Anatomical Package

class nidata.anatomical.OasisVbmDataset(*args, **kwargs)[source]

Bases: nidata.core.datasets.NilearnDataset

Methods

fetch(n_subjects=None, dartel_version=True, url=None, resume=True, force=False, verbose=1)[source]
fetcher_function = 'nilearn.datasets.fetch_oasis_vbm'
nilearn_name = 'oasis1'
class nidata.anatomical.PINGDataset(*args, **kwargs)[source]

Bases: nidata.core.datasets.AuthenticatedHttpDataset

TODO: PING docstring.

Methods

PASSWD_ENV_VAR = 'PING_PASSWORD'
USERNAME_ENV_VAR = 'PING_USERNAME'
dependencies = OrderedDict([('pandas', 'pandas'), ('ping', 'git+https://github.com/guruucsd/PING')])
fetch(n_subjects=1, url=None, resume=True, force=False, verbose=1)[source]
mod = 'pandas'
nidata.anatomical.fetch_oasis_vbm(data_dir=None, n_subjects=None, dartel_version=True, url=None, resume=True, verbose=1)[source]

Atlas Package

Datasets defining cortical parcellations.

Core Package

Common functions for dataset fetching and image utilities.

Diffusion Package

exception nidata.diffusion.FetcherError[source]

Bases: exceptions.Exception

nidata.diffusion.check_md5(filename, stored_md5)[source]

Computes the md5 of filename and check if it matches with the supplied string md5

nidata.diffusion.fetch_data(files, folder)[source]

Downloads files to folder and checks their md5 checksums

Parameters:

files : dictionary

For each file in files the value should be (url, md5). The file will be downloaded from url if the file does not already exist or if the file exists but the md5 checksum does not match.

folder : str

The directory where to save the file, the directory will be created if it does not already exist.
Raises:

FetcherError

Raises if the md5 checksum of the file does not match the expected value. The downloaded file is not deleted when this error is raised.
nidata.diffusion.fetch_isbi2013_2shell()[source]

Download a 2-shell software phantom dataset

nidata.diffusion.fetch_scil_b0()[source]

Download b=0 datasets from multiple MR systems (GE, Philips, Siemens) and different magnetic fields (1.5T and 3T)

nidata.diffusion.fetch_sherbrooke_3shell()[source]

Download a 3shell HARDI dataset with 192 gradient directions

nidata.diffusion.fetch_stanford_hardi()[source]

Download a HARDI dataset with 160 gradient directions

nidata.diffusion.fetch_stanford_labels()[source]

Download reduced freesurfer aparc image from stanford web site.

nidata.diffusion.fetch_stanford_pve_maps()[source]
nidata.diffusion.fetch_stanford_t1()[source]
nidata.diffusion.fetch_syn_data()[source]

Download t1 and b0 volumes from the same session

nidata.diffusion.fetch_taiwan_ntu_dsi()[source]

Download a DSI dataset with 203 gradient directions

nidata.diffusion.read_isbi2013_2shell()[source]

Load ISBI 2013 2-shell synthetic dataset

Returns:

img : obj,

Nifti1Image

gtab : obj,

GradientTable
nidata.diffusion.read_scil_b0()[source]

Load GE 3T b0 image form the scil b0 dataset.

Returns:

img : obj,

Nifti1Image
nidata.diffusion.read_sherbrooke_3shell()[source]

Load Sherbrooke 3-shell HARDI dataset

Returns:

img : obj,

Nifti1Image

gtab : obj,

GradientTable
nidata.diffusion.read_siemens_scil_b0()[source]

Load Siemens 1.5T b0 image form the scil b0 dataset.

Returns:

img : obj,

Nifti1Image
nidata.diffusion.read_stanford_hardi()[source]

Load Stanford HARDI dataset

Returns:

img : obj,

Nifti1Image

gtab : obj,

GradientTable
nidata.diffusion.read_stanford_labels()[source]

Read stanford hardi data and label map

nidata.diffusion.read_stanford_pve_maps()[source]
nidata.diffusion.read_stanford_t1()[source]
nidata.diffusion.read_syn_data()[source]

Load t1 and b0 volumes from the same session

Returns:

t1 : obj,

Nifti1Image

b0 : obj,

Nifti1Image
nidata.diffusion.read_taiwan_ntu_dsi()[source]

Load Taiwan NTU dataset

Returns:

img : obj,

Nifti1Image

gtab : obj,

GradientTable

nidata.version module

Module contents

TODO: Module docstring for nidata