agramfort
commented
6 years ago this example runs on your system:
?
Closed EhsanTadayon closed 6 years ago
agramfort
commented
6 years ago this example runs on your system:
?
EhsanTadayon
commented
6 years ago Hi,
thanks. Nope. I ran my code on another machine ( macOS) and it works just fine. I updated my mayavi ( conda), reinstalled my pysurfer and changed my browser. But nothing worked on my office Macbook (macOS Sierra).
thanks
agramfort
commented
6 years ago maybe you can try to follow these instructions:
http://martinos.org/mne/stable/install_mne_python.html#get-mne-and-its-dependencies
it works well for me on a mac.
fliem
commented
6 years ago Hi,
I have the same issue with add_annotation on OSX. Interestingly, add_label is working as expected.
Here is my conda list
# packages in environment at /anaconda3/envs/py2:
#
# Name Version Build Channel
alabaster 0.7.10 py27h9dd7d6e_0
anaconda custom py27h2cfa9e9_0
anaconda-client 1.6.9 py27_0
anaconda-project 0.8.2 py27h2dc806c_0
appnope 0.1.0 py27hb466136_0
appscript 1.0.1 py27h451298e_1
apptools 4.4.0 py27_1
asn1crypto 0.24.0 py27_0
astroid 1.6.1 py27_0
astropy 2.0.3 py27h1de35cc_0
attrs 17.4.0 py27_0
babel 2.5.3 py27_0
backports 1.0 py27hb4f9756_1
backports.functools_lru_cache 1.4 py27h2aca819_1
backports.shutil_get_terminal_size 1.0.0 py27hc9115de_2
backports_abc 0.5 py27h6972548_0
beautifulsoup4 4.6.0 py27h9416283_1
bitarray 0.8.1 py27h1de35cc_1
bkcharts 0.2 py27haafc882_0
blas 1.0 mkl
blaze 0.11.3 py27hb49378a_0
bleach 2.1.2 py27_0
bokeh 0.12.13 py27h5233db4_0
boto 2.48.0 py27hacdd0fd_1
bottleneck 1.2.1 py27h71f98a3_0
bzip2 1.0.6 hd86a083_4
ca-certificates 2018.03.07 0
cdecimal 2.3 py27h1de35cc_3
certifi 2018.8.24 py27_1
cffi 1.11.4 py27h342bebf_0
chardet 3.0.4 py27h2842e91_1
click 6.7 py27h2b86a94_0
cloudpickle 0.5.2 py27_1
clyent 1.2.2 py27hc0ae608_0
colorama 0.3.9 py27hbbe92b6_0
configobj 5.0.6 py27_1
configparser 3.5.0 py27hc7edf1b_0
contextlib2 0.5.5 py27h9cb85f4_0
cryptography 2.1.4 py27hdbc5e8f_0
curl 7.58.0 ha441bb4_0
cycler 0.10.0 py27hfc73c78_0
cython 0.27.3 py27h6429b90_0
cytoolz 0.9.0 py27h1de35cc_0
dask 0.16.1 py27_0
dask-core 0.16.1 py27_0
datashape 0.5.4 py27hd6a1745_0
dbus 1.12.2 h5243cc1_1
decorator 4.2.1 py27_0
distributed 1.20.2 py27_0
docutils 0.14 py27h0befae3_0
entrypoints 0.2.3 py27hd680fb1_2
enum34 1.1.6 py27hf475452_1
envisage 4.7.0 py27_0
et_xmlfile 1.0.1 py27hc42f929_0
expat 2.2.5 hb8e80ba_0
fastcache 1.0.2 py27h1de35cc_2
filelock 2.0.13 py27h2c227fa_0
flask 0.12.2 py27h3ac5568_0
flask-cors 3.0.3 py27h13db576_0
freetype 2.8 h12048fb_1
funcsigs 1.0.2 py27hb9f6266_0
functools32 3.2.3.2 py27h8ceab06_1
future 0.16.0 py27_2
futures 3.2.0 py27h1b80678_0
