector = [ 1 0 -1 0];
+    otherwise
+        error('Incorrect number of conditions detected: %d', numel(conditions));
+end
+
+for crun = 1:nrun
+		inputs{1, crun} = { statsdir }; % fMRI model specification: Directory  - cfg_entry
+		
+		% fMRI model specification: Directory  - cfg_entry
+		for index = 1:length(images)
+			offset = (index - 1) .* 3;
+			inputs{offset + 2, crun}  = CreateFunctionalVolumeStruct(statsdir, images{index}, image_boldreps{index}); % fMRI model specification: Scans - cfg_entry
+			inputs{offset + 3, crun}  = { strcat(statsdir, conditions{index} ) };    % fMRI model specification: Multiple Conditions File - cfg_entry
+			inputs{offset + 4, crun}  = { strcat(statsdir, regressors{index} ) };    % fMRI model specification: Multiple Regressors File - cfg_entry
+		end
+
+		image_offset = (length(images) .* 3) + 1;
+		inputs{image_offset + 1, crun}  = 'Omnibus F';				% fMRI model specification: Omnibus Title - cfg_entry
+    inputs{image_offset + 2, crun}  = fcontrast_vector;		% fMRI model specification: Omnibus Contrast - cfg_entry
+
+		inputs{image_offset + 3, crun}  = 'NV > PV';					% fMRI model specification: T Contrast 1 Title - cfg_entry
+		inputs{image_offset + 4, crun}  = tcontrast_1_vector; % fMRI model specification: T Contrast 1 Vector - cfg_entry
+
+		inputs{image_offset + 5, crun}  = 'PV > NV';   				% fMRI model specification: T Contrast 2 Title - cfg_entry
+		inputs{image_offset + 6, crun} = tcontrast_2_vector; 	% fMRI model specification: T Contrast 2 Vector - cfg_entry
+
+end
+
+
+
+spm_jobman('serial', jobs, '', inputs{:});

data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats.rb

@@ -0,0 +1,67 @@
+# require 'logfile'
+module JohnsonTbiLongitudinalSnodStats
+
+	DEFAULT_CONDITIONS = [:new, :old]
+  
+  # runs the complete set of tasks using data in a subject's "proc" directory and a preconfigured template spm job.
+	def run_first_level_stats
+		flash "Highway to the dangerzone..."
+		setup_directory(@statsdir, "STATS")
+		
+		Dir.chdir(@statsdir) do
+			link_files_from_proc_directory(File.join(@procdir, "sw*.nii"), File.join(@procdir, "rp*.txt"))
+			setup_onsets
+			run_stats_spm_job
+		end
+	end
+
+	alias_method :perform, :run_first_level_stats
+	
+	def setup_onsets
+	  setup_conditions
+    create_or_link_onsets_files
+  end
+  
+  def setup_conditions
+    @conditions = @conditions ? @conditions.collect {|c| c.to_sym if c.respond_to? :to_sym } : DEFAULT_CONDITIONS 
+  end
+  
+  def create_or_link_onsets_files
+    if @onsetsfiles.nil?
+		  if @responses.nil?
+		    raise ScriptError, "Condition vectors cannot be created because neither log response files nor onsets mat files have been specified."
+	    else
+	      @onsetsfiles = create_onsets_files(@responses, conditions)
+      end
+    else
+	    link_onsets_files
+		end
+  end
+  
+  # Finally runs the stats job 
+  def run_stats_spm_job
+    images = @scan_labels ? @scan_labels.collect! { |label| Dir.glob("sw*#{label}*.nii").to_s } : Dir.glob(File.join(@origdir, "sw*#{@subid}*.nii"))
+    raise ScriptError, "Can't find any smoothed, warped images in #{@statsdir}" if images.empty?
+    unless @onsetsfiles.length == @regressorsfiles.length && @regressorsfiles.length == @bold_reps.length
+      raise ScriptError, "Mismatch between #{@bold_reps.length} reps, #{@onsetsfiles.length} onsets and #{@regressorsfiles.length} regressors files."
+    end
+    
+    queue = MatlabQueue.new
+	  queue.paths << [
+	    '/Applications/spm/spm8/spm8_current', 
+	    '/apps/spm/spm8_current',
+      File.join(@libdir, 'custom_methods'), 
+      File.join(@libdir, 'matlab_helpers')    ]
+
+	  queue << "JohnsonTbiLongitudinalSnodStats('#{@statsdir}/', \
+    { #{images.collect {|im| "'#{File.basename(im)}'"}.join(' ')} },  \
+    { #{@bold_reps.join(' ') } }, \
+    { #{@onsetsfiles.collect { |file| "'#{File.basename(file)}'"}.join(' ') } }, \
+    { #{@regressorsfiles.collect { |file| "'#{File.basename(file)}'"}.join(' ') } }, \
+    'JohnsonTbiLongitudinalSnodStats_job.m')"
+    
+    # puts queue.to_s
+    queue.run!
+  end
+  
+end

