Merge branch 'expand_tree2' into 'master'

Expand trees

See merge request fsl/fslpy!104

fsl/utils/filetree/filetree.py

@@ -185,7 +185,7 @@ class FileTree(object):
         """
         return tuple(self.extract_variables(short_name, fn) for fn in self.get_all(short_name, glob_vars=glob_vars))
 
-    def get_all_trees(self, short_name: str, global_vars=()) -> Tuple["FileTree"]:
+    def get_all_trees(self, short_name: str, glob_vars=()) -> Tuple["FileTree"]:
         """
         Gets all the trees that generate the existing files matching the pattern
 
@@ -197,7 +197,7 @@ class FileTree(object):
             If glob_vars is set to 'all', all undefined variables will be used to look up matches.
         :return: sequence of FileTrees used to generate each file on disk matching the pattern of `short_name`
         """
-        return tuple(self.update(**vars) for vars in self.get_all_vars(short_name, glob_vars=global_vars))
+        return tuple(self.update(**vars) for vars in self.get_all_vars(short_name, glob_vars=glob_vars))
 
     def update(self, **variables) -> "FileTree":
         """

fsl/utils/filetree/trees/HCP_Surface.tree

@@ -17,6 +17,9 @@
 {subject}.{hemi}.sphere.reg.reg_LR.native.surf.gii (sphere_reg_LR)
 {subject}.{hemi}.sphere.MSMSulc.native.surf.gii (sphere_MSMSulc)
 {subject}.{hemi}.sphere.MSMAll.native.surf.gii (sphere_msm)
+{subject}.{hemi}.BA.32k_fs_LR.label.gii (BA_gifti)
+{subject}.{hemi}.aparc.32k_fs_LR.label.gii (aparc_gifti)
+{subject}.{hemi}.aparc.a2009s.32k_fs_LR.label.gii (aparc2009_gifti)
 {subject}.{space}.wb.spec (spec)
 {subject}.sulc.{space}.dscalar.nii (sulc_cifti)
 {subject}.thickness.{space}.dscalar.nii (thick_cifti)
@@ -24,3 +27,6 @@
 {subject}.sulc_MSMAll.{space}.dscalar.nii (sulc_msm_cifti)
 {subject}.thickness_MSMAll.{space}.dscalar.nii (thick_msm_cifti)
 {subject}.curvature_MSMAll.{space}.dscalar.nii (curv_msm_cifti)
+{subject}.BA.32k_fs_LR.dlabel.nii (BA_cifti))
+{subject}.aparc.32k_fs_LR.dlabel.nii (aparc_cifti)
+{subject}.aparc.a2009s.32k_fs_LR.dlabel.nii (aparc2009_cifti)

fsl/utils/filetree/trees/HCP_directory.tree

@@ -24,6 +24,11 @@
             NonlinearRegJacobians.nii.gz
             acpc_dc2standard.nii.gz
             standard2acpc_dc.nii.gz
+        Results
+            rfMRI_REST{run_id}_{phase_encoding}
+                Movement_RelativeRMS_mean.txt
+                rfMRI_REST{run_id}_{phase_encoding}_Atlas_MSMAll_hp2000_clean.dtseries.nii (resting_cifti)
+                rfMRI_REST{run_id}_{phase_encoding}_hp2000_clean.nii.gz (resting_nifti)
     T1w (acpc_dc)
         Diffusion
             ->Diffusion (Diffusion)