Merge pull request #638 from Remi-Gau/fix_skip_segment

[FIX] properly skip segment and sullstrip

Author: Remi-Gau

src/WIP/makeStandalone.m WIP/makeStandalone.msrc/WIP/makeStandalone.m renamed to WIP/makeStandalone.m

@@ -50,7 +50,7 @@
 cpp_spm();
 
 %% Dopwnload the dataset
-download_data = true;
+download_data = false;
 clean = true;
 download_moae_ds(download_data, clean);
 

src/WIP/miss_hit.cfg WIP/miss_hit.cfgsrc/WIP/miss_hit.cfg renamed to WIP/miss_hit.cfg

@@ -19,6 +19,7 @@ regex_parameter_name: "[A-Z]+(_[A-Z]+)*|[a-z]+([A-Z]+[a-z]*)*"
 
 exclude_dir: "lib"
 exclude_dir: "docs"
+exclude_dir: "WIP"
 
 copyright_entity: "JH"
 copyright_entity: "DSS"
@@ -37,5 +38,5 @@ tab_width: 2
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
 metric "cnest": limit 5
 metric "file_length": limit 600
-metric "cyc": limit 18
+metric "cyc": limit 19
 metric "parameters": limit 7

demos/MoAE/moae_01_bids_app.m

@@ -138,6 +138,11 @@
 end
 
 function biasCorrectedImage = getBiasCorrectedImage(matlabbatch, BIDS, opt)
+  %
+  % tries to grab a previously computed bias corrected image
+  % if this fails we assume we are in a bidsSpatialPreproc workflow
+  % and we rely on the batch dependency
+  %
 
   biasCorrectedImage = '';
 
@@ -161,6 +166,11 @@
 end
 
 function [gmTpm, wmTpm, csfTpm] = getTpms(matlabbatch, BIDS, opt)
+  %
+  % tries to grab a previously tissue probability maps
+  % if this fails we assume we are in a bidsSpatialPreproc workflow
+  % and we rely on the batch dependency
+  %
 
   gmTpm = '';
   wmTpm = '';
@@ -205,6 +215,11 @@
 end
 
 function skullstrippedImage = getSkullstrippedImage(matlabbatch, BIDS, opt)
+  %
+  % tries to grab a skullstripped image
+  % if this fails we assume we are in a bidsSpatialPreproc workflow
+  % and we rely on the batch dependency
+  %
 
   skullstrippedImage = '';
 
@@ -226,6 +241,11 @@
 end
 
 function skullstripMask = getSkullstripMask(matlabbatch, BIDS, opt)
+  %
+  % tries to grab a skullstripped mask
+  % if this fails we assume we are in a bidsSpatialPreproc workflow
+  % and we rely on the batch dependency
+  %
 
   skullstripMask = '';
 

miss_hit.cfg

@@ -1,4 +1,4 @@
-function matlabbatch = setBatchSegmentation(matlabbatch, opt, imageToSegment)
+function [matlabbatch, opt] = setBatchSegmentation(matlabbatch, opt, imageToSegment)
   %
   % Creates a batch to segment the anatomical image
   %
@@ -16,24 +16,35 @@
   %
   % (C) Copyright 2020 CPP_SPM developers
 
+  if ~opt.segment.do
+    opt.orderBatches.segment = 0;
+    return
+  else
+    opt.orderBatches.segment = numel(matlabbatch) + 1;
+  end
+
   printBatchName('Segmentation anatomical image', opt);
 
   % define SPM folder
   spmLocation = spm('dir');
 
   % save bias correction field = false
   % save bias corrected image = true
-  matlabbatch{end + 1}.spm.spatial.preproc.channel.write = [false true];
+  preproc.channel.write = [false true];
 
+  % firts part assumes we are in the bidsSpatialPreproc workflow
   if isfield(opt, 'orderBatches') && isfield(opt.orderBatches, 'selectAnat')
 
     % SAVE BIAS CORRECTED IMAGE
-    matlabbatch{end}.spm.spatial.preproc.channel.vols(1) = ...
-        cfg_dep('Named File Selector: Anatomical(1) - Files', ...
-                returnDependency(opt, 'selectAnat'), ...
-                substruct('.', 'files', '{}', {1}));
+    preproc.channel.vols(1) = cfg_dep('Named File Selector: Anatomical(1) - Files', ...
+                                      returnDependency(opt, 'selectAnat'), ...
+                                      substruct('.', 'files', '{}', {1}));
   else
 
