[REF] Support spm25 for pet-surface (aramis-lab#1609)

* Refactor reformat_surfname

* Refactor reformat_surfname 2

* Remove typo

* Modify m file

* Remove command depending on platform

* Revert m file

* Correct m file

* No spm12 hardcoding

* Modify m script for standalone

* Fix typo in m script

* Get rid of matlab setup

* Modify script lines

* Remove unnecessary spacing

Author: AliceJoubert

clinica/pipelines/pet_surface/applyInverseDeformationField.m

@@ -284,7 +284,6 @@ def _build_core_nodes(self):
                     "acq_label",
                     "csv_segmentation",
                     "suvr_reference_region",
-                    "matscript_folder_inverse_deformation",
                     "desikan_left",
                     "desikan_right",
                     "destrieux_left",
@@ -329,9 +328,6 @@ def _build_core_nodes(self):
                 "label_conversion_gtmsegmentation.csv",
             )
         )
-        full_pipe.inputs.matscript_folder_inverse_deformation = os.path.abspath(
-            os.path.dirname(os.path.realpath(__file__))
-        )
         full_pipe.inputs.is_longitudinal = self.parameters["longitudinal"]
 
         # Connection

clinica/pipelines/pet_surface/pet_surface_pipeline.py

@@ -202,8 +202,6 @@ def isclose(a, b, rel_tol=1e-9, abs_tol=0.0):
     dst_val = numpy.asarray(dst)
     dst_val = dst_val.astype("int")
 
-    reg = list(convert_lut.REGION)
-
     # Check that each label of original volume (old_label) has a matching transformation in the csv file
     for i in range(old_labels.size):
         index = numpy.argwhere(src_val == old_labels[i])
@@ -212,15 +210,12 @@ def isclose(a, b, rel_tol=1e-9, abs_tol=0.0):
             raise Exception(
                 f"Could not find label {old_labels[i]} on conversion table. Add it manually in CSV file to correct error"
             )
-        # else:
-        #     cprint(str(old_labels[i]) + " has been found on conversion table")
 
     # Instantiation of final volume, with same dtype as original volume
     new_volume = numpy.zeros(volume.shape, dtype=volume.dtype)
     # Computing the transformation
     for i in range(len(src)):
         new_volume[volume == src_val[i]] = dst_val[i]
-        # cprint("Region " + reg[i] + " transformed")
     # Get unique list of new label
     new_labels = numpy.unique(new_volume)
     new_labels = new_labels.astype("int")
@@ -235,7 +230,6 @@ def isclose(a, b, rel_tol=1e-9, abs_tol=0.0):
         current_path = os.path.abspath(current_path)
         nib.save(myNifti, current_path)
         list_of_regions.append(current_path)
-        # cprint("Label " + str(new_labels[i]) + " created in " + current_path)
         allsum = allsum + region_volume
 
     # The sum of a voxel location across the fourth dimension should be 1
@@ -248,61 +242,66 @@ def isclose(a, b, rel_tol=1e-9, abs_tol=0.0):
     return list_of_regions
 
 
-def runApplyInverseDeformationField_SPM_standalone(
-    target, deformation_field, img, matscript_folder
-):
+def runApplyInverseDeformationField_SPM_standalone(target, deformation_field, img):
     """
     This function does the exact same job as runApplyInverseDeformationField but with SPM standalone. We directly create
     a batch file that SPM standalone can run. This function does not check whether SPM standalone must be used. Previous
     check when building the pipeline ensures that all the env vars exists ($SPMSTANDALONE_HOME and $MCR_HOME)
     """
     import os
-    import platform
     import subprocess
     from os.path import abspath, basename, exists, join
+    from textwrap import dedent
+
+    from clinica.utils.check_dependency import get_spm_standalone_home
+    from clinica.utils.spm import _get_real_spm_standalone_file
 
     prefix = "subject_space_"
 
