Comments (8)
annapasca
commented on August 17, 2024
Output key: raw_file Template: /home/mainak/Desktop/projects/github_repos/BIDS-examples/sample_BIDS_omega/*sub-0003/ses-0001/meg/sub-0003*rest*ica.fif returned no file
I put sub-0003_task-rest_run-01_meg_raw_filt_dsamp_ica.fif in the Dropbox :)
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jasmainak
commented on August 17, 2024
hmm ... now my script is stuck. Output so far.
In [1]: %run examples/plot_02_power.py
*** main_path -> /home/mainak/Desktop/projects/github_repos/BIDS-examples/sample_BIDS_omega ***
180916-22:30:49,489 nipype.workflow INFO:
Generated workflow graph: /home/mainak/Desktop/projects/github_repos/BIDS-examples/sample_BIDS_omega/power_pipeline/graph.png (graph2use=colored, simple_form=True).
180916-22:30:49,630 nipype.workflow INFO:
Workflow power_pipeline settings: ['check', 'execution', 'logging', 'monitoring']
180916-22:30:49,687 nipype.workflow INFO:
Running in parallel.
180916-22:30:49,704 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 27.95/27.95, Free processors: 3/3.
180916-22:30:49,788 nipype.workflow INFO:
[Node] Setting-up "power_pipeline.datasource" in "/home/mainak/Desktop/projects/github_repos/BIDS-examples/sample_BIDS_omega/power_pipeline/_sess_index_ses-0001_subject_id_sub-0003/datasource".
180916-22:30:49,812 nipype.workflow INFO:
[Node] Running "datasource" ("nipype.interfaces.io.DataGrabber")
180916-22:30:49,823 nipype.workflow INFO:
[Node] Finished "power_pipeline.datasource".
180916-22:30:51,694 nipype.workflow INFO:
[Job 0] Completed (power_pipeline.datasource).
180916-22:30:51,698 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 27.95/27.95, Free processors: 3/3.
180916-22:30:51,776 nipype.workflow INFO:
[Node] Setting-up "power_pipeline.power.power" in "/home/mainak/Desktop/projects/github_repos/BIDS-examples/sample_BIDS_omega/power_pipeline/power/_sess_index_ses-0001_subject_id_sub-0003/power".
180916-22:30:51,814 nipype.workflow INFO:
[Node] Running "power" ("ephypype.interfaces.mne.power.Power")
in Power
Opening raw data file /home/mainak/Desktop/projects/github_repos/BIDS-examples/sample_BIDS_omega/sub-0003/ses-0001/meg/sub-0003_task-rest_run-01_meg_raw_filt_dsamp_ica.fif...
ephypype/power.py:18: RuntimeWarning: This filename (/home/mainak/Desktop/projects/github_repos/BIDS-examples/sample_BIDS_omega/sub-0003/ses-0001/meg/sub-0003_task-rest_run-01_meg_raw_filt_dsamp_ica.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz
epochs = read_raw_fif(data_fname, preload=True)
This filename (/home/mainak/Desktop/projects/github_repos/BIDS-examples/sample_BIDS_omega/sub-0003/ses-0001/meg/sub-0003_task-rest_run-01_meg_raw_filt_dsamp_ica.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz
Read 5 compensation matrices
Range : 0 ... 479999 = 0.000 ... 599.999 secs
Ready.
Current compensation grade : 3
Reading 0 ... 479999 = 0.000 ... 599.999 secs...
180916-22:30:53,694 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 27.75/27.95, Free processors: 2/3.
Currently running:
* power_pipeline.power.power
Effective window size : 0.320 (s)
(270, 48)
*** save /home/mainak/Desktop/projects/github_repos/BIDS-examples/sample_BIDS_omega/power_pipeline/power/_sess_index_ses-0001_subject_id_sub-0003/power/sub-0003_task-rest_run-01_meg_raw_filt_dsamp_ica-psds.npz ***from ephypype.
annapasca
commented on August 17, 2024
HI @jasmainak I have just run the power analysis and it works for me. I don't understand the problem.
