Merge pull request #44 from khanlab/xfm-patch

added missing final transform as target rule, updated documentation

docs/getting_started/outputs.rst

@@ -41,11 +41,11 @@ ITK transforms to warp images from the ``T1w`` space to the ``unfold`` space are
 
     sub-{subject}
      └── seg_T2w
-         └── sub-{subject}_hemi-{L,R}_from-corobl_to-unfold_mode-image_xfm.nii.gz
+         └── sub-{subject}_hemi-{L,R}_from-T1w_to-unfold_mode-image_xfm.nii.gz
 
 This is an ITK transform that can transform any image that is in ``T1w`` space (can be any resolution and FOV, as long as aligned to ``T1w``), to the ``unfold`` hippocampal volume space. You can use the warp itself as a reference image, e.g.::
 
-    antsApplyTransforms -i sub-001_space-T1w_FA.nii.gz -o sub-001_hemi-L_space-unfold_FA.nii.gz -t sub-001_hemi-L_from-corobl_to-unfold_mode-image_xfm.nii.gz -r sub-001_hemi-L_from-corobl_to-unfold_mode-image_xfm.nii.gz -v
+    antsApplyTransforms -i sub-001_space-T1w_FA.nii.gz -o sub-001_hemi-L_space-unfold_FA.nii.gz -t sub-001_hemi-L_from-T1w_to-unfold_mode-image_xfm.nii.gz -r sub-001_hemi-L_from-T1w_to-unfold_mode-image_xfm.nii.gz -v
 
 
 Subfield segmentations

hippunfold/workflow/Snakefile

@@ -86,6 +86,19 @@ def get_final_coords():
 
     return coords
 
+def get_final_transforms():
+    transforms = []
+    for modality in config['modality']:
+        mod_index = get_modality_key(modality)
+        transforms = transforms + \
+            expand(bids(root='results',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi}',from_='T1w',to='unfold',mode='image'),
+                modality=modality,
+                hemi=['L','R'],
+                subject=config['input_lists'][mod_index]['subject'],
+                session=config['sessions'])
+
+    return transforms
+
 def get_final_anat():
     anat = []
     for modality in config['modality']:
@@ -129,6 +142,7 @@ rule all:
     input: 
         get_final_specs(),
         get_final_subfields(),
+        get_final_transforms(),
         get_final_coords(),
         get_final_anat(),
         get_final_qc(),