https://github.com/0rc0/neuromet_mp2rage_pypes
Pipelines for structural analysis for NeuroMet Project
Science Score: 23.0%
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○CITATION.cff file
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○Scientific vocabulary similarity
Low similarity (4.3%) to scientific vocabulary
Keywords
7-tesla
7t
freesurfer
fsl
mp2rage
mri
neuroimaging
neuroimaging-analysis
notebook
structural-analysis
Last synced: 5 months ago
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Pipelines for structural analysis for NeuroMet Project
Basic Info
Statistics
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 3
- Releases: 0
Topics
7-tesla
7t
freesurfer
fsl
mp2rage
mri
neuroimaging
neuroimaging-analysis
notebook
structural-analysis
Created over 5 years ago
· Last pushed over 3 years ago
Metadata Files
Readme
License
README.md
NeuroMET MP2RAGE pipeline
Structural preprocesing pipeline for MP2Rage
The pipeline
The T1wUNI image from the MP2Rage sequence has an optimal contrast for the brain, but its high background noise, caused by the high (7 T) magnetic field, makes it difficult to use this image as-is with various software packages. On the other hand, the T1w denoised (T1wDEN) image loses contrast with the denoising process. This pipeline processes the T1w images to achieve an image with the brain from the UNI image and the background from DEN image and thus an optimal contrast.
Usage
See Example Notebook. Only the variables in Settings section should be modified.
Owner
- Name: Andrea Dell'Orco
- Login: 0rC0
- Kind: user
- Location: Berlin
- Repositories: 55
- Profile: https://github.com/0rC0
Sharing code for neuroimaging research. Credits for profile picture: @lastknight"
GitHub Events
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Dependencies
requirements.txt
pypi
- alembic =1.4.2=py_0
- asn1crypto =1.3.0=py36_0
- async_generator =1.10=py_0
- attrs =19.3.0=py_0
- backcall =0.1.0=py36_0
- blas =1.0=mkl
- bleach =3.1.4=py_0
- blinker =1.4=py36_0
- ca-certificates =2020.1.1=0
- certifi =2020.4.5.1=py36_0
- certipy =0.1.3=py_0
- cffi =1.14.0=py36h2e261b9_0
- chardet =3.0.4=py36_1003
- ci-info =0.2.0=pyh9f0ad1d_0
- click =7.1.2=py_0
- configurable-http-proxy =4.0.1=node6_0
- cryptography =2.3.1=py36hc365091_0
- cycler =0.10.0=py36_0
- decorator =4.4.2=py_0
- defusedxml =0.6.0=py_0
- entrypoints =0.3=py36_0
- etelemetry =0.2.1=pyh9f0ad1d_0
- filelock =3.0.12=py_0
- freetype =2.9.1=h8a8886c_1
- gmp =6.1.2=h6c8ec71_1
- h5py =2.10.0=py36h7918eee_0
- hdf5 =1.10.4=hb1b8bf9_0
- html5lib =1.0.1=py_0
- icu =58.2=he6710b0_3
- idna =2.9=py_1
- importlib_metadata =1.5.0=py36_0
- intel-openmp =2020.1=217
- ipykernel =5.1.4=py36h39e3cac_0
- ipython =7.13.0=py36h5ca1d4c_0
- ipython_genutils =0.2.0=py36_0
- isodate =0.6.0=py_1
- jedi =0.17.0=py36_0
- jinja2 =2.11.2=py_0
- joblib =0.13.2=py36_0
- json5 =0.9.5=py_0