data/lib/custom_methods/JohnsonTbiLongitudinalSnodStats_job.m

@@ -0,0 +1,59 @@
+%-----------------------------------------------------------------------
+% Job configuration created by cfg_util (rev $Rev: 3599 $)
+%-----------------------------------------------------------------------
+%% Specification
+matlabbatch{1}.spm.stats.fmri_spec.dir = '<UNDEFINED>';
+matlabbatch{1}.spm.stats.fmri_spec.timing.units = 'scans';
+matlabbatch{1}.spm.stats.fmri_spec.timing.RT = 2;
+matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t = 16;
+matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t0 = 1;
+for i = 1:2
+	matlabbatch{1}.spm.stats.fmri_spec.sess(i).scans = '<UNDEFINED>';
+	matlabbatch{1}.spm.stats.fmri_spec.sess(i).cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {});
+	matlabbatch{1}.spm.stats.fmri_spec.sess(i).multi = '<UNDEFINED>';
+	matlabbatch{1}.spm.stats.fmri_spec.sess(i).regress = struct('name', {}, 'val', {});
+	matlabbatch{1}.spm.stats.fmri_spec.sess(i).multi_reg = '<UNDEFINED>';
+	matlabbatch{1}.spm.stats.fmri_spec.sess(i).hpf = 128;
+end
+matlabbatch{1}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});
+matlabbatch{1}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];
+matlabbatch{1}.spm.stats.fmri_spec.volt = 1;
+matlabbatch{1}.spm.stats.fmri_spec.global = 'None';
+matlabbatch{1}.spm.stats.fmri_spec.mask = {''};
+matlabbatch{1}.spm.stats.fmri_spec.cvi = 'AR(1)';
+%% Estimation
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep;
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tname = 'Select SPM.mat';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tgt_spec{1}(1).name = 'filter';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tgt_spec{1}(1).value = 'mat';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tgt_spec{1}(2).name = 'strtype';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).tgt_spec{1}(2).value = 'e';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).sname = 'fMRI model specification: SPM.mat File';
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).src_exbranch = substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1});
+matlabbatch{2}.spm.stats.fmri_est.spmmat(1).src_output = substruct('.','spmmat');
+matlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;
+%% Contrast Creation
+matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep;
+matlabbatch{3}.spm.stats.con.spmmat(1).tname = 'Select SPM.mat';
+matlabbatch{3}.spm.stats.con.spmmat(1).tgt_spec{1}(1).name = 'filter';
+matlabbatch{3}.spm.stats.con.spmmat(1).tgt_spec{1}(1).value = 'mat';
+matlabbatch{3}.spm.stats.con.spmmat(1).tgt_spec{1}(2).name = 'strtype';
+matlabbatch{3}.spm.stats.con.spmmat(1).tgt_spec{1}(2).value = 'e';
+matlabbatch{3}.spm.stats.con.spmmat(1).sname = 'Model estimation: SPM.mat File';
+matlabbatch{3}.spm.stats.con.spmmat(1).src_exbranch = substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1});
+matlabbatch{3}.spm.stats.con.spmmat(1).src_output = substruct('.','spmmat');
+matlabbatch{3}.spm.stats.con.consess{1}.fcon.name       = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{1}.fcon.convec{1}  = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{1}.fcon.sessrep    = 'repl';
+matlabbatch{3}.spm.stats.con.consess{2}.tcon.name       = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{2}.tcon.convec     = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{2}.tcon.sessrep    = 'repl';
+matlabbatch{3}.spm.stats.con.consess{3}.tcon.name       = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{3}.tcon.convec     = '<UNDEFINED>';
+matlabbatch{3}.spm.stats.con.consess{3}.tcon.sessrep    = 'repl';
+matlabbatch{3}.spm.stats.con.delete = 0;
+
+% NOTE! F-contrasts expect cells containing contrast arrays, while
+% T-contrasts expect the arrays themslves (hence the cell reference in
+% F-contrast definition (convec{1} = [];) but not in T-contrast definition
+% (convec = [];)

