Merge pull request #1976 from chrisfilo/enh/toptup_out_warp

Output warp fields and jacobian correction files in TOPUP.

Author: effigies

nipype/interfaces/fsl/epi.py

@@ -26,7 +26,7 @@
 
 from ..base import (traits, TraitedSpec, InputMultiPath, File,
                     isdefined)
-from .base import FSLCommand, FSLCommandInputSpec
+from .base import FSLCommand, FSLCommandInputSpec, Info
 
 
 class PrepareFieldmapInputSpec(FSLCommandInputSpec):
@@ -140,6 +140,13 @@ class TOPUPInputSpec(FSLCommandInputSpec):
     out_field = File(argstr='--fout=%s', hash_files=False,
                      name_source=['in_file'], name_template='%s_field',
                      desc='name of image file with field (Hz)')
+    out_warp_prefix = traits.Str("warpfield", argstr='--dfout=%s', hash_files=False,
+                                 desc='prefix for the warpfield images (in mm)',
+                                 usedefault=True)
+    out_jac_prefix = traits.Str("jac", argstr='--jacout=%s',
+                                 hash_files=False,
+                                 desc='prefix for the warpfield images',
+                                 usedefault=True)
     out_corrected = File(argstr='--iout=%s', hash_files=False,
                          name_source=['in_file'], name_template='%s_corrected',
                          desc='name of 4D image file with unwarped images')
@@ -212,6 +219,8 @@ class TOPUPOutputSpec(TraitedSpec):
     out_movpar = File(exists=True, desc='movpar.txt output file')
     out_enc_file = File(desc='encoding directions file output for applytopup')
     out_field = File(desc='name of image file with field (Hz)')
+    out_warps = traits.List(File(exists=True), desc='warpfield images')
+    out_jacs = traits.List(File(exists=True), desc='Jacobian images')
     out_corrected = File(desc='name of 4D image file with unwarped images')
     out_logfile = File(desc='name of log-file')
 
@@ -237,7 +246,8 @@ class TOPUP(FSLCommand):
     >>> topup.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE
     'topup --config=b02b0.cnf --datain=topup_encoding.txt \
 --imain=b0_b0rev.nii --out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz \
---fout=b0_b0rev_field.nii.gz --logout=b0_b0rev_topup.log'
+--fout=b0_b0rev_field.nii.gz --jacout=jac --logout=b0_b0rev_topup.log \
+--dfout=warpfield'
     >>> res = topup.run() # doctest: +SKIP
 
     """
@@ -270,6 +280,16 @@ def _list_outputs(self):
         outputs['out_movpar'] = self._gen_fname(base, suffix='_movpar',
                                                 ext='.txt', cwd=base_path)
 
+        n_vols = nb.load(self.inputs.in_file).shape[-1]
+        ext = Info.output_type_to_ext(self.inputs.output_type)
+        fmt = os.path.abspath('{prefix}_{i:02d}{ext}').format
+        outputs['out_warps'] = [
+            fmt(prefix=self.inputs.out_warp_prefix, i=i, ext=ext)
+            for i in range(1, n_vols + 1)]
+        outputs['out_jacs'] = [
+            fmt(prefix=self.inputs.out_jac_prefix, i=i, ext=ext)
+            for i in range(1, n_vols + 1)]
+
         if isdefined(self.inputs.encoding_direction):
             outputs['out_enc_file'] = self._get_encfilename()
         return outputs

nipype/interfaces/fsl/tests/test_auto_TOPUP.py

@@ -54,6 +54,14 @@ def test_TOPUP_inputs():
     name_source=['in_file'],
     name_template='%s_field',
     ),
+    out_warp_prefix=dict(argstr='--dfout=%s',
+    hash_files=False,
+    usedefault=True,
+    ),
+    out_jac_prefix=dict(argstr='--jacout=%s',
+    hash_files=False,
+    usedefault=True,
+    ),
     out_logfile=dict(argstr='--logout=%s',
     hash_files=False,
     keep_extension=True,
@@ -98,6 +106,8 @@ def test_TOPUP_outputs():
     out_fieldcoef=dict(),
     out_logfile=dict(),
     out_movpar=dict(),
+    out_warps=dict(),
+    out_jacs=dict(),
     )
     outputs = TOPUP.output_spec()