Merge branch 'noMatlabDep'. Adds options to run pipelines using SPM

standalone.

clinica/pipelines/fmri_preprocessing/fmri_preprocessing_pipeline.py

@@ -275,7 +275,7 @@ class fMRIPreprocessing(cpe.Pipeline):
         import nipype.interfaces.spm as spm
         import nipype.pipeline.engine as npe
         from clinica.utils.io import zip_nii, unzip_nii
-
+        
         # Zipping
         # =======
         unzip_node = npe.MapNode(name='Unzipping',

clinica/pipelines/fmri_preprocessing/fmri_preprocessing_utils.py

 """
 
-"""
 
+"""
 
 from __future__ import print_function, division, unicode_literals, absolute_import
 from nipype.utils.filemanip import (fname_presuffix, filename_to_list, list_to_filename)
@@ -11,6 +11,15 @@ import nipype.pipeline.engine as npe
 import nipype.interfaces.spm as spm
 import nipype.interfaces.fsl as fsl
 
+import os
+
+if 'SPMSTANDALONE_HOME' in os.environ:
+    if 'MCR_HOME' in os.environ:
+        matlab_cmd = os.path.join(os.environ['SPMSTANDALONE_HOME'],
+                '/run_spm12.sh') \
+                + ' ' + os.environ['MCR_HOME'] \
+                + ' script'
+        spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
 
 class RealignUnwarpInputSpec(SPMCommandInputSpec):
     scans = traits.Either(traits.List(File(exists=True)), File(exists=True),

clinica/pipelines/pet_volume/pet_volume_pipeline.py

@@ -357,6 +357,18 @@ class PETVolume(cpe.Pipeline):
         from clinica.utils.io import unzip_nii
         import clinica.pipelines.pet_volume.pet_volume_utils as utils
 
+        import os
+
+
+        if 'SPMSTANDALONE_HOME' in os.environ:
+            if 'MCR_HOME' in os.environ:
+                matlab_cmd = os.path.join(os.environ['SPMSTANDALONE_HOME'],
+                        '/run_spm12.sh') \
+                        + ' ' + os.environ['MCR_HOME'] \
+                        + ' script'
+                spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+        
+ 
         # Unzipping
         # =========
         unzip_pet_image = npe.Node(nutil.Function(input_names=['in_file'],

clinica/pipelines/t1_volume_create_dartel/t1_volume_create_dartel_pipeline.py

@@ -193,17 +193,38 @@ class T1VolumeCreateDartel(cpe.Pipeline):
         mlab.MatlabCommand.set_default_matlab_cmd(mlab_home)
         mlab.MatlabCommand.set_default_paths(spm_home)
 
-        version = spm.Info.version()
-
+        
+        if 'SPMSTANDALONE_HOME' in os.environ:
+            if 'MCR_HOME' in os.environ:
+                matlab_cmd = os.path.join(os.environ['SPMSTANDALONE_HOME'],
+                        'run_spm12.sh') \
+                        + ' ' + os.environ['MCR_HOME'] \
+                        + ' script'
+                spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+                version = spm.SPMCommand().version
+        else:
+            version = spm.Info.version()
+        
+                
         if version:
-            if version['name'] == 'SPM8':
-                print 'You are using SPM version 8. The recommended version to use with Clinica is SPM 12. ' \
-                      'Please upgrade your SPM toolbox.'
-            elif version['name'] != 'SPM12':
-                raise RuntimeError('SPM version 8 or 12 could not be found. Please upgrade your SPM toolbox.')
+            if isinstance(version, dict):
+                spm_path = version['path']
+                if version['name'] == 'SPM8':
+                    print 'You are using SPM version 8. The recommended version to use with Clinica is SPM 12. ' \
+                          'Please upgrade your SPM toolbox.'
+                    tissue_map = os.path.join(spm_path, 'toolbox/Seg/TPM.nii')
+                elif version['name'] == 'SPM12':
+                    tissue_map = os.path.join(spm_path, 'tpm/TPM.nii')
+                else:
+                    raise RuntimeError('SPM version 8 or 12 could not be found. Please upgrade your SPM toolbox.')
+            if isinstance(version, unicode):
+                if version == '12.7169':
+                    tissue_map = os.path.join(unicode(spm_home), 'spm12_mcr/spm/spm12/tpm/TPM.nii')
+                else:
+                    raise RuntimeError('SPM standalone version not supported. Please upgrade SPM standalone.')
         else:
             raise RuntimeError('SPM could not be found. Please verify your SPM_HOME environment variable.')
-
+        
         # Unzipping
         # =========
         unzip_node = npe.MapNode(nutil.Function(input_names=['in_file'],

clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_pipeline.py

@@ -241,17 +241,38 @@ class T1VolumeDartel2MNI(cpe.Pipeline):
         mlab.MatlabCommand.set_default_matlab_cmd(mlab_home)
         mlab.MatlabCommand.set_default_paths(spm_home)
 
-        version = spm.Info.version()
-
+        
+        if 'SPMSTANDALONE_HOME' in os.environ:
+            if 'MCR_HOME' in os.environ:
+                matlab_cmd = os.path.join(os.environ['SPMSTANDALONE_HOME'],
+                        'run_spm12.sh') \
+                        + ' ' + os.environ['MCR_HOME'] \
+                        + ' script'
+                spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+                version = spm.SPMCommand().version
+        else:
+            version = spm.Info.version()
+        
+                
         if version:
-            if version['name'] == 'SPM8':
-                print 'You are using SPM version 8. The recommended version to use with Clinica is SPM 12. ' \
-                      'Please upgrade your SPM toolbox.'
-            elif version['name'] != 'SPM12':
-                raise RuntimeError('SPM version 8 or 12 could not be found. Please upgrade your SPM toolbox.')
+            if isinstance(version, dict):
+                spm_path = version['path']
+                if version['name'] == 'SPM8':
+                    print 'You are using SPM version 8. The recommended version to use with Clinica is SPM 12. ' \
+                          'Please upgrade your SPM toolbox.'
+                    tissue_map = os.path.join(spm_path, 'toolbox/Seg/TPM.nii')
+                elif version['name'] == 'SPM12':
+                    tissue_map = os.path.join(spm_path, 'tpm/TPM.nii')
+                else:
+                    raise RuntimeError('SPM version 8 or 12 could not be found. Please upgrade your SPM toolbox.')
+            if isinstance(version, unicode):
+                if version == '12.7169':
+                    tissue_map = os.path.join(unicode(spm_home), 'spm12_mcr/spm/spm12/tpm/TPM.nii')
+                else:
+                    raise RuntimeError('SPM standalone version not supported. Please upgrade SPM standalone.')
         else:
             raise RuntimeError('SPM could not be found. Please verify your SPM_HOME environment variable.')
-
+        
         # Unzipping
         # =========
         unzip_tissues_node = npe.MapNode(nutil.Function(input_names=['in_file'],

clinica/pipelines/t1_volume_existing_template/t1_volume_existing_template_utils.py

@@ -21,6 +21,14 @@ __email__ = "jorge.samper-gonzalez@inria.fr"
 __status__ = "Development"
 
 
+if 'SPMSTANDALONE_HOME' in os.environ:
+    if 'MCR_HOME' in os.environ:
+        matlab_cmd = os.environ['SPMSTANDALONE_HOME'] \
+                + '/run_spm12.sh ' \
+                + os.environ['MCR_HOME'] \
+                + ' script'
+        SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+
 class DARTELExistingTemplateInputSpec(SPMCommandInputSpec):
     image_files = traits.List(traits.List(File(exists=True)),
                               desc="A list of files to be segmented",

clinica/pipelines/t1_volume_new_template/t1_volume_new_template_pipeline.py

@@ -321,22 +321,37 @@ class T1VolumeNewTemplate(cpe.Pipeline):
         mlab.MatlabCommand.set_default_matlab_cmd(mlab_home)
         mlab.MatlabCommand.set_default_paths(spm_home)
 