     # Write SPM batch command directly in a script that is readable by SPM standalone
     script_location = abspath("./m_script.m")
-    script_file = open(script_location, "w+")
-    script_file.write(
-        "jobs{1}.spm.util.defs.comp{1}.inv.comp{1}.def = {'"
-        + deformation_field
-        + "'};\n"
+    script_file = dedent(
+        """
+        spm('Defaults', 'fMRI');
+        spm_jobman('initcfg');
+
+        jobs{{1}}.spm.util.defs.comp{{1}}.inv.comp{{1}}.def   = {{'{deformation_field}'}};
+        jobs{{1}}.spm.util.defs.comp{{1}}.inv.space           = {{'{target}'}};
+        jobs{{1}}.spm.util.defs.out{{1}}.pull.fnames          = {{'{img}'}};
+        jobs{{1}}.spm.util.defs.out{{1}}.pull.savedir.saveusr = {{'{output_dir}'}};
+        jobs{{1}}.spm.util.defs.out{{1}}.pull.interp          = 4;
+        jobs{{1}}.spm.util.defs.out{{1}}.pull.mask            = 1;
+        jobs{{1}}.spm.util.defs.out{{1}}.pull.fwhm            = [0 0 0];
+        jobs{{1}}.spm.util.defs.out{{1}}.pull.prefix          = '{prefix}';
+
+        spm_jobman('run', jobs);
+        """
     )
-    script_file.write("jobs{1}.spm.util.defs.comp{1}.inv.space = {'" + target + "'};\n")
-    script_file.write("jobs{1}.spm.util.defs.out{1}.pull.fnames = {'" + img + "'};\n")
-    script_file.write(
-        "jobs{1}.spm.util.defs.out{1}.pull.savedir.saveusr = {'"
-        + abspath(os.getcwd())
-        + "'};\n"
+
+    script_file = script_file.format(
+        deformation_field=deformation_field,
+        target=target,
+        img=img,
+        output_dir=abspath(os.getcwd()),
+        prefix=prefix,
     )
-    script_file.write("jobs{1}.spm.util.defs.out{1}.pull.interp = 4;\n")
-    script_file.write("jobs{1}.spm.util.defs.out{1}.pull.mask = 1;\n")
-    script_file.write("jobs{1}.spm.util.defs.out{1}.pull.fwhm = [0 0 0];\n")
-    script_file.write("jobs{1}.spm.util.defs.out{1}.pull.prefix = '" + prefix + "';\n")
-    script_file.close()
-
-    # Generate command line to run
-    # SPM standalone must be run directly from its root folder
-    if platform.system() == "Darwin":
-        # Mac OS
-        cmdline = f"cd $SPMSTANDALONE_HOME && ./run_spm12.sh $MCR_HOME batch {script_location}"
-    elif platform.system() == "Linux":
-        # Linux OS
-        cmdline = f"$SPMSTANDALONE_HOME/run_spm12.sh $MCR_HOME batch {script_location}"
-    else:
-        raise SystemError("Only support Mac OS and Linux")
+
+    with open(script_location, "w", encoding="utf-8") as f:
+        f.write(script_file)
+
+    # TODO : This might not even be needed with cmd line setting done prior
+    spm_file = _get_real_spm_standalone_file(get_spm_standalone_home())
+    cmdline = f"$SPMSTANDALONE_HOME/{spm_file} $MCR_HOME batch {script_location}"
+
     subprocess_run = subprocess.run(
         cmdline,
         shell=True,
         stdout=subprocess.DEVNULL,
         stderr=subprocess.DEVNULL,
     )
-    if subprocess_run.returncode != 0:
+    if code := subprocess_run.returncode != 0:
         raise ValueError(
-            "runApplyInverseDeformationField_SPM_standalone failed, returned non-zero code"
+            f"runApplyInverseDeformationField_SPM_standalone failed, returned non-zero code with {code}"
         )
 
     output_file = join(abspath("./"), prefix + basename(img))
@@ -317,40 +316,6 @@ def runApplyInverseDeformationField_SPM_standalone(
     return output_file
 
