Fixed bug on resampling where the EPI dimensions weren't used. Also n…

…ow download specific version of twolevel_dbm.

install.sh

@@ -44,5 +44,8 @@ csv_labels=$template_dir/DSURQE_40micron_R_mapping.csv
 python $RABIES/gen_masks.py $DSURQE_100micron_labels $csv_labels $template_dir/DSURQE_100micron
 
 # install twolevel_ants_dbm
-git clone https://github.com/CobraLab/twolevel_ants_dbm $RABIES/twolevel_ants_dbm && \
+git clone https://github.com/CoBrALab/twolevel_ants_dbm.git $RABIES/twolevel_ants_dbm
+cd twolevel_ants_dbm
+git checkout bde563f3ee017eb7f374b72e8599f2102a69c1da
+cd ..
 echo 'export PATH=$RABIES/twolevel_ants_dbm:$PATH' >> $HOME/.bashrc

rabies/preprocess_bold_pkg/resampling.py

@@ -26,9 +26,9 @@ def init_bold_preproc_trans_wf(resampling_dim, name='bold_preproc_trans_wf'):
     bold_transform.inputs.resampling_dim = resampling_dim
     bold_transform.inputs.data_type = os.environ["rabies_data_type"]
 
-    merge = pe.Node(Merge(), name='merge', mem_gb=5)
+    merge = pe.Node(Merge(), name='merge', mem_gb=3)
     merge.inputs.data_type = os.environ["rabies_data_type"]
-    merge.plugin_args = {'qsub_args': '-pe smp %s' % (str(4*int(os.environ["min_proc"]))), 'overwrite': True}
+    merge.plugin_args = {'qsub_args': '-pe smp %s' % (str(3*int(os.environ["min_proc"]))), 'overwrite': True}
 
     # Generate a new BOLD reference
     bold_reference_wf = init_bold_reference_wf()
@@ -72,9 +72,9 @@ def init_bold_commonspace_trans_wf(resampling_dim, name='bold_commonspace_trans_
     bold_transform.inputs.resampling_dim = resampling_dim
     bold_transform.inputs.data_type = os.environ["rabies_data_type"]
 
-    merge = pe.Node(Merge(), name='merge', mem_gb=5)
+    merge = pe.Node(Merge(), name='merge', mem_gb=3)
     merge.inputs.data_type = os.environ["rabies_data_type"]
-    merge.plugin_args = {'qsub_args': '-pe smp %s' % (str(4*int(os.environ["min_proc"]))), 'overwrite': True}
+    merge.plugin_args = {'qsub_args': '-pe smp %s' % (str(3*int(os.environ["min_proc"]))), 'overwrite': True}
 
     # Generate a new BOLD reference
     bold_reference_wf = init_bold_reference_wf()

rabies/preprocess_bold_pkg/utils.py

@@ -336,7 +336,13 @@ def _run_interface(self, runtime):
         import nibabel as nb
         import os
         img=nb.load(self.inputs.in_file)
-        resample_image(nb.load(self.inputs.ref_file), self.inputs.data_type, img_dim=self.inputs.resampling_dim).to_filename('resampled.nii.gz')
+
+        if not self.inputs.resampling_dim=='origin':
+            resample_image(nb.load(self.inputs.ref_file), self.inputs.data_type, img_dim=self.inputs.resampling_dim).to_filename('resampled.nii.gz')
+        else:
+            shape=img.header.get_zooms()
+            dims="%sx%sx%s" % (shape[0],shape[1],shape[2])
+            resample_image(nb.load(self.inputs.ref_file), self.inputs.data_type, img_dim=dims).to_filename('resampled.nii.gz')
 
         #tranforms is a list of transform files, set in order of call within antsApplyTransforms
         transform_string=""