-        version = spm.Info.version()
-        #TODO: remove check for SPM
-
+        if 'SPMSTANDALONE_HOME' in os.environ:
+            if 'MCR_HOME' in os.environ:
+                matlab_cmd = os.path.join(os.environ['SPMSTANDALONE_HOME'],
+                        'run_spm12.sh') \
+                        + ' ' + os.environ['MCR_HOME'] \
+                        + ' script'
+                spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+                version = spm.SPMCommand().version
+        else:
+            version = spm.Info.version()
+        
+                
         if version:
-            spm_path = version['path']
-            if version['name'] == 'SPM8':
-                print 'You are using SPM version 8. The recommended version to use with Clinica is SPM 12. ' \
-                      'Please upgrade your SPM toolbox.'
-                tissue_map = op.join(spm_path, 'toolbox/Seg/TPM.nii')
-            elif version['name'] == 'SPM12':
-                tissue_map = op.join(spm_path, 'tpm/TPM.nii')
-            else:
-                raise RuntimeError('SPM version 8 or 12 could not be found. Please upgrade your SPM toolbox.')
+            if isinstance(version, dict):
+                spm_path = version['path']
+                if version['name'] == 'SPM8':
+                    print 'You are using SPM version 8. The recommended version to use with Clinica is SPM 12. ' \
+                          'Please upgrade your SPM toolbox.'
+                    tissue_map = os.path.join(spm_path, 'toolbox/Seg/TPM.nii')
+                elif version['name'] == 'SPM12':
+                    tissue_map = os.path.join(spm_path, 'tpm/TPM.nii')
+                else:
+                    raise RuntimeError('SPM version 8 or 12 could not be found. Please upgrade your SPM toolbox.')
+            if isinstance(version, unicode):
+                if version == '12.7169':
+                    tissue_map = os.path.join(unicode(spm_home), 'spm12_mcr/spm/spm12/tpm/TPM.nii')
+                else:
+                    raise RuntimeError('SPM standalone version not supported. Please upgrade SPM standalone.')
         else:
             raise RuntimeError('SPM could not be found. Please verify your SPM_HOME environment variable.')
-
+        
         # Unzipping
         # ===============================
         unzip_node = npe.MapNode(nutil.Function(input_names=['in_file'],

clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_pipeline.py

@@ -201,21 +201,36 @@ class T1VolumeTissueSegmentation(cpe.Pipeline):
         mlab.MatlabCommand.set_default_matlab_cmd(mlab_home)
         mlab.MatlabCommand.set_default_paths(spm_home)
 
-        version = spm.Info.version()
-
+        if 'SPMSTANDALONE_HOME' in os.environ:
+            if 'MCR_HOME' in os.environ:
+                matlab_cmd = os.path.join(os.environ['SPMSTANDALONE_HOME'],
+                        'run_spm12.sh') \
+                        + ' ' + os.environ['MCR_HOME'] \
+                        + ' script'
+                spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)
+                version = spm.SPMCommand().version
+        else:
+            version = spm.Info.version()
+                
         if version:
-            spm_path = version['path']
-            if version['name'] == 'SPM8':
-                print 'You are using SPM version 8. The recommended version to use with Clinica is SPM 12. ' \
-                      'Please upgrade your SPM toolbox.'
-                tissue_map = op.join(spm_path, 'toolbox/Seg/TPM.nii')
-            elif version['name'] == 'SPM12':
-                tissue_map = op.join(spm_path, 'tpm/TPM.nii')
-            else:
-                raise RuntimeError('SPM version 8 or 12 could not be found. Please upgrade your SPM toolbox.')
+            if isinstance(version, dict):
+                spm_path = version['path']
+                if version['name'] == 'SPM8':
+                    print 'You are using SPM version 8. The recommended version to use with Clinica is SPM 12. ' \
+                          'Please upgrade your SPM toolbox.'
+                    tissue_map = os.path.join(spm_path, 'toolbox/Seg/TPM.nii')
+                elif version['name'] == 'SPM12':
+                    tissue_map = os.path.join(spm_path, 'tpm/TPM.nii')
+                else:
+                    raise RuntimeError('SPM version 8 or 12 could not be found. Please upgrade your SPM toolbox.')
+            if isinstance(version, unicode):
+                if version == '12.7169':
+                    tissue_map = os.path.join(unicode(spm_home), 'spm12_mcr/spm/spm12/tpm/TPM.nii')
+                else:
+                    raise RuntimeError('SPM standalone version not supported. Please upgrade SPM standalone.')
         else:
             raise RuntimeError('SPM could not be found. Please verify your SPM_HOME environment variable.')
-
+        
         # Unzipping
         # ===============================
         unzip_node = npe.MapNode(nutil.Function(input_names=['in_file'],