NEW FEATURE: MPM

MRC-CBU · Jul 2, 2017 · 334d46a · 334d46a
1 parent 6bda156
commit 334d46a
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Showing 5 changed files with 80 additions and 1 deletion.
diff --git a/aa_engine/aa_init.m b/aa_engine/aa_init.m
@@ -142,6 +142,16 @@
     end;
 end;
 
+% Path to VBQ
+if ~isempty(aap.directory_conventions.VBQdir)
+    addpath(aap.directory_conventions.VBQdir);
+else
+    % Check whether already in path, give warning if not
+    if isempty(which('vbq_mpr_b0_b1'))
+       aas_log(aap,false,sprintf('VBQ toolbox not found, if you need this you should add it to the matlab path manually, or set aap.directory_conventions.VBQdir'));
+    end;
+end;
+
 % Path to DCMTK
 if isfield(aap.directory_conventions,'DCMTKdir') && ~isempty(aap.directory_conventions.DCMTKdir)
     setenv('PATH',[aacache.path.bcp_shellpath ':' fullfile(aap.directory_conventions.DCMTKdir,'bin')]);
@@ -210,6 +220,14 @@
     end
 end
 
+% VBQ
+if ~isempty(aap.directory_conventions.VBQdir)
+    p_ind = cell_index(p,aap.directory_conventions.VBQdir);
+    for ip = p_ind
+        reqpath{end+1} = p{ip};
+    end
+end
+
 % clean
 reqpath=reqpath(strcmp('',reqpath)==0);
 exc = cell_index(reqpath,'.git');

diff --git a/aa_modules/aamod_MPM.m b/aa_modules/aamod_MPM.m
@@ -0,0 +1,37 @@
+function [aap,resp]=aamod_MPM(aap,task,subj)
+
+resp='';
+
+switch task
+    case 'report'
+
+    case 'doit'
+
+        mpmfns = cellstr(aas_getfiles_bystream(aap,'special_session',[subj,cell_index({aap.acq_details.special_sessions.name},'MPM')],'MPM'));
+
+        job.b1_type = '3D_EPI_v2b';
+
+        job.data_spec.subj.raw_fld.b0 = [...
+            mpmfns(cell_index(mpmfns,'serie01')),...
+            {''},...
+            mpmfns(cell_index(mpmfns,'serie02')),...
+            ];
+        job.data_spec.subj.raw_fld.b1 = mpmfns(cell_index(mpmfns,'serie03'))';
+        job.data_spec.subj.raw_mpm.MT = mpmfns(cell_index(mpmfns,'serie04'))';
+        job.data_spec.subj.raw_mpm.PD = mpmfns(cell_index(mpmfns,'serie05'))';
+        job.data_spec.subj.raw_mpm.T1 = mpmfns(cell_index(mpmfns,'serie06'))';
+
+        aas_makedir(aap,fullfile(aas_getsubjpath(aap,subj),'MPM'));
+        job.data_spec.subj.output.outdir = cellstr(fullfile(aas_getsubjpath(aap,subj),'MPM'));
+
+        out = vbq_mpr_b0_b1(job);
+
+        aap=aas_desc_outputs(aap,'subject',subj,'mt',out.MT{1});
+        aap=aas_desc_outputs(aap,'subject',subj,'pd',strrep(out.A{1},'_A.nii','_PDw.nii'));
+        aap=aas_desc_outputs(aap,'subject',subj,'r1',out.R1{1});
+        aap=aas_desc_outputs(aap,'subject',subj,'r2star',out.R2s{1});
+        aap=aas_desc_outputs(aap,'subject',subj,'t1',out.T1w{1});
+
+    case 'checkrequirements'
+
+end
diff --git a/aa_modules/aamod_MPM.xml b/aa_modules/aamod_MPM.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="utf-8"?>
+<aap>
+    <tasklist>
+        <currenttask domain='subject' desc='Calculate MP maps using VBQ toolbox' modality='X'>
+
+            <b1_type>3D_EPI_v2b</b1_type>
+
+            <inputstreams>
+                <stream>MPM</stream>
+            </inputstreams>
+
+            <outputstreams>
+                <stream isrenameable='1'>mt</stream>
+                <stream isrenameable='1'>pd</stream>
+                <stream isrenameable='1'>r1</stream>
+                <stream isrenameable='1'>r2star</stream>
+                <stream isrenameable='1'>t1</stream>
+            </outputstreams>
+
+        </currenttask>
+    </tasklist>
+</aap>
diff --git a/aa_recipes_and_parametersets/aap_parameters_defaults.xml b/aa_recipes_and_parametersets/aap_parameters_defaults.xml
@@ -52,6 +52,7 @@
         <ANTSdir desc='Path to Advanced Normalisation Tools (ANTS)' ui='dir'></ANTSdir>
         <fieldtripdir desc='Path to fieltrip toolbox' ui='dir'></fieldtripdir>
         <BrainWaveletdir desc='Path to BrainWavelet toolbox' ui='dir'></BrainWaveletdir>
+        <VBQdir desc='Path to VBQ toolbox' ui='dir'></VBQdir>
         <DCMTKdir desc='Path to DICOM Toolkit' ui='dir'></DCMTKdir>
         <FaceMaskingdir desc='Path to FaceMasking (WUSTL NRG)' ui='dir'></FaceMaskingdir>
         <allowremotecache desc='Allow local caching of files from remote server' ui='optionlist'>1</allowremotecache>

