[STORY] segment T1-weighted anatomical MRI images (Bugs to fix) #230

[arkiev]

Metadata

Epic: #17
Feature: #79
Feature Release:
Required knowledge: mid-level

Bugs to address related to [STORY] segment T1-weighted anatomical MRI images

• from fileformats.medimage import MghZip should allow to use .mgz files within a workflow (ie., just as from fileformats.medimage import NiftiGz permits use of .nii.gz. However, there seems to be an error with how .mgz files are handled, described as described below. Workaround has been to create an intermediate .nii.gz' raise FormatMismatchError( #237
  raise FormatMismatchError( fileformats.core.exceptions.FormatMismatchError: Magic number of file "1f8b0800" doesn't match expected "504B0304"
• labelconvert_.py has repeating arguments in the input_spec. Workaround solution has been to change the second lut_out to path_out (line 41 and 132).
• "output_file_template": "image_out.mif" argument is problematic - workaround solution has been to comment-out this line in the following files: labelconvert_.py and fivett2vis_.py
• mrconvert_.py several lines commented out to avoid errors (see file for details)