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Workflows and interfaces for neuroimaging packages
https://nipype.readthedocs.org/en/latest/
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Failure on MRTrix2TrackVis with nipype 0.13 but not the older 0.12 #1802

Closed dorianps closed 7 years ago

dorianps commented 7 years ago

Summary

The same code fails if I use the developer version of nipype 0.13 but works with the older release 0.12. Sorry for not giving too much details, it's my first time using nipype and I did not keep track of everything (who would have thought that it was the nipype version).

Actual behavior

The ".trk" file produce with the new version is 1kb with nothing in it. It loads in TrackVis but has not streamlines to show.

Expected behavior

The ".trk" file should be dependent on the number of streamlines, and larger than 1kb. It should also be loadable in TrackVis.

How to replicate the behavior

tck2trk = mrt.MRTrix2TrackVis()
tck2trk.inputs.in_file = 'temp.tck'
tck2trk.inputs.image_file = 'meanb0.nii.gz'
tck2trk.inputs.out_filename = 'temp.trk'
tck2trk.run()

Platform details:

please paste the output of: python -c "import nipype; print(nipype.get_info())" This is what's working well. {'nibabel_version': '2.1.0', 'networkx_version': '1.11', 'numpy_version': '1.12.0', 'sys_platform': 'linux2', 'sys_version': '2.7.13 |Anaconda 4.3.0 (64-bit)| (default, Dec 20 2016, 23:09:15) \n[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]', 'commit_source': 'installation', 'commit_hash': u'a4d1e07', 'pkg_path': '/data/jag/dpustina/engine/anaconda/lib/python2.7/site-packages/nipype', 'sys_executable': '/data/jag/dpustina/engine/anaconda/bin/python', 'traits_version': '4.6.0', 'scipy_version': '0.18.1'}

I am trying to upload a zip file to help you replicate the error but it's not allowing it.

mgxd commented 7 years ago

Hi @dorianps, This seems weird, if you could share some data with me to replicate this I'd like to take a look

dorianps commented 7 years ago

Follow up: I have installed nipype in 3-4 computers in the last two days, and I finally realized that all packages need to be updated for the Trackvis conversion to work. That said, once everything works on nipype 0.12.1 upgrading to 0.13 brings a charset error, as below.

Files can be located here (rar file): https://www.wetransfer.com/downloads/0b7d2283bc6ce3f5e26d6774d9d3274e20170209031546/0e81ee06f00c6dca76fb3839aa98861720170209031546/b34e3b