@davidmeunier79 @dmalt some idea?
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annapasca
commented on August 17, 2024
(mne) pasca@pasca-XPS-13-9360:~/Tools/python/packages/neuropycon/examples$ conda list
# packages in environment at /home/pasca/anaconda3/envs/mne:
#
# Name Version Build Channel
alabaster 0.7.11 py36_0
apipkg 1.5 <pip>
appdirs 1.4.3 py36h28b3542_0
apptools 4.4.0 <pip>
asn1crypto 0.24.0 py36_0
astroid 2.0.4 py36_0
atomicwrites 1.2.1 py36_0
attrs 18.2.0 py36h28b3542_0
automat 0.7.0 py36_0
babel 2.6.0 py36_0
backcall 0.1.0 py36_0
blas 1.0 mkl
bleach 2.1.4 py36_0
ca-certificates 2018.03.07 0
certifi 2018.8.24 py36_1
cffi 1.11.5 py36he75722e_1
chardet 3.0.4 py36_1
click 6.7 <pip>
cloudpickle 0.5.5 py36_0
codespell 1.13.0 <pip>
configobj 5.0.6 <pip>
configparser 3.5.0 <pip>
constantly 15.1.0 py36h28b3542_0
coverage 4.5.1 py36h14c3975_0
cryptography 2.3.1 py36hc365091_0
cycler 0.10.0 py36_0
cython 0.28.5 py36hf484d3e_0
dbus 1.13.2 h714fa37_1
decorator 4.3.0 py36_0
dipy 0.14.0 <pip>
docutils 0.14 py36_0
entrypoints 0.2.3 py36_2
envisage 4.7.0 <pip>
ephypype 0.1.dev0 <pip>
execnet 1.5.0 <pip>
expat 2.2.6 he6710b0_0
flake8 3.5.0 py36_1
fontconfig 2.12.6 h49f89f6_0
freetype 2.8 hab7d2ae_1
funcsigs 1.0.2 <pip>
future 0.16.0 py36_0
glib 2.56.2 hd408876_0
gmp 6.1.2 h6c8ec71_1
graphpype 0.0.2 <pip>
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
h5py 2.8.0 py36h39dcb92_0
hdf5 1.8.18 h6792536_1
html5lib 1.0.1 py36_0
hyperlink 18.0.0 py36_0
icu 58.2 h9c2bf20_1
idna 2.7 py36_0
imagesize 1.1.0 py36_0
incremental 17.5.0 py36_0
intel-openmp 2018.0.3 0
ipykernel 4.9.0 py36_0
ipython 6.5.0 py36_0
ipython_genutils 0.2.0 py36_0
ipywidgets 7.4.1 py36_0
isodate 0.6.0 <pip>
isort 4.3.4 py36_0
jedi 0.12.1 py36_0
jeepney 0.3.1 py36_0
jinja2 2.10 py36_0
joblib 0.12.3 py36_0
jpeg 9b h024ee3a_2
jsoncpp 1.8.3 h3a67955_0
jsonschema 2.6.0 py36_0
jupyter 1.0.0 py36_4
jupyter_client 5.2.3 py36_0
jupyter_console 5.2.0 py36_1
jupyter_core 4.4.0 py36_0
keyring 13.2.1 py36_0
kiwisolver 1.0.1 py36hf484d3e_0
lazy-object-proxy 1.3.1 py36h14c3975_2
libedit 3.1.20170329 h6b74fdf_2
libffi 3.2.1 hd88cf55_4
libgcc-ng 8.2.0 hdf63c60_1
libgfortran-ng 7.3.0 hdf63c60_0
libpng 1.6.34 hb9fc6fc_0
libsodium 1.0.16 h1bed415_0
libstdcxx-ng 8.2.0 hdf63c60_1
libtiff 4.0.9 he85c1e1_2
libxcb 1.13 h1bed415_1