+    % TODO
+    % implement the opt.segment.do and opt.segment.force
+    % with segmentationAlreadyDone ?
+
     % in case a cell was given as input
     if iscell(imageToSegment)
       imageToSegment = char(imageToSegment);
@@ -42,60 +53,56 @@
     % add all the images to segment
     for iImg = 1:size(imageToSegment, 1)
       file = validationInputFile([], deblank(imageToSegment(iImg, :)));
-      matlabbatch{end}.spm.spatial.preproc.channel.vols{iImg, 1} = file;
+      preproc.channel.vols{iImg, 1} = file;
     end
 
   end
 
-  matlabbatch{end}.spm.spatial.preproc.channel.biasreg = 0.001;
-  matlabbatch{end}.spm.spatial.preproc.channel.biasfwhm = opt.segment.biasfwhm;
+  preproc.channel.biasreg = 0.001;
+  preproc.channel.biasfwhm = opt.segment.biasfwhm;
 
   % CREATE SEGMENTS IN NATIVE SPACE OF GM, WM AND CSF
   nativeSpace = 1;
   dartelSpace = 0;
   native = [nativeSpace dartelSpace];
-  matlabbatch{end}.spm.spatial.preproc.tissue(1).tpm = ...
-      {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',1']};
-  matlabbatch{end}.spm.spatial.preproc.tissue(1).ngaus = 1;
-  matlabbatch{end}.spm.spatial.preproc.tissue(1).native = native;
-  matlabbatch{end}.spm.spatial.preproc.tissue(1).warped = [0 0];
-
-  matlabbatch{end}.spm.spatial.preproc.tissue(2).tpm = ...
-      {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',2']};
-  matlabbatch{end}.spm.spatial.preproc.tissue(2).ngaus = 1;
-  matlabbatch{end}.spm.spatial.preproc.tissue(2).native = native;
-  matlabbatch{end}.spm.spatial.preproc.tissue(2).warped = [0 0];
-
-  matlabbatch{end}.spm.spatial.preproc.tissue(3).tpm = ...
-      {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',3']};
-  matlabbatch{end}.spm.spatial.preproc.tissue(3).ngaus = 2;
-  matlabbatch{end}.spm.spatial.preproc.tissue(3).native = native;
-  matlabbatch{end}.spm.spatial.preproc.tissue(3).warped = [0 0];
-
-  matlabbatch{end}.spm.spatial.preproc.tissue(4).tpm = ...
-      {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',4']};
-  matlabbatch{end}.spm.spatial.preproc.tissue(4).ngaus = 3;
-  matlabbatch{end}.spm.spatial.preproc.tissue(4).native = [0 0];
-  matlabbatch{end}.spm.spatial.preproc.tissue(4).warped = [0 0];
-
-  matlabbatch{end}.spm.spatial.preproc.tissue(5).tpm = ...
-      {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',5']};
-  matlabbatch{end}.spm.spatial.preproc.tissue(5).ngaus = 4;
-  matlabbatch{end}.spm.spatial.preproc.tissue(5).native = [0 0];
-  matlabbatch{end}.spm.spatial.preproc.tissue(5).warped = [0 0];
-
-  matlabbatch{end}.spm.spatial.preproc.tissue(6).tpm = ...
-      {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',6']};
-  matlabbatch{end}.spm.spatial.preproc.tissue(6).ngaus = 2;
-  matlabbatch{end}.spm.spatial.preproc.tissue(6).native = [0 0];
-  matlabbatch{end}.spm.spatial.preproc.tissue(6).warped = [0 0];
+  preproc.tissue(1).tpm = {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',1']};
+  preproc.tissue(1).ngaus = 1;
+  preproc.tissue(1).native = native;
+  preproc.tissue(1).warped = [0 0];
+
+  preproc.tissue(2).tpm = {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',2']};
+  preproc.tissue(2).ngaus = 1;
+  preproc.tissue(2).native = native;
+  preproc.tissue(2).warped = [0 0];
+
+  preproc.tissue(3).tpm = {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',3']};
+  preproc.tissue(3).ngaus = 2;
+  preproc.tissue(3).native = native;
+  preproc.tissue(3).warped = [0 0];
+
+  preproc.tissue(4).tpm = {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',4']};
+  preproc.tissue(4).ngaus = 3;
+  preproc.tissue(4).native = [0 0];
+  preproc.tissue(4).warped = [0 0];
+
+  preproc.tissue(5).tpm = {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',5']};
+  preproc.tissue(5).ngaus = 4;
+  preproc.tissue(5).native = [0 0];
+  preproc.tissue(5).warped = [0 0];
+
+  preproc.tissue(6).tpm = {[fullfile(spmLocation, 'tpm', 'TPM.nii') ',6']};
+  preproc.tissue(6).ngaus = 2;
+  preproc.tissue(6).native = [0 0];
+  preproc.tissue(6).warped = [0 0];
 