get_terminal_size 1.0.0 h7520d66_0
gettext 0.19.8.1 h15daf44_3
gevent 1.2.2 py27hc02608c_0
glib 2.53.6 h33f6a65_2
glob2 0.6 py27h55c9705_0
gmp 6.1.2 hb37e062_1
gmpy2 2.0.8 py27h4bc979a_2
greenlet 0.4.12 py27h081ed54_0
grin 1.2.1 py27_4
h5py 2.7.1 py27h75626f5_0
hdf5 1.10.1 ha036c08_1
heapdict 1.0.0 py27_2
html5lib 1.0.1 py27h5233db4_0
icu 58.2 h4b95b61_1
idna 2.6 py27hedea723_1
imageio 2.2.0 py27h37746d9_0
imagesize 0.7.1 py27h4f7bcc8_0
intel-openmp 2018.0.0 h8158457_8
ipaddress 1.0.19 py27_0
ipykernel 4.8.0 py27_0
ipython 5.4.1 py27_2
ipython_genutils 0.2.0 py27h8b9a179_0
ipywidgets 7.1.1 py27_0
isort 4.2.15 py27h5bf637f_0
itsdangerous 0.24 py27h3948ded_1
jbig 2.1 h4d881f8_0
jdcal 1.3 py27hfeaf94f_0
jedi 0.11.1 py27_0
jinja2 2.10 py27h70b8dc5_0
jpeg 9b he5867d9_2
jsoncpp 1.8.3 ha5298f7_0
jsonschema 2.6.0 py27hd9b497e_0
jupyter 1.0.0 py27_4
jupyter_client 5.2.2 py27_0
jupyter_console 5.2.0 py27h9702a86_1
jupyter_core 4.4.0 py27h5ea6ba4_0
jupyterlab 0.31.5 py27_0
jupyterlab_launcher 0.10.2 py27_0
lazy-object-proxy 1.3.1 py27h712ce3f_0
libcurl 7.58.0 hf30b1f0_0
libcxx 4.0.1 h579ed51_0
libcxxabi 4.0.1 hebd6815_0
libedit 3.1 hb4e282d_0
libffi 3.2.1 h475c297_4
libgfortran 3.0.1 h93005f0_2
libiconv 1.15 hdd342a3_7
libpng 1.6.34 he12f830_0
libsodium 1.0.15 hd9e47c5_0
libssh2 1.8.0 h322a93b_4
libtiff 4.0.9 h0dac147_0
libxml2 2.9.7 hab757c2_0
libxslt 1.1.32 hb819dd2_0
llvmlite 0.21.0 py27hac8ee23_0
locket 0.2.0 py27ha10513d_1
lxml 4.1.1 py27hef8c89e_1
lzo 2.10 h362108e_2
markupsafe 1.0 py27hd3c86fa_1
matplotlib 2.1.2 py27h6d6146d_0
mayavi 4.5.0 py27_0
mccabe 0.6.1 py27h1f69e8d_0
mistune 0.8.3 py27_0
mkl 2018.0.1 hfbd8650_4
mkl-service 1.1.2 py27hcba3029_4
mpc 1.0.3 h7a72875_5
mpfr 3.1.5 h711e7fd_2
mpmath 1.0.0 py27h6b0eff6_2
msgpack-python 0.5.1 py27h04f5b5a_0
multipledispatch 0.4.9 py27h10993aa_0
nbconvert 5.3.1 py27h6455e4c_0
nbformat 4.4.0 py27hddc86d0_0
ncurses 6.0 hd04f020_2
networkx 2.1 py27_0
nibabel 2.3.0 <pip>
nltk 3.2.5 py27h2e86947_0
nose 1.3.7 py27h2ee3cb8_2
notebook 5.4.0 py27_0
numba 0.36.2 np114py27he3a832a_0
numexpr 2.6.4 py27hf375000_0
numpy 1.14.0 py27h8a80b8c_1
numpydoc 0.7.0 py27h022f19e_0
odo 0.5.1 py27h992a9f7_0
olefile 0.45.1 py27_0
openpyxl 2.4.10 py27_0
openssl 1.0.2p h1de35cc_0
packaging 16.8 py27h24b219a_0
pandas 0.22.0 py27h0a44026_0
pandoc 1.19.2.1 ha5e8f32_1
pandocfilters 1.4.2 py27hed78c4e_1
parso 0.1.1 py27he57c4c6_0
partd 0.3.8 py27h7560dbf_0
path.py 10.5 py27h0d68f8b_0
pathlib2 2.3.0 py27he09da1e_0
patsy 0.5.0 py27_0
pcre 8.41 hfb6ab37_1
pep8 1.7.1 py27_0
pexpect 4.3.1 py27_0
pickleshare 0.7.4 py27h37e3d41_0
pillow 5.0.0 py27hfcce615_0
pip 9.0.1 py27h1567d89_4
pkginfo 1.4.1 py27ha9221e7_0
pluggy 0.6.0 py27had36429_0
ply 3.10 py27h6279b8a_0