diff --git a/aa_recipes_and_parametersets/aap_parameters_defaults_CBSU.xml b/aa_recipes_and_parametersets/aap_parameters_defaults_CBSU.xml
@@ -23,7 +23,7 @@
             <protocol_t2 ui='text'>t2_spc</protocol_t2>
             <dicomfilter ui='text'>*.dcm</dicomfilter>
             <megsubjectoutputformat desc='sprintf formatting string to get subject directory from number' ui='text'>meg%02d_%04d*</megsubjectoutputformat>
-            <spmdir desc="Path(s) to SPM (>SPM12 r6470 required)" ui="dir">/imaging/local/software/spm_cbu_svn/releases/spm12_fil_r6685</spmdir>
+            <spmdir desc="Path(s) to SPM (>SPM12 r6470 required)" ui="dir">/imaging/local/software/spm_cbu_svn/releases/spm12_fil_r6906</spmdir>
 			<spmtoolsdir desc='Path(s) to SPM tools' ui='dir'>/imaging/local/software/spm_toolbox/vbm8</spmtoolsdir>
             <linuxshell desc='Linux shell used to run linux commands' ui='text'>bash</linuxshell>
             <fsldir desc='Path to fsl' ui='dir'>/imaging/local/software/fsl/latest/x86_64/fsl</fsldir>
@@ -43,6 +43,7 @@
             <ANTSdir desc='Path to Advanced Normalisation Tools (ANTS)' ui='dir'>/imaging/local/software/ANTs/v1.9</ANTSdir>
             <fieldtripdir desc='Path to fieltrip toolbox' ui='dir'></fieldtripdir>
             <BrainWaveletdir desc='Path to BrainWavelet toolbox' ui='dir'>/imaging/local/software/BrainWavelet</BrainWaveletdir>
+            <VBQdir desc='Path to VBQ toolbox' ui='dir'>/imaging/local/software/spm_toolbox/VBQ</VBQdir>
             <DCMTKdir desc='Path to DICOM Toolkit' ui='dir'>/imaging/local/software/dcmtk/v3.6.0/dcmtk</DCMTKdir>
             <FaceMaskingdir desc='Path to FaceMasking (WUSTL NRG)' ui='dir'>/imaging/local/software/FaceMasking/FaceMasking-06.30.2015</FaceMaskingdir>
             <allowremotecache desc='Allow local caching of files from remote server' ui='optionlist'>1</allowremotecache>