libxml2 2.9.8 h26e45fe_1
lxml 4.2.4 <pip>
markupsafe 1.0 py36h14c3975_1
matplotlib 2.2.2 py36h0e671d2_1
mayavi 4.6.2 <pip>
mccabe 0.6.1 py36_1
mistune 0.8.3 py36h14c3975_1
mkl 2018.0.3 1
mkl_fft 1.0.4 py36h4414c95_1
mkl_random 1.0.1 py36h4414c95_1
mne 0.16.2 <pip>
mock 2.0.0 <pip>
more-itertools 4.3.0 py36_0
nbconvert 5.3.1 py36_0
nbformat 4.4.0 py36_0
ncurses 6.1 hf484d3e_0
neo 0.6.1 <pip>
networkx 1.9 <pip>
nibabel 2.3.0 <pip>
nilearn 0.4.2 <pip>
nipype 1.1.2 <pip>
nitime 0.7 <pip>
notebook 5.6.0 py36_0
numexpr 2.6.8 py36hd89afb7_0
numpy 1.15.1 py36h1d66e8a_0
numpy-base 1.15.1 py36h81de0dd_0
numpydoc 0.8.0 py36_0
olefile 0.45.1 py36_0
openssl 1.0.2p h14c3975_0
packaging 17.1 py36_0
pandas 0.23.4 py36h04863e7_0
pandoc 2.2.3.2 0
pandocfilters 1.4.2 py36_1
parso 0.3.1 py36_0
patsy 0.5.0 py36_0
pbr 4.2.0 <pip>
pcre 8.42 h439df22_0
pexpect 4.6.0 py36_0
pickleshare 0.7.4 py36_0
pillow 5.1.0 py36h3deb7b8_0
pip 10.0.1 py36_0
pluggy 0.7.1 py36h28b3542_0
prometheus_client 0.3.1 py36h28b3542_0
prompt_toolkit 1.0.15 py36_0
prov 1.5.0 <pip>
psutil 5.4.7 py36h14c3975_0
ptyprocess 0.6.0 py36_0
py 1.6.0 py36_0
pyasn1 0.4.4 py36h28b3542_0
pyasn1-modules 0.2.2 py36_0
pycodestyle 2.3.1 py36hf609f19_0
pycparser 2.18 py36_1
pydocstyle 2.1.1 <pip>
pydot 1.2.4 <pip>
pydotplus 2.0.2 <pip>
pyface 6.0.0 py36_0
pyflakes 1.6.0 py36_0
pygments 2.2.0 py36_0
PyHamcrest 1.9.0 <pip>
pylint 2.1.1 py36_0
pyopenssl 18.0.0 py36_0
pyparsing 2.2.0 py36_1
pyqt 5.9.2 py36h751905a_0
PyQt5 5.11.2 <pip>
PyQt5_sip 4.19.12 <pip>
pysocks 1.6.8 py36_0
pysurfer 0.8.0 <pip>
pytest 3.7.4 py36_0
pytest-cov 2.6.0 py36_0
pytest-faulthandler 1.5.0 <pip>
pytest-forked 0.2 <pip>
pytest-sugar 0.9.1 <pip>
pytest-xdist 1.23.0 <pip>
python 3.6.6 hc3d631a_0
python-dateutil 2.7.3 py36_0
python-picard 0.3 <pip>
pytz 2018.5 py36_0
pyzmq 17.1.2 py36h14c3975_0
qt 5.9.5 h7e424d6_0
qtawesome 0.4.4 py36_0
qtconsole 4.4.1 py36_0
qtpy 1.5.0 py36_0
quantities 0.12.2 <pip>
rdflib 4.2.2 <pip>
readline 7.0 h7b6447c_5
requests 2.19.1 py36_0
rope 0.11.0 py36_0
scikit-learn 0.19.1 py36hedc7406_0
scipy 1.1.0 py36hfa4b5c9_1
secretstorage 3.1.0 py36_0
send2trash 1.5.0 py36_0
service_identity 17.0.0 py36h28b3542_0
setuptools 40.2.0 py36_0
simplegeneric 0.8.1 py36_2
simplejson 3.16.0 <pip>
sip 4.19.12 py36he6710b0_0
six 1.11.0 py36_1
snowballstemmer 1.2.1 py36_0
