Including voxel size & BB selection

The warped images were generated with the SPM default value of 1.5 x 1.5
x 1.5 mm3 for the US (and pipeline), which was not ideal.
-> adding the option in the batch and the *_run_*.m functions

hmri_run_proc_US.m

@@ -65,10 +65,12 @@
     end
 
     % Prepare and run 'spm_preproc' -> get tissue maps + deformation
-    defsa.channel = job.subjc(nm).channel;
-    defsa.tissue  = job.tissue;
-    defsa.warp    = job.warp;
-    out.subjc(nm) = spm_preproc_run(defsa);
+    defsa.channel  = job.subjc(nm).channel;
+    defsa.tissue   = job.tissue;
+    defsa.warp     = job.warp;
+    defsa.warp.vox = mean(job.many_sdatas.vox);
+    defsa.warp.bb  = job.many_sdatas.bb;
+    out.subjc(nm)  = spm_preproc_run(defsa);
 
     % Move segmentation output (if requested) and update 'out' structure:
     % all *c*.nii images, deformation field (y_*.nii), parameters 

hmri_run_proc_pipeline.m

@@ -27,6 +27,9 @@
     job_US.many_sdatas.vols_pm = job.vols_pm;
 end
 job_US.many_sdatas.channel.vols = job.s_vols;
+% Set voxel sizes & BB
+job_US.many_sdatas.vox = job.vox;
+job_US.many_sdatas.bb  = job.bb;
 
 % Only spit out CSF in native space (no Dartel imported) & warped (no modulation)
 job_US.tissue(3).native = [1 0];
@@ -47,7 +50,7 @@
 %         maps
 % .def  : cell-array with the deformations for each subject.
 
-% 2/ Proceed with dartel (only of requested)
+% 2/ Proceed with dartel (only if requested)
 %-------------------------------------------
 % including template create and warping into MNI space
 
@@ -107,6 +110,9 @@
     job_Dnorm.multsdata.vols_pm = job.vols_pm;
     % get the warps
     job_Dnorm.multsdata.vols_field = out_Dwarp.files;
+    % Set voxel sizes
+    job_Dnorm.vox = job.vox;
+    job_Dnorm.bb  = job.bb;
     % get the output directory
     job_Dnorm.output = job.output;
 

tbx_scfg_hmri_proc_US.m

@@ -122,13 +122,38 @@
 many_pams.help       = {['Select whole brain parameter maps (e.g. MT, ',...
     'R2*, FA, etc.) from all subjects for processing, one type per entry.']};
 
+% ---------------------------------------------------------------------
+% vox Voxel sizes
+% ---------------------------------------------------------------------
+vox          = cfg_entry;
+vox.tag      = 'vox';
+vox.name     = 'Voxel sizes';
+vox.num      = [1 3];
+vox.strtype  = 'e';
+vox.val      = {[1 1 1]};
+vox.help     = {[...
+'Specify the voxel sizes of the deformation field and tissue classes ',...
+'to be produced. Non-finite values will default to the voxel sizes of ',...
+'the template image that was originally used to estimate the deformation.']};
+
+%--------------------------------------------------------------------------
+% bb Bounding box
+%--------------------------------------------------------------------------
+bb         = cfg_entry;
+bb.tag     = 'bb';
+bb.name    = 'Bounding box';
+bb.help    = {'The bounding box (in mm) of the volume which is to be written (relative to the anterior commissure).'};
+bb.strtype = 'r';
+bb.num     = [2 3];
+bb.def     = @(val)spm_get_defaults('normalise.write.bb', val{:});
+
 % ---------------------------------------------------------------------
 % many_sdatas Many subjects data
 % ---------------------------------------------------------------------
 many_sdatas = cfg_branch;
 many_sdatas.tag = 'many_sdatas';
 many_sdatas.name = 'Data & options';
-many_sdatas.val = {output unlimit(rstruct) many_pams};
+many_sdatas.val = {output unlimit(rstruct) many_pams vox bb};
 many_sdatas.help = {'Specify images for many subjects at once.' , ...
     ['Processing will work on 1 subject at the time, using his ',...
     'structural image(s) to estimate the segmentation and warping parameters. ', ...

tbx_scfg_hmri_proc_pipeline.m

@@ -133,6 +133,31 @@
     'Gaussian blurring kernel in mm. Three values should be entered',...
     'denoting the FWHM in the x, y and z directions.']};
 
+% ---------------------------------------------------------------------
+% vox Voxel sizes
+% ---------------------------------------------------------------------
+vox          = cfg_entry;
+vox.tag      = 'vox';
+vox.name     = 'Voxel sizes';
+vox.num      = [1 3];
+vox.strtype  = 'e';
+vox.val      = {[1 1 1]};
+vox.help     = {[...
+'Specify the voxel sizes of the deformation field and tissue classes ',...
+'to be produced. Non-finite values will default to the voxel sizes of ',...
+'the template image that was originally used to estimate the deformation.']};
+
+%--------------------------------------------------------------------------
+% bb Bounding box
+%--------------------------------------------------------------------------
+bb         = cfg_entry;
+bb.tag     = 'bb';
+bb.name    = 'Bounding box';
+bb.help    = {'The bounding box (in mm) of the volume which is to be written (relative to the anterior commissure).'};
+bb.strtype = 'r';
+bb.num     = [2 3];
+bb.def     = @(val)spm_get_defaults('normalise.write.bb', val{:});
+
 % ---------------------------------------------------------------------
 % proc_pipel Preprocess maps -> pipelines
 % ---------------------------------------------------------------------
@@ -149,7 +174,7 @@
     ['- US+Dartel+Smooth -> applies US, builds Dartel template and warps' ...
     'into MNI, then smoothes (weighted-average)']
     }'; %#ok<*NBRAK>
-proc_pipel.val  = {output vols many_pams fwhm pipe_c};
+proc_pipel.val  = {output vols many_pams vox bb fwhm pipe_c};
 proc_pipel.prog = @hmri_run_proc_pipeline;
 proc_pipel.vout = @vout_proc_pipeline;
 proc_pipel.check = @check_data;