 
-def runApplyInverseDeformationField(target, deformation_field, img, matscript_folder):
-    import os
-    import sys
-
-    from nipype.interfaces.matlab import MatlabCommand, get_matlab_command
-
-    prefix = "subject_space_"
-
-    MatlabCommand.set_default_matlab_cmd(get_matlab_command())
-    matlab = MatlabCommand()
-    if sys.platform.startswith("linux"):
-        matlab.inputs.args = "-nosoftwareopengl"
-
-    matlab.inputs.paths = matscript_folder
-    matlab.inputs.script = """
-    applyInverseDeformationField('%s', '%s', '%s', './', '%s')
-    """ % (
-        target,
-        deformation_field,
-        img,
-        prefix,
-    )
-    matlab.inputs.single_comp_thread = False
-    matlab.inputs.logfile = os.path.join("./", "matlab_output.log")
-    matlab.run()
-
-    output_file = os.path.join(os.path.abspath("./"), prefix + os.path.basename(img))
-    if not os.path.exists(output_file):
-        raise IOError(
-            f"Something went wrong, please check {os.path.abspath(matlab.inputs.logfile)} for more information"
-        )
-    return output_file
-
-
 def suvr_normalization(pet_path, mask):
     """suvr_normalization is a way of getting suvr from your pet image, based on the segmentation performed by
     gtmsegmentation. The Standard Uptake Value ratio is computed by dividing the whole PET volume by the mean value
@@ -789,16 +754,13 @@ def get_mid_surface(in_surfaces):
 
 
 def reformat_surfname(hemi, left_surface, right_surface):
-    res = None
     if hemi == "lh":
-        res = left_surface
-    elif hemi == "rh":
-        res = right_surface
-    else:
-        raise Exception(
-            "First input of this reformat_surfname function must be either lh or rh"
-        )
-    return res
+        return left_surface
+    if hemi == "rh":
+        return right_surface
+    raise ValueError(
+        f"First input of this reformat_surfname function must be either lh or rh. Here it is : {hemi}"
+    )
 
 
 def produce_tsv(pet, atlas_files):
@@ -890,7 +852,6 @@ def get_wf(
     acq_label: str,
     csv_segmentation,
     suvr_reference_region: str,
-    matscript_folder_inverse_deformation,
     destrieux_left,
     destrieux_right,
     desikan_left,
@@ -912,7 +873,6 @@ def get_wf(
         acq_label (string):
         csv_segmentation (string): Path to the CSV for the segmentation (problems encountered while using __file__)
         suvr_reference_region (string): Label of the SUVR reference region
-        matscript_folder_inverse_deformation (string): Path to the current folder containing the matlab script used to call the spm function for the inverse deformation
         destrieux_left (string):
         destrieux_right (string):
         desikan_left (string):
@@ -1037,23 +997,14 @@ def get_wf(
         name="normalize_to_MNI",
     )
 
-    if using_spm_standalone:
-        fun_apply_inverse_deformation = (
-            utils.runApplyInverseDeformationField_SPM_standalone
-        )
-    else:
-        fun_apply_inverse_deformation = utils.runApplyInverseDeformationField
     apply_inverse_deformation = pe.Node(
         niu.Function(
-            input_names=["target", "deformation_field", "img", "matscript_folder"],
+            input_names=["target", "deformation_field", "img"],
             output_names=["freesurfer_space_eroded_mask"],
-            function=fun_apply_inverse_deformation,
+            function=utils.runApplyInverseDeformationField_SPM_standalone,
         ),
         name="applyInverseDeformation",
     )
-    apply_inverse_deformation.inputs.matscript_folder = (
-        matscript_folder_inverse_deformation
-    )
 
     pons_normalization = pe.Node(
         niu.Function(
@@ -1222,7 +1173,6 @@ def get_wf(
         name="inputnode",
         mandatory_inputs=True,
     )
-
     inputnode.inputs.orig_nu = orig_nu
     inputnode.inputs.pet = pet
     inputnode.inputs.psf = pvc_psf_tsv