sphinx 1.7.8 py36_0
sphinxcontrib 1.0 py36_1
sphinxcontrib-websupport 1.1.0 py36_1
spyder 3.3.1 py36_1
spyder-kernels 0.2.6 py36_0
sqlite 3.24.0 h84994c4_0
statsmodels 0.9.0 py36h035aef0_0
tbb 2018.0.5 h6bb024c_0
termcolor 1.1.0 <pip>
terminado 0.8.1 py36_1
testpath 0.3.1 py36_0
tk 8.6.8 hbc83047_0
tornado 5.1 py36h14c3975_0
traitlets 4.3.2 py36_0
traits 4.6.0 py36h7b6447c_3
traitsui 6.0.0 py36_1
twisted 18.7.0 py36h14c3975_1
typed-ast 1.1.0 py36h14c3975_0
urllib3 1.23 py36_0
vtk 8.1.1 <pip>
vtk 8.1.0 py36h9686630_201
wcwidth 0.1.7 py36_0
webencodings 0.5.1 py36_1
wheel 0.31.1 py36_0
widgetsnbextension 3.4.1 py36_0
wrapt 1.10.11 py36h14c3975_2
xz 5.2.4 h14c3975_4
zeromq 4.2.5 hf484d3e_1
zlib 1.2.11 ha838bed_2
zope 1.0 py36_1
zope.interface 4.5.0 py36h14c3975_0
(mne) pasca@pasca-XPS-13-9360:~/Tools/python/packages/neuropycon/examples$
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annapasca
commented on August 17, 2024
this is my output
`(mne) pasca@pasca-XPS-13-9360:~/Tools/python/packages/neuropycon/examples$ python run_power_analysis.py
main_path /media/pasca/paska/meg_data/omega/sample_BIDS_omega/
*** main_path -> /media/pasca/paska/meg_data/omega/sample_BIDS_omega/ ***
180917-12:57:13,319 nipype.workflow INFO:
Workflow power_pipeline settings: ['check', 'execution', 'logging', 'monitoring']
180917-12:57:14,59 nipype.workflow INFO:
Running in parallel.
180917-12:57:14,71 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 14.00/14.00, Free processors: 3/3.
180917-12:57:14,146 nipype.workflow INFO:
[Node] Setting-up "power_pipeline.datasource" in "/media/pasca/paska/meg_data/omega/sample_BIDS_omega/power_pipeline/_sess_index_ses-0001_subject_id_sub-0003/datasource".
180917-12:57:14,151 nipype.workflow INFO:
[Node] Running "datasource" ("nipype.interfaces.io.DataGrabber")
180917-12:57:14,165 nipype.workflow INFO:
[Node] Finished "power_pipeline.datasource".
180917-12:57:16,69 nipype.workflow INFO:
[Job 0] Completed (power_pipeline.datasource).
180917-12:57:16,72 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 14.00/14.00, Free processors: 3/3.
180917-12:57:16,117 nipype.workflow INFO:
[Node] Setting-up "power_pipeline.power.power" in "/media/pasca/paska/meg_data/omega/sample_BIDS_omega/power_pipeline/power/_sess_index_ses-0001_subject_id_sub-0003/power".