prompt_toolkit 1.0.15 py27h4a7b9c2_0
psutil 5.4.3 py27h1de35cc_0
ptyprocess 0.5.2 py27h70f6364_0
py 1.5.2 py27he6783ac_0
pyaudio 0.2.7 py27h3777516_1
pycodestyle 2.3.1 py27h5b634e0_0
pycosat 0.6.3 py27h6c51c7e_0
pycparser 2.18 py27h0d28d88_1
pycrypto 2.6.1 py27h1de35cc_7
pycurl 7.43.0.1 py27hdbc3d79_0
pyface 6.0.0 py27_0
pyflakes 1.6.0 py27h4446e76_0
pygments 2.2.0 py27h1a556bb_0
pylint 1.8.2 py27_0
pyodbc 4.0.22 py27h0a44026_0
pyopenssl 17.5.0 py27hfda213f_0
pyparsing 2.2.0 py27h5bb6aaf_0
pyqt 4.11.4 py27_4
pysocks 1.6.7 py27h1cff6a6_1
pysurfer 0.8.0 <pip>
pytables 3.4.2 py27ha4551b8_2
pytest 3.3.2 py27_0
python 2.7.14 hde5916a_29
python-dateutil 2.6.1 py27hd56c96b_1
python.app 2 py27hf2d5e94_7
pytz 2017.3 py27h803c07a_0
pywavelets 0.5.2 py27hd99e88a_0
pyyaml 3.12 py27ha7932d0_1
pyzmq 16.0.3 py27h91ccc67_0
qt 4.8.7 4
qtawesome 0.4.4 py27hdeb2f59_0
qtconsole 4.3.1 py27hdc90b4f_0
qtpy 1.3.1 py27h39159f8_0
readline 7.0 hc1231fa_4
requests 2.18.4 py27h9b2b37c_1
rope 0.10.7 py27hffa1879_0
ruamel_yaml 0.15.35 py27h1de35cc_1
scandir 1.6 py27h97aa1ee_0
scikit-image 0.13.1 py27h1de35cc_1
scikit-learn 0.19.1 py27h9788993_0
scipy 1.0.0 py27h793f721_0
seaborn 0.8.1 py27h6bd0ddc_0
send2trash 1.4.2 py27_0
setuptools 38.4.0 py27_0
simplegeneric 0.8.1 py27_2
singledispatch 3.4.0.3 py27he22c18d_0
sip 4.18 py27_0
six 1.11.0 py27h7252ba3_1
snowballstemmer 1.2.1 py27h68ac032_0
sortedcollections 0.5.3 py27h8094be4_0
sortedcontainers 1.5.9 py27_0
sphinx 1.6.6 py27_0
sphinxcontrib 1.0 py27hd2ed746_1
sphinxcontrib-websupport 1.0.1 py27h857890b_1
spyder 3.2.6 py27_0
sqlalchemy 1.2.1 py27h1de35cc_0
sqlite 3.22.0 h3efe00b_0
ssl_match_hostname 3.5.0.1 py27h8780752_2
statsmodels 0.8.0 py27h6d68dbf_0
subprocess32 3.2.7 py27h24b2887_0
sympy 1.1.1 py27hce55102_0
tbb 2018.0.5 h04f5b5a_0
tblib 1.3.2 py27ha684fc4_0
terminado 0.8.1 py27_1
testpath 0.3.1 py27h72d81a5_0
tk 8.6.7 h35a86e2_3
toolz 0.9.0 py27_0
tornado 4.5.3 py27_0
traitlets 4.3.2 py27hcf08151_0
traits 4.6.0 py27h1de35cc_3
traitsui 6.0.0 py27_1
typing 3.6.2 py27h646fea0_0
unicodecsv 0.14.1 py27h170f95c_0
unixodbc 2.3.4 h4cb4dde_1
urllib3 1.22 py27hc3787e9_0
vtk 6.3.0 py27_1
wcwidth 0.1.7 py27h817c265_0
webencodings 0.5.1 py27h19a9f58_1
werkzeug 0.14.1 py27_0
wheel 0.30.0 py27h677a027_1
widgetsnbextension 3.1.0 py27_0
wrapt 1.10.11 py27hd341262_0
xlrd 1.1.0 py27hbd41ed1_1
xlsxwriter 1.0.2 py27h7f1064a_0
xlwings 0.11.5 py27_0
xlwt 1.2.0 py27hbeec4ae_0
xz 5.2.3 h0278029_2
yaml 0.1.7 hc338f04_2
zeromq 4.2.2 ha360ad0_2
zict 0.1.3 py27h5fff8b1_0
zlib 1.2.11 hf3cbc9b_2The mne environment is also not working:
File "/anaconda3/envs/mne/lib/python3.6/site-packages/surfer/viz.py", line 461, in __init__
interaction)