data/lib/custom_methods/ReconWithHello.rb

@@ -0,0 +1,7 @@
+module ReconWithHello
+	
+	def hello
+		"=== Hello World! ==="
+	end
+	
+end

data/lib/default_logger.rb

@@ -0,0 +1,13 @@
+require 'log4r'
+
+# Setup Command and General Logs to point to STDOUT if not defined.
+module DefaultLogger
+  def setup_logger
+    %w{$Log $CommandLog}.each do |log|
+      unless eval(log)
+        eval("#{log} = Log4r::Logger.new('output')")
+        eval("#{log}.add Log4r::StdoutOutputter.new(:stdout)")
+      end
+    end
+  end
+end

data/lib/default_methods/default_preproc.rb

@@ -0,0 +1,76 @@
+module DefaultPreproc
+	
+	# Runs the preprocessing job, including spm job customization, run spm job, and handling motion issues.
+	# This function assumes a destination directory is set up; it will overwrite preexisting data.	Careful!
+	def preproc_visit
+		$Log.info "Spatial Preprocessing Subject: #{@subid}"
+		
+		setup_directory(@procdir, "PREPROC")
+		
+		Dir.chdir(@procdir) do
+			link_files_into_proc
+			customize_templates
+			run_spm_jobs
+			deal_with_motion
+		end
+	end
+	
+	alias_method :perform, :preproc_visit
+	
+	# Links all the slice timing corrected data from the source "orig" directory using a wildcard a${subid}*.nii,
+	# where subid is the subject id specified in the preproc_spec hash.
+	def link_files_into_proc
+		flash "Linking files from #{@origdir} into #{@procdir}"
+		wildcard = File.join(@origdir,"a*#{@subid}*.nii")
+		files = Dir.glob(wildcard)
+		unless files.empty?
+		  system("ln -s #{wildcard} #{@procdir}")
+	  else
+	    raise(IOError, "No files matching #{wildcard} found.")
+    end
+	end
+	
+	def check_permissions(files)
+	  unwritable = []
+	  files.collect { |file| unwritable << file unless File.writable?(file) }
+    raise IOError, "Cannot write to #{unwritable.join(", ")} files." unless unwritable.empty?
+  end
+	
+	# Customizes the template job in preproc_spec to be specific for this particular preproc job.
+	# Performs to recursive string replacements inside the spm job:
+	# - path inside template is replaced with destination "proc" directory
+	# - subid inside template is replaced with the current subid
+	def customize_templates
+		flash "Customizing template SPM job: #{@tspec['job']}"
+		replacecmd = "spmjobStringReplace.sh"
+		
+		templatejob = File.join(@spmdir, @tspec['job'])
+		thisjob = @subid + '_preproc.mat'
+		
+		File.copy(templatejob, thisjob)
+		system("#{replacecmd} #{thisjob} #{@tspec['path']} #{@procdir} #{thisjob}")
+		system("#{replacecmd} #{thisjob} #{@tspec['subid']} #{@subid} #{thisjob}")
+	end
+	
+	# Runs the customized spm job using the shell script runSpmJob.sh.	Make sure this is available at your site.
+	def run_spm_jobs
+		thisjob = "#{@subid}_preproc.mat"
+		flash "Running spatial preprocessing SPM job: #{thisjob}"
+		system("runSpmJob.sh #{thisjob}")
+	end
+	
+  # Calculates the realignment motion derivatives and checks that displacement
+  # in all directions was less than the MOTION_THRESHOLD. Operates on all files
+  # in the current working directory that match rp_a*txt (SPM convention). Uses
+  # two shell scripts that must both be available on the local machine: 
+  # - calc_derivs.sh 
+  # - fmri_motion_check.sh
+	def deal_with_motion
+		flash "Calculating motion derivatives and checking for excessive motion"
+		Dir.glob("rp_a*txt").each do |rp|
+			run("calc_derivs.sh #{rp}")
+			run("fmri_motion_check.sh #{rp} #{@motion_threshold}")
+		end
+	end
+	
+end