   % SAVE FORWARD DEFORMATION FIELD FOR NORMALISATION
-  matlabbatch{end}.spm.spatial.preproc.warp.mrf = 1;
-  matlabbatch{end}.spm.spatial.preproc.warp.cleanup = 1;
-  matlabbatch{end}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
-  matlabbatch{end}.spm.spatial.preproc.warp.affreg = 'mni';
-  matlabbatch{end}.spm.spatial.preproc.warp.fwhm = 0;
-  matlabbatch{end}.spm.spatial.preproc.warp.samp = opt.segment.samplingDistance;
-  matlabbatch{end}.spm.spatial.preproc.warp.write = [1 1];
+  preproc.warp.mrf = 1;
+  preproc.warp.cleanup = 1;
+  preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
+  preproc.warp.affreg = 'mni';
+  preproc.warp.fwhm = 0;
+  preproc.warp.samp = opt.segment.samplingDistance;
+  preproc.warp.write = [1 1];
+
+  matlabbatch{end + 1}.spm.spatial.preproc = preproc;
 end

src/batches/preproc/setBatchNormalizationSpatialPrepro.m

@@ -48,11 +48,11 @@
 
   printBatchName('skull stripping', opt);
 
-  [imageToSkullStrip, dataDir] = getAnatFilename(BIDS, opt, subLabel);
-
   % if the input image is mean func image instead of anatomical
   if opt.skullstrip.mean
     [imageToSkullStrip, dataDir] = getMeanFuncFilename(BIDS, subLabel, opt);
+  else
+    [imageToSkullStrip, dataDir] = getAnatFilename(BIDS, opt, subLabel);
   end
 
   bf = bids.File(imageToSkullStrip, 'use_schema', false);
@@ -68,7 +68,9 @@
   % if this is part of a pipeline we get the segmentation dependency to get
   % the input from.
   % Otherwise the files to process are stored in a cell
-  if isfield(opt, 'orderBatches') && isfield(opt.orderBatches, 'segment')
+  if isfield(opt, 'orderBatches') && ...
+      isfield(opt.orderBatches, 'segment') && ...
+      opt.orderBatches.segment > 0
 
     input(1) = cfg_dep('Segment: Bias Corrected (1)', ...
                        returnDependency(opt, 'segment'), ...
@@ -92,10 +94,8 @@
 
   else
 
-    anatImage  = getAnatFilename(BIDS, opt, subLabel);
-
     % bias corrected image
-    anatFile = bids.File(anatImage);
+    anatFile = bids.File(imageToSkullStrip);
     filter = struct('suffix',  anatFile.suffix, ...
                     'sub', anatFile.entities.sub, ...
                     'prefix', '', ...

src/batches/preproc/setBatchSegmentation.m

@@ -8,11 +8,14 @@
   %
   % :param matlabbatch: list of SPM batches
   % :type matlabbatch: structure
+  %
   % :param BIDS: BIDS layout returned by ``getData``.
   % :type BIDS: structure
+  %
   % :param opt: structure or json filename containing the options. See
   %             ``checkOptions()`` and ``loadAndCheckOptions()``.
   % :type opt: structure
+  %
   % :param subLabel: subject label
   % :type subLabel: string
   %

src/batches/preproc/setBatchSkullStripping.m

@@ -10,11 +10,13 @@
   %   [anatImage, anatDataDir] = getAnatFilename(BIDS, subLabel, opt)
   %
   % :param BIDS:
-  % :type BIDS:         structure
+  % :type BIDS:      structure
+  %
   % :param subLabel:
-  % :param subLabel:    string
+  % :param subLabel:  char
+  %
   % :type opt:
-  % :param opt:         structure
+  % :param opt:      structure
   %
   % :returns: - :anatImage: (string)
   %           - :anatDataDir: (string)
@@ -55,7 +57,7 @@
   anat = anat{1};
   anatImage = unzipAndReturnsFullpathName(anat);
 
-  msg = sprintf('selecting anat file: %s\n', pathToPrint(anat));
+  msg = sprintf('  selecting anat file: %s\n', pathToPrint(anat));
   printToScreen(msg, opt);
 
   [anatDataDir, anatImage, ext] = spm_fileparts(anatImage);

src/batches/setBatchSelectAnat.m

@@ -308,12 +308,14 @@
   fieldsToSet.useFieldmaps = true;
 
   %% Options for segmentation
+  fieldsToSet.segment.do = true;
   fieldsToSet.segment.force = false;
   fieldsToSet.segment.biasfwhm = 60;
   fieldsToSet.segment.samplingDistance = 3;
 
   %% Options for skullstripping
   fieldsToSet.skullstrip.do = true;
+  fieldsToSet.skullstrip.force = false;
   fieldsToSet.skullstrip.threshold = 0.75;
   fieldsToSet.skullstrip.mean = false;