- jsonschema =3.2.0=py36_0
- jupyter_client =6.1.3=py_0
- jupyter_core =4.6.3=py36_0
- jupyterhub =1.0.0=py36_0
- jupyterlab =1.2.6=pyhf63ae98_0
- jupyterlab_server =1.1.4=py_0
- keepalive =0.5=py_1
- kiwisolver =1.2.0=py36hfd86e86_0
- ld_impl_linux-64 =2.33.1=h53a641e_7
- libcurl =7.61.1=heec0ca6_0
- libedit =3.1.20181209=hc058e9b_0
- libffi =3.2.1=hd88cf55_4
- libgcc =7.2.0=h69d50b8_2
- libgcc-ng =9.1.0=hdf63c60_0
- libgfortran-ng =7.3.0=hdf63c60_0
- libpng =1.6.37=hbc83047_0
- libsodium =1.0.16=h1bed415_0
- libssh2 =1.8.0=h9cfc8f7_4
- libstdcxx-ng =9.1.0=hdf63c60_0
- libxml2 =2.9.9=hea5a465_1
- libxslt =1.1.33=h7d1a2b0_0
- lmfit =0.9.7=py36_0
- lxml =4.5.0=py36hefd8a0e_0
- mako =1.1.3=py_0
- markupsafe =1.1.1=py36h7b6447c_0
- matplotlib-base =3.1.3=py36hef1b27d_0
- mistune =0.8.4=py36h7b6447c_0
- mkl =2020.1=217
- mkl-service =2.3.0=py36he904b0f_0
- mkl_fft =1.0.15=py36ha843d7b_0
- mkl_random =1.1.0=py36hd6b4f25_0
- nbconvert =5.6.1=py36_0
- nbformat =5.0.6=py_0
- ncurses =6.2=he6710b0_1
- networkx =2.4=py_0
- neurdflib =5.0.1=py_0
- nibabel =3.1.0=py_0
- nipype =1.5.0rc1=py36h9f0ad1d_0
- nodejs =6.11.2=h3db8ef7_0
- notebook =6.0.3=py36_0
- numpy =1.18.1=py36h4f9e942_0
- numpy-base =1.18.1=py36hde5b4d6_1
- oauthlib =3.1.0=py_0
- openssl =1.0.2u=h7b6447c_0
- packaging =20.3=py_0
- pamela =1.0.0=py_0
- pandas =1.0.3=py36h0573a6f_0
- pandoc =2.2.3.2=0
- pandocfilters =1.4.2=py36_1
- parse =1.8.4=py36_0
- parso =0.7.0=py_0
- pexpect =4.8.0=py36_0
- pickleshare =0.7.5=py36_0
- pip =20.0.2=py36_3
- prometheus_client =0.7.1=py_0
- prompt-toolkit =3.0.4=py_0
- prompt_toolkit =3.0.4=0
- prov =1.5.3=py_0
- psutil =5.7.0=py36h7b6447c_0
- ptyprocess =0.6.0=py36_0
- pycparser =2.20=py_0
- pycurl =7.43.0.2=py36hb7f436b_0
- pydicom =1.4.2=py_0
- pydotplus =2.0.2=py_1
- pygments =2.6.1=py_0
- pyjwt =1.7.1=py36_0
- pyopenssl =19.0.0=py36_0
- pyparsing =2.4.7=py_0
- pyrsistent =0.16.0=py36h7b6447c_0
- pysocks =1.7.1=py36_0
- python =3.6.5=hc3d631a_2
- python-dateutil =2.8.1=py_0
- python-editor =1.0.4=py_0
- python_abi =3.6=1_cp36m
- pytz =2020.1=py_0
- pyzmq =18.1.1=py36he6710b0_0
- rdflib =5.0.0=py36h9f0ad1d_2
- readline =7.0=h7b6447c_5
- requests =2.23.0=py36_0
- scikit-learn =0.23.1=py36h7ea95a0_0
- scipy =1.4.1=py36h0b6359f_0
- send2trash =1.5.0=py36_0
- setuptools =46.4.0=py36_0
- simplejson =3.17.0=py36h7b6447c_0
- six =1.14.0=py36_0
- sparqlwrapper =1.8.5=py36h9f0ad1d_1003
- sqlalchemy =1.3.17=py36h7b6447c_0
- sqlite =3.31.1=h62c20be_1
- suspect =0.4.3=py36hd000896_1
- terminado =0.8.3=py36_0
- testpath =0.4.4=py_0
- tk =8.6.8=hbc83047_0
- tornado =6.0.4=py36h7b6447c_1
- traitlets =4.3.3=py36_0
- traits =6.0.0=py36h14c3975_0
- urllib3 =1.25.8=py36_0
- wcwidth =0.1.9=py_0
- webencodings =0.5.1=py36_1
- wheel =0.34.2=py36_0
- xlrd =1.2.0=py_0
- xvfbwrapper =0.2.9=py36_1001
- xz =5.2.5=h7b6447c_0
- zeromq =4.3.1=he6710b0_3
- zipp =3.1.0=py_0
- zlib =1.2.11=h7b6447c_3