data/lib/default_methods/default_recon.rb

@@ -0,0 +1,80 @@
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__), '..', '..', '..',  'physionoise/lib')
+
+require 'metamri/core_additions'
+require 'physionoise'
+require 'pathname'
+require 'default_methods/recon/physionoise_helper'
+require 'default_methods/recon/raw_sequence'
+
+module DefaultRecon
+	
+	# Reconstructs, strips, and slice timing corrects all scans specified in the recon_spec.
+	# This function assumes a destination directory is set up in the filesystem and begins writing
+	# to it with no further checking.	 It will overwrite data if it already exists, be careful.
+	def recon_visit
+		
+		setup_directory(@origdir, "RECON")
+		
+		Dir.chdir(@origdir) do		  
+			@scans.each_with_index do |scan_spec, i|
+				outfile = "%s_%s.nii" % [@subid, scan_spec['label']]
+				
+				reconstruct_scan(scan_spec, outfile)
+				
+				if scan_spec['type'] == "func"
+          # if scan_spec['physio_files']
+          #   create_physiosnoise_regressors(scan_spec)
+          #   outfile = run_retroicor(scan_spec['physio_files'], outfile)
+          # end
+				  
+					slice_time_correct(outfile)
+				else
+					File.copy('tmp.nii', outfile)
+				end
+				
+				File.delete('tmp.nii') if File.exist? 'tmp.nii'
+			end
+		end
+	end
+	
+	alias_method :perform, :recon_visit
+	
+  # Reconstructs a scan from dicoms or pfile to nifti, anatomical or functional.
+  # Uses a scan_spec hash to drive. Writes the result in current working
+  # directory. Raises an error if to3d system call fails. Conventions: I****.dcm
+  # filenaming, I0002.dcm is second file in series,
+	def reconstruct_scan(scan_spec, outfile)	
+		if scan_spec['dir']
+		  sequence = DicomRawSequence.new(scan_spec, @rawdir)
+		  sequence.prepare('tmp.nii')
+			strip_leading_volumes('tmp.nii', outfile, @volume_skip, scan_spec['bold_reps'])
+	  elsif scan_spec['pfile']
+	    sequence = PfileRawSequence.new(scan_spec, @rawdir)
+	    sequence.prepare(outfile)
+    else 
+      raise ConfigError, "Scan must list either a pfile or a dicom directory."
+    end
+	end
+	
+	# Removes the specified number of volumes from the beginning of a 4D functional nifti file.
+	# In most cases this will be 3 volumes. Writes result in current working directory.
+	def strip_leading_volumes(infile, outfile, volume_skip, bold_reps)
+		$Log.info "Stripping #{volume_skip.to_s} leading volumes: #{infile}"
+		cmd_fmt = "fslroi %s %s %s %s"
+		cmd_options = [infile, outfile, volume_skip.to_s, bold_reps.to_s]
+		cmd = cmd_fmt % cmd_options
+		unless run(cmd)
+		  raise ScriptError, "Failed to strip volumes: #{cmd}"
+	  end
+	end
+	
+	# Uses to3d to slice time correct a 4D functional nifti file.	 Writes result in the current working directory.
+	def slice_time_correct(infile)
+		$Log.info "Slice Timing Correction: #{infile}"
+		cmd = "3dTshift -tzero 0 -tpattern alt+z -prefix a#{infile} #{infile}"
+		unless run(cmd)
+		  raise ScriptError, "Failed to slice time correct: #{cmd}"
+	  end
+	end
+	
+end