Add fetch automatically template for StatisticsVolumeCorrection pipel…

…ine if it doesn't exist (#80) * Add fetch automatically template for pipeline if it doesn't exist * Fix code style issue * Add T1_linear brief description on the cli * Fix, add import statements * Fix import statement syntax
aramis-lab · Apr 1, 2020 · 60ba3e2 · 60ba3e2
1 parent c665422
commit 60ba3e2
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Showing 2 changed files with 15 additions and 3 deletions.
diff --git a/clinica/pipelines/statistics_volume_correction/statistics_volume_correction_pipeline.py b/clinica/pipelines/statistics_volume_correction/statistics_volume_correction_pipeline.py
@@ -58,9 +58,10 @@ def build_output_node(self):
     def build_core_nodes(self):
         """Build and connect the core nodes of the pipeline."""
         import clinica.pipelines.statistics_volume_correction.statistics_volume_correction_utils as utils
+        from clinica.utils.inputs import fetch_file
         import nipype.interfaces.utility as nutil
         import nipype.pipeline.engine as npe
-        from os.path import join, abspath, pardir, dirname
+        from os.path import join, abspath, pardir, dirname, exists
         import numpy as np
 
         peak_correction_FWE = npe.Node(name='peak_correction_FWE',
@@ -91,7 +92,18 @@ def build_core_nodes(self):
                                                        output_names=['figs'],
                                                        function=utils.produce_figures))
         produce_fig_FWE_peak_correction.inputs.n_cuts = self.parameters['n_cuts']
-        produce_fig_FWE_peak_correction.inputs.template = join(dirname(abspath(__file__)), pardir, pardir, 'resources', 'mni_icbm152_t1_tal_nlin_sym_09a.nii.gz')
+
+        root = dirname(abspath(join(abspath(__file__), pardir, pardir)))
+        path_to_mask = join(root, 'resources', 'masks')
+        produce_fig_FWE_peak_correction.inputs.template = join(path_to_mask, 'mni_icbm152_t1_tal_nlin_sym_09a.nii.gz')
+
+        url = "https://aramislab.paris.inria.fr/files/data/img_t1_linear/mni_icbm152_t1_tal_nlin_sym_09c.nii"
+
+        if not(exists(produce_fig_FWE_peak_correction.inputs.template)):
+            try:
+                fetch_file(url, produce_fig_FWE_peak_correction.inputs.template)
+            except IOError as err:
+                cprint('Unable to download required template (mni_icbm152) for processing:', err)
 
         produce_fig_FDR_peak_correction = produce_fig_FWE_peak_correction.clone(name='produce_figure_FDR_peak_correction')
         produce_fig_FWE_cluster_correction = produce_fig_FWE_peak_correction.clone(name='produce_figure_FWE_cluster_correction')

diff --git a/clinica/pipelines/t1_linear/t1_linear_cli.py b/clinica/pipelines/t1_linear/t1_linear_cli.py
@@ -14,7 +14,7 @@ def define_name(self):
     def define_description(self):
         """Define a description of this pipeline.
         """
-        self._description = ('Brief description:\n'
+        self._description = ('Affine registration of T1w images to the MNI standard space:\n'
                              'http://clinica.run/doc/Pipelines/T1Linear/')
 
     def define_options(self):