File "/anaconda3/envs/mne/lib/python3.6/site-packages/surfer/viz.py", line 215, in _make_viewer
figure = mlab.figure(title, size=(w, h))
File "/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/figure.py", line 64, in figure
engine = get_engine()
File "/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/engine_manager.py", line 92, in get_engine
return self.new_engine()
File "/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/engine_manager.py", line 137, in new_engine
check_backend()
File "/anaconda3/envs/mne/lib/python3.6/site-packages/mayavi/tools/engine_manager.py", line 40, in check_backend
raise ImportError(msg)
ImportError: Could not import backend for traitsui. Make sure you
have a suitable UI toolkit like PyQt/PySide or wxPython
installed.Any ideas? Thanks.
agramfort
commented
6 years ago you're using python 2.7 for which I agree it should not (yet) be broken.
in the mean time can you try to install a python 3 env as explained here:
http://martinos.org/mne/stable/install_mne_python.html#get-a-python-interpreter
fliem
commented
6 years ago Thanks for the reply. Here it says "PySurfer requires Python 2.7, and it does not work on Python 3."
The MNE env gives me an error (see bottom of previous post). Thanks.
mwaskom
commented
6 years ago Might be a breaking change in the latest nibabel
fliem
commented
6 years ago Thanks @mwaskom. That's it. Annotations display correctly with nibabel 2.2.1
mwaskom
commented
6 years ago Great, ideally we should sort out exactly what the issue is and report upstream
larsoner
commented
6 years ago With something like:
import nibabel as nib
labels, cmap, _ = nib.freesurfer.read_annot('/Users/larsoner/mne_data/MNE-sample-data/subjects/fsaverage/label/lh.aparc.annot', orig_ids=True)The third column of cmap has changed from 255 in 2.2.2 to 0 in nibabel master at least. Also the data type changed from int64 to uint32. And finally, the first entry of HCPMMP1 annot has changed from [255, 255, 255, 255, 16777215] in 2.2.2 to [255, 255, 255, 255, -1] in master.
I think this has to do with the weird format that annot files use, related to this PR:
larsoner
commented
6 years ago mwaskom
commented
6 years ago I’m confused about how someone on the west coast was able to figure this all out before I even was able to make coffee! Thanks @larsoner
larsoner
commented
6 years ago Don't worry, I'm not currently on the west coast :)
EhsanTadayon
commented
6 years ago Thanks, @larsoner. Now, It works for me as well.
Hi,
I am trying to display Freesurfer annotation using brain.add_annotation('aparc'). However, pysurfer does not display the annotation. I'm using Mac OS and qt backend. I appreciate any input on this.
thanks Ehsan.