don't load the whole thing into memory

Author: Shoshana Berleant

nipype/interfaces/fsl/epi.py

@@ -354,14 +354,14 @@ class ApplyTOPUP(FSLCommand):
 
     >>> from nipype.interfaces.fsl import ApplyTOPUP
     >>> applytopup = ApplyTOPUP()
-    >>> applytopup.inputs.in_files = ["epi.nii", "epi_rev.nii"]
+    >>> applytopup.inputs.in_files = ["ds003_sub-01_mc.nii.gz", "ds003_sub-01_mc.nii.gz"]
     >>> applytopup.inputs.encoding_file = "topup_encoding.txt"
     >>> applytopup.inputs.in_topup_fieldcoef = "topup_fieldcoef.nii.gz"
     >>> applytopup.inputs.in_topup_movpar = "topup_movpar.txt"
     >>> applytopup.inputs.output_type = "NIFTI_GZ"
     >>> applytopup.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE
-    'applytopup --datain=topup_encoding.txt --imain=epi.nii,epi_rev.nii \
---inindex=1,2 --topup=topup --out=epi_corrected.nii.gz'
+    'applytopup --datain=topup_encoding.txt --imain=ds003_sub-01_mc.nii.gz,ds003_sub-01_mc.nii.gz \
+--inindex=1,2 --topup=topup --out=ds003_sub-01_mc_corrected.nii.gz'
     >>> res = applytopup.run() # doctest: +SKIP
 
     """
@@ -374,7 +374,7 @@ def _parse_inputs(self, skip=None):
             skip = []
 
         for filename in self.inputs.in_files:
-            ndims = nib.load(filename).get_data().ndim
+            ndims = nib.load(filename).header['dim'][0]
             if ndims != 4:
                 raise ValueError('Input in_files for ApplyTopUp must be 4-D. {} is {}-D.'
                                  .format(filename, ndims))