180917-12:57:16,121 nipype.workflow INFO:
[Node] Running "power" ("ephypype.interfaces.mne.power.Power")
in Power
Opening raw data file /media/pasca/paska/meg_data/omega/sample_BIDS_omega/sub-0003/ses-0001/meg/sub-0003_task-rest_run-01_meg_raw_short_filt_dsamp_ica.fif...
/home/pasca/Tools/python/packages/neuropycon/ephypype/ephypype/power.py:18: RuntimeWarning: This filename (/media/pasca/paska/meg_data/omega/sample_BIDS_omega/sub-0003/ses-0001/meg/sub-0003_task-rest_run-01_meg_raw_short_filt_dsamp_ica.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz
epochs = read_raw_fif(data_fname, preload=True)
This filename (/media/pasca/paska/meg_data/omega/sample_BIDS_omega/sub-0003/ses-0001/meg/sub-0003_task-rest_run-01_meg_raw_short_filt_dsamp_ica.fif) does not conform to MNE naming conventions. All raw files should end with raw.fif, raw_sss.fif, raw_tsss.fif, raw.fif.gz, raw_sss.fif.gz or raw_tsss.fif.gz
Read 5 compensation matrices
Range : 0 ... 144000 = 0.000 ... 180.000 secs
Ready.
Current compensation grade : 3
Reading 0 ... 144000 = 0.000 ... 180.000 secs...
Effective window size : 0.320 (s)
(270, 48)
*** save /media/pasca/paska/meg_data/omega/sample_BIDS_omega/power_pipeline/power/_sess_index_ses-0001_subject_id_sub-0003/power/sub-0003_task-rest_run-01_meg_raw_short_filt_dsamp_ica-psds.npz ***
*** save /media/pasca/paska/meg_data/omega/sample_BIDS_omega/power_pipeline/power/_sess_index_ses-0001_subject_id_sub-0003/power/sub-0003_task-rest_run-01_meg_raw_short_filt_dsamp_ica-psds.png ***
180917-12:57:17,824 nipype.workflow INFO:
[Node] Finished "power_pipeline.power.power".
180917-12:57:18,70 nipype.workflow INFO:
[Job 1] Completed (power_pipeline.power.power).
180917-12:57:18,73 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 14.00/14.00, Free processors: 3/3.
180917-12:57:18,156 nipype.workflow INFO:
[Node] Setting-up "power_pipeline.power.power_band" in "/media/pasca/paska/meg_data/omega/sample_BIDS_omega/power_pipeline/power/_sess_index_ses-0001_subject_id_sub-0003/power_band".
180917-12:57:18,165 nipype.workflow INFO:
[Node] Running "power_band" ("ephypype.nodes.power_tools.PowerBand")
the .npz file contain ['psds', 'freqs']
psds is a matrix (270, 48)
freqs contains 48 frequencies
*** frequency band [2, 4] ***
*** frequency band [5, 7] ***
*** frequency band [8, 12] ***
*** frequency band [13, 29] ***
*** frequency band [30, 59] ***
*** frequency band [60, 90] ***
(270, 6)
180917-12:57:18,215 nipype.workflow INFO:
[Node] Finished "power_pipeline.power.power_band".
180917-12:57:20,72 nipype.workflow INFO:
[Job 2] Completed (power_pipeline.power.power_band).
180917-12:57:20,75 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 14.00/14.00, Free processors: 3/3.
(mne) pasca@pasca-XPS-13-9360:~/Tools/python/packages/neuropycon/examples$
`
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jasmainak
commented on August 17, 2024
@annapasca did you try using my environment file that I provided in this comment? You can save it in an environment.yml and create an environment:
$ conda env create -f environment.ymlThen activate the environment and run the examples again ...
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jasmainak
commented on August 17, 2024
I suspect though that it's not related to the environment, just the data files. So, we should try to fix automatic dataset fetching. This is done in my pull request #30 . Let us test it and make it work ...
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jasmainak
commented on August 17, 2024
Okay I think this issue can be closed now.
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Related Issues (20)
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