Python 2.7.13 |Anaconda 4.3.0 (64-bit)| (default, Dec 20 2016, 23:09:15)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import nipype.interfaces.mrtrix as mrt
tck2trk = mrt.MRTrix2TrackVis()
tck2trk.inputs.in_file = 'LeftTempSingleSeed_tracks.tck'
tck2trk.inputs.image_file = 'meanb0.nii.gz'
tck2trk.inputs.out_filename = 'LeftTempSingleSeed_tracks.trk'
tck2trk.run()  >>> tck2trk = mrt.MRTrix2TrackVis()
>>> tck2trk.inputs.in_file = 'LeftTempSingleSeed_tracks.tck'
>>> tck2trk.inputs.image_file = 'meanb0.nii.gz'
>>> tck2trk.inputs.out_filename = 'LeftTempSingleSeed_tracks.trk'
>>> tck2trk.run()
170208-22:07:13,340 interface INFO:
         Reading header data...
170208-22:07:13,340 interface INFO:
         ...adding "3" to header for key "downsample_factor"
170208-22:07:13,340 interface INFO:
         ...adding "0.25" to header for key "fod_power"
170208-22:07:13,340 interface INFO:
         ...adding "0.100000001" to header for key "init_threshold"
170208-22:07:13,340 interface INFO:
         ...adding "8" to header for key "lmax"
170208-22:07:13,340 interface INFO:
         ...adding "60" to header for key "max_angle"
170208-22:07:13,340 interface INFO:
         ...adding "243.00621" to header for key "max_dist"
170208-22:07:13,340 interface INFO:
         ...adding "200000" to header for key "max_num_attempts"
170208-22:07:13,340 interface INFO:
         ...adding "2000" to header for key "max_num_tracks"
170208-22:07:13,340 interface INFO:
         ...adding "1" to header for key "max_seed_attempts"
170208-22:07:13,340 interface INFO:
         ...adding "1000" to header for key "max_trials"
170208-22:07:13,340 interface INFO:
         ...adding "iFOD2" to header for key "method"
170208-22:07:13,340 interface INFO:
         ...adding "12.1503105" to header for key "min_dist"
170208-22:07:13,340 interface INFO:
         ...adding "0.3.15-285-g68589079" to header for key "mrtrix_version"
170208-22:07:13,340 interface INFO:
         ...adding "1" to header for key "output_step_size"
170208-22:07:13,340 interface INFO:
         ...adding "0" to header for key "rk4"
170208-22:07:13,340 interface INFO:
         ...adding "4" to header for key "samples_per_step"
170208-22:07:13,340 interface INFO:
         ...adding "1" to header for key "sh_precomputed"
170208-22:07:13,340 interface INFO:
         ...adding "WMfod.mif" to header for key "source"
170208-22:07:13,340 interface INFO:
         ...adding "1" to header for key "step_size"
170208-22:07:13,340 interface INFO:
         ...adding "0" to header for key "stop_on_all_include"
170208-22:07:13,340 interface INFO:
         ...adding "0.100000001" to header for key "threshold"
170208-22:07:13,340 interface INFO:
         ...adding "1486486988.2982976437" to header for key "timestamp"
170208-22:07:13,340 interface INFO:
         ...adding "0" to header for key "unidirectional"
170208-22:07:13,340 interface INFO:
         ...adding "seed LeftTempSingleSeed.mif" to header for key "roi"
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/mnt/c/Users/dp/Desktop/localmrtrixHCP/src/nipype/nipype/interfaces/base.py", line 1085, in run
    runtime = self._run_wrapper(runtime)
  File "/mnt/c/Users/dp/Desktop/localmrtrixHCP/src/nipype/nipype/interfaces/base.py", line 1033, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/mnt/c/Users/dp/Desktop/localmrtrixHCP/src/nipype/nipype/interfaces/mrtrix/convert.py", line 190, in _run_interface
    header, streamlines = read_mrtrix_tracks(self.inputs.in_file, as_generator=True)
  File "/mnt/c/Users/dp/Desktop/localmrtrixHCP/src/nipype/nipype/interfaces/mrtrix/convert.py", line 52, in read_mrtrix_tracks
    header = read_mrtrix_header(in_file)
  File "/mnt/c/Users/dp/Desktop/localmrtrixHCP/src/nipype/nipype/interfaces/mrtrix/convert.py", line 61, in read_mrtrix_header
    for line in fileobj:
  File "/home/dp/anaconda2/lib/python2.7/codecs.py", line 314, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf8' codec can't decode byte 0xf5 in position 128: invalid start byte

Rolling back to 0.12 fixes the conversion, everything works fine again:

dp@EDITING:/mnt/c/Users/dp/Desktop/localmtrtrix$ pip uninstall nipype
Uninstalling nipype-0.13.0-g61978ad.dev:
  /home/dp/anaconda2/bin/nipypecli
  /home/dp/anaconda2/lib/python2.7/site-packages/nipype.egg-link
Proceed (y/n)? y
  Successfully uninstalled nipype-0.13.0-g61978ad.dev
dp@EDITING:/mnt/c/Users/dp/Desktop/localmtrtrix$ pip install nipype
Collecting nipype
  Using cached nipype-0.12.1-py2.py3-none-any.whl
Requirement already satisfied: mock in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: nibabel>=2.0.1 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: python-dateutil>=1.5 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: simplejson>=3.8.0 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: future>=0.15.2 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: scipy>=0.11 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: numpy>=1.6.2 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: nose>=1.2 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: networkx>=1.7 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: xvfbwrapper in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: traits>=4.3 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: prov>=1.4.0 in /home/dp/anaconda2/lib/python2.7/site-packages (from nipype)
Requirement already satisfied: funcsigs>=1; python_version < "3.3" in /home/dp/anaconda2/lib/python2.7/site-packages (from mock->nipype)
Requirement already satisfied: six>=1.9 in /home/dp/anaconda2/lib/python2.7/site-packages (from mock->nipype)
Requirement already satisfied: pbr>=0.11 in /home/dp/anaconda2/lib/python2.7/site-packages (from mock->nipype)
Requirement already satisfied: decorator>=3.4.0 in /home/dp/anaconda2/lib/python2.7/site-packages (from networkx>=1.7->nipype)
Requirement already satisfied: lxml in /home/dp/anaconda2/lib/python2.7/site-packages (from prov>=1.4.0->nipype)
Requirement already satisfied: rdflib>=4.2.1 in /home/dp/anaconda2/lib/python2.7/site-packages (from prov>=1.4.0->nipype)
Requirement already satisfied: isodate in /home/dp/anaconda2/lib/python2.7/site-packages (from rdflib>=4.2.1->prov>=1.4.0->nipype)
Requirement already satisfied: pyparsing in /home/dp/anaconda2/lib/python2.7/site-packages (from rdflib>=4.2.1->prov>=1.4.0->nipype)
Installing collected packages: nipype
Successfully installed nipype-0.12.1
dp@EDITING:/mnt/c/Users/dp/Desktop/localmtrtrix$ ^C
dp@EDITING:/mnt/c/Users/dp/Desktop/localmtrtrix$ python
Python 2.7.13 |Anaconda 4.3.0 (64-bit)| (default, Dec 20 2016, 23:09:15)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import nipype.interfaces.mrtrix as mrt
tck2trk = mrt.MRTrix2TrackVis()
tck2trk.inputs.in_file = 'LeftTempSingleSeed_tracks.tck'
tck2trk.inputs.image_file = 'meanb0.nii.gz'
tck2trk.inputs.out_filename = 'LeftTempSingleSeed_tracks.trk'
tck2trk.run()  >>> tck2trk = mrt.MRTrix2TrackVis()
>>> tck2trk.inputs.in_file = 'LeftTempSingleSeed_tracks.tck'
>>> tck2trk.inputs.image_file = 'meanb0.nii.gz'
>>> tck2trk.inputs.out_filename = 'LeftTempSingleSeed_tracks.trk'
>>> tck2trk.run()
170208-22:09:14,793 interface INFO:
         Reading header data...
170208-22:09:14,793 interface INFO:
         ...adding "3" to header for key "downsample_factor"
170208-22:09:14,793 interface INFO:
         ...adding "0.25" to header for key "fod_power"
170208-22:09:14,793 interface INFO:
         ...adding "0.100000001" to header for key "init_threshold"
170208-22:09:14,793 interface INFO:
         ...adding "8" to header for key "lmax"
170208-22:09:14,793 interface INFO:
         ...adding "60" to header for key "max_angle"
170208-22:09:14,793 interface INFO:
         ...adding "243.00621" to header for key "max_dist"
170208-22:09:14,793 interface INFO:
         ...adding "200000" to header for key "max_num_attempts"
170208-22:09:14,793 interface INFO:
         ...adding "2000" to header for key "max_num_tracks"
170208-22:09:14,793 interface INFO:
         ...adding "1" to header for key "max_seed_attempts"
170208-22:09:14,793 interface INFO:
         ...adding "1000" to header for key "max_trials"
170208-22:09:14,793 interface INFO:
         ...adding "iFOD2" to header for key "method"
170208-22:09:14,793 interface INFO:
         ...adding "12.1503105" to header for key "min_dist"
170208-22:09:14,793 interface INFO:
         ...adding "0.3.15-285-g68589079" to header for key "mrtrix_version"
170208-22:09:14,793 interface INFO:
         ...adding "1" to header for key "output_step_size"
170208-22:09:14,793 interface INFO:
         ...adding "0" to header for key "rk4"
170208-22:09:14,793 interface INFO:
         ...adding "4" to header for key "samples_per_step"
170208-22:09:14,793 interface INFO:
         ...adding "1" to header for key "sh_precomputed"
170208-22:09:14,793 interface INFO:
         ...adding "WMfod.mif" to header for key "source"
170208-22:09:14,793 interface INFO:
         ...adding "1" to header for key "step_size"
170208-22:09:14,793 interface INFO:
         ...adding "0" to header for key "stop_on_all_include"
170208-22:09:14,793 interface INFO:
         ...adding "0.100000001" to header for key "threshold"
170208-22:09:14,793 interface INFO:
         ...adding "1486486988.2982976437" to header for key "timestamp"
170208-22:09:14,793 interface INFO:
         ...adding "0" to header for key "unidirectional"
170208-22:09:14,793 interface INFO:
         ...adding "seed LeftTempSingleSeed.mif" to header for key "roi"
170208-22:09:14,793 interface INFO:
         ...adding "mask bmask.nii.gz" to header for key "roi"
170208-22:09:14,793 interface INFO:
         ...adding "mask bmask.nii.gz" to header for key "roi"
170208-22:09:14,793 interface INFO:
         ...adding "Float32LE" to header for key "datatype"
170208-22:09:14,793 interface INFO:
         ...adding ". 640" to header for key "file"
170208-22:09:14,793 interface INFO:
         ...adding "2000" to header for key "count"
170208-22:09:14,793 interface INFO:
         ...adding "2925" to header for key "total_count"
170208-22:09:14,793 interface INFO:
         Reached the end of the header!
170208-22:09:14,793 interface INFO:
         Identifying the number of points per tract...
170208-22:09:14,809 interface INFO:
         MRTrix Header:
170208-22:09:14,809 interface INFO:
         {'roi': 'mask bmask.nii.gz', 'mrtrix_version': '0.3.15-285-g68589079', 'max_dist': '243.00621', 'file': '. 640', 'threshold': '0.100000001',
'output_step_size': '1', 'max_num_attempts': '200000', 'downsample_factor': '3', 'source': 'WMfod.mif', 'step_size': '1', 'method': 'iFOD2', 'rk4': '0
', 'min_dist': '12.1503105', 'init_threshold': '0.100000001', 'timestamp': '1486486988.2982976437', 'samples_per_step': '4', 'offset': 640, 'fod_power
': '0.25', 'stop_on_all_include': '0', 'max_angle': '60', 'count': 2000, 'max_seed_attempts': '1', 'max_num_tracks': '2000', 'sh_precomputed': '1', 't
otal_count': '2925', 'max_trials': '1000', 'datatype': 'Float32LE', 'lmax': '8', 'unidirectional': '0'}
170208-22:09:14,809 interface INFO:
         Applying transformation from scanner coordinates to meanb0.nii.gz
170208-22:09:14,809 interface INFO:
         Reading tracks...
170208-22:09:14,809 interface INFO:
         1% : 20 tracks read
170208-22:09:14,809 interface INFO:
         2% : 40 tracks read
170208-22:09:14,809 interface INFO:
         3% : 60 tracks read
170208-22:09:14,809 interface INFO:
         4% : 80 tracks read
170208-22:09:14,809 interface INFO:
         5% : 100 tracks read
170208-22:09:14,824 interface INFO:
         6% : 120 tracks read
170208-22:09:14,824 interface INFO:
         7% : 140 tracks read
170208-22:09:14,824 interface INFO:
         8% : 160 tracks read
170208-22:09:14,824 interface INFO:
         9% : 180 tracks read
170208-22:09:14,824 interface INFO:
         10% : 200 tracks read
170208-22:09:14,824 interface INFO:
         11% : 220 tracks read
170208-22:09:14,824 interface INFO:
         12% : 240 tracks read
170208-22:09:14,824 interface INFO:
         13% : 260 tracks read
170208-22:09:14,824 interface INFO:
         14% : 280 tracks read
170208-22:09:14,824 interface INFO:
         15% : 300 tracks read
170208-22:09:14,824 interface INFO:
         16% : 320 tracks read
170208-22:09:14,840 interface INFO:
         17% : 340 tracks read
170208-22:09:14,840 interface INFO:
         18% : 360 tracks read
170208-22:09:14,840 interface INFO:
         19% : 380 tracks read
170208-22:09:14,840 interface INFO:
         20% : 400 tracks read
170208-22:09:14,840 interface INFO:
         21% : 420 tracks read
170208-22:09:14,840 interface INFO:
         22% : 440 tracks read
170208-22:09:14,840 interface INFO:
         23% : 460 tracks read
170208-22:09:14,840 interface INFO:
         24% : 480 tracks read
170208-22:09:14,840 interface INFO:
         25% : 500 tracks read
170208-22:09:14,840 interface INFO:
         26% : 520 tracks read
170208-22:09:14,856 interface INFO:
         27% : 540 tracks read
170208-22:09:14,856 interface INFO:
         28% : 560 tracks read
170208-22:09:14,856 interface INFO:
         28% : 580 tracks read
170208-22:09:14,856 interface INFO:
         30% : 600 tracks read
170208-22:09:14,856 interface INFO:
         31% : 620 tracks read
170208-22:09:14,856 interface INFO:
         32% : 640 tracks read
170208-22:09:14,856 interface INFO:
         33% : 660 tracks read
170208-22:09:14,856 interface INFO:
         34% : 680 tracks read
170208-22:09:14,856 interface INFO:
         35% : 700 tracks read
170208-22:09:14,856 interface INFO:
         36% : 720 tracks read
170208-22:09:14,871 interface INFO:
         37% : 740 tracks read
170208-22:09:14,871 interface INFO:
         38% : 760 tracks read
170208-22:09:14,871 interface INFO:
         39% : 780 tracks read
170208-22:09:14,871 interface INFO:
         40% : 800 tracks read
170208-22:09:14,871 interface INFO:
         41% : 820 tracks read
170208-22:09:14,871 interface INFO:
         42% : 840 tracks read
170208-22:09:14,871 interface INFO:
         43% : 860 tracks read
170208-22:09:14,871 interface INFO:
         44% : 880 tracks read
170208-22:09:14,871 interface INFO:
         45% : 900 tracks read
170208-22:09:14,871 interface INFO:
         46% : 920 tracks read
170208-22:09:14,871 interface INFO:
         47% : 940 tracks read
170208-22:09:14,887 interface INFO:
         48% : 960 tracks read
170208-22:09:14,887 interface INFO:
         49% : 980 tracks read
170208-22:09:14,887 interface INFO:
         50% : 1000 tracks read
170208-22:09:14,887 interface INFO:
         51% : 1020 tracks read
170208-22:09:14,887 interface INFO:
         52% : 1040 tracks read
170208-22:09:14,887 interface INFO:
         53% : 1060 tracks read
170208-22:09:14,887 interface INFO:
         54% : 1080 tracks read
170208-22:09:14,887 interface INFO:
         55% : 1100 tracks read
170208-22:09:14,887 interface INFO:
         56% : 1120 tracks read
170208-22:09:14,887 interface INFO:
         56% : 1140 tracks read
170208-22:09:14,887 interface INFO:
         57% : 1160 tracks read
170208-22:09:14,887 interface INFO:
         59% : 1180 tracks read
170208-22:09:14,902 interface INFO:
         60% : 1200 tracks read
170208-22:09:14,902 interface INFO:
         61% : 1220 tracks read
170208-22:09:14,902 interface INFO:
         62% : 1240 tracks read
170208-22:09:14,902 interface INFO:
         63% : 1260 tracks read
170208-22:09:14,902 interface INFO:
         64% : 1280 tracks read
170208-22:09:14,902 interface INFO:
         65% : 1300 tracks read
170208-22:09:14,902 interface INFO:
         66% : 1320 tracks read
170208-22:09:14,902 interface INFO:
         67% : 1340 tracks read
170208-22:09:14,902 interface INFO:
         68% : 1360 tracks read
170208-22:09:14,902 interface INFO:
         69% : 1380 tracks read
170208-22:09:14,918 interface INFO:
         70% : 1400 tracks read
170208-22:09:14,918 interface INFO:
         71% : 1420 tracks read
170208-22:09:14,918 interface INFO:
         72% : 1440 tracks read
170208-22:09:14,918 interface INFO:
         73% : 1460 tracks read
170208-22:09:14,918 interface INFO:
         74% : 1480 tracks read
170208-22:09:14,918 interface INFO:
         75% : 1500 tracks read
170208-22:09:14,918 interface INFO:
         76% : 1520 tracks read
170208-22:09:14,918 interface INFO:
         77% : 1540 tracks read
170208-22:09:14,918 interface INFO:
         78% : 1560 tracks read
170208-22:09:14,918 interface INFO:
         79% : 1580 tracks read
170208-22:09:14,918 interface INFO:
         80% : 1600 tracks read
170208-22:09:14,918 interface INFO:
         81% : 1620 tracks read
170208-22:09:14,934 interface INFO:
         82% : 1640 tracks read
170208-22:09:14,934 interface INFO:
         83% : 1660 tracks read
170208-22:09:14,934 interface INFO:
         84% : 1680 tracks read
170208-22:09:14,934 interface INFO:
         85% : 1700 tracks read
170208-22:09:14,934 interface INFO:
         86% : 1720 tracks read
170208-22:09:14,934 interface INFO:
         87% : 1740 tracks read
170208-22:09:14,934 interface INFO:
         88% : 1760 tracks read
170208-22:09:14,934 interface INFO:
         89% : 1780 tracks read
170208-22:09:14,934 interface INFO:
         90% : 1800 tracks read
170208-22:09:14,934 interface INFO:
         91% : 1820 tracks read
170208-22:09:14,934 interface INFO:
         92% : 1840 tracks read
170208-22:09:14,949 interface INFO:
         93% : 1860 tracks read
170208-22:09:14,949 interface INFO:
         94% : 1880 tracks read
170208-22:09:14,949 interface INFO:
         95% : 1900 tracks read
170208-22:09:14,949 interface INFO:
         96% : 1920 tracks read
170208-22:09:14,949 interface INFO:
         97% : 1940 tracks read
170208-22:09:14,949 interface INFO:
         98% : 1960 tracks read
170208-22:09:14,949 interface INFO:
         99% : 1980 tracks read
170208-22:09:14,949 interface INFO:
         100% : 2000 tracks read
170208-22:09:14,949 interface INFO:
         Saving Trackvis file as /mnt/c/Users/dp/Desktop/localmtrtrix/LeftTempSingleSeed_tracks.trk
170208-22:09:14,949 interface INFO:
         TrackVis Header:
170208-22:09:14,949 interface INFO:
         ('TRACK', [96, 96, 52], [ 2.39582992,  2.39582992,  2.5       ], [ 0.,  0.,  0.], 0, ['', '', '', '', '', '', '', '', '', ''], 0, ['', '', ''
, '', '', '', '', '', '', ''], [[ -2.38634968e+00,  -4.16538902e-02,  -2.17889369e-01,   1.19886192e+02], [ -5.98501377e-02,   2.38603210e+00,   2.170
60238e-01,  -1.19028839e+02], [ -2.04339847e-01,  -2.12408915e-01,   2.48100972e+00,  -1.34701786e+01], [  0.00000000e+00,   0.00000000e+00,   0.00000
000e+00,   1.00000000e+00]], '', 'LAS', '', [ 0.,  0.,  0.,  0.,  0.,  0.], '', '', '', '', '', '', '', 2000, 2, 1000)
<nipype.interfaces.base.InterfaceResult object at 0x7fa1eaab97d0>
mgxd commented 7 years ago

@dorianps thanks for the info - i've submitted a patch for this that ignores the problem. This seemed to have been caused from switching over to unicode encoding.

satra commented 7 years ago

@dorianps - can you verify the fix from mathias' branch?