Group analysis of resting-state fMRI with dictionary learning: DictLearningΒΆ

An example applying dictionary learning to resting-state data. This example applies it to 20 subjects of the ADHD200 datasets.

Dictionary learning is a sparsity based decomposition method for extracting spatial maps.

  • Gael Varoquaux et al.

Multi-subject dictionary learning to segment an atlas of brain spontaneous activity Information Processing in Medical Imaging, 2011, pp. 562-573, Lecture Notes in Computer Science

Pre-prints for paper is available on hal https://hal.inria.fr/inria-00588898/en/

../../_images/plot_dict_learning_resting_state_001.png

Script output:

First functional nifti image (4D) is at: /home/ubuntu/nilearn_data/adhd/data/0010042/0010042_rest_tshift_RPI_voreg_mni.nii.gz
[Example] Learning maps using CanICA model
[CanICA] Learning mask
[MultiNiftiMasker.fit] Loading data from [/home/ubuntu/nilearn_data/adhd/data/0010042/0010042_rest_tshift_RPI_voreg_mni.nii.gz, /home/ubuntu/nilearn_data/adhd/data/0010064/0010064_rest_tshift_RPI_voreg_mni.nii.gz, /home/ubuntu/nilearn_data/a
[MultiNiftiMasker.fit] Computing mask
________________________________________________________________________________
[Memory] Calling nilearn.masking.compute_multi_epi_mask...
compute_multi_epi_mask([ '/home/ubuntu/nilearn_data/adhd/data/0010042/0010042_rest_tshift_RPI_voreg_mni.nii.gz',
  '/home/ubuntu/nilearn_data/adhd/data/0010064/0010064_rest_tshift_RPI_voreg_mni.nii.gz',
  '/home/ubuntu/nilearn_data/adhd/data/0010128/0010128_rest_tshift_RPI_voreg_mni.nii.gz',
  '/home/ubuntu/nilearn_data/adhd/data/0021019/0021019_rest_tshift_RPI_voreg_mni.nii.gz',
  '/home/ubuntu/nilearn_data/adhd/data/0023008/0023008_rest_tshift_RPI_voreg_mni.nii.gz',
  '/home/ubuntu/nilearn_data/adhd/data/0023012/0023012_rest_tshift_RPI_voreg_mni.nii.gz',
  '/home/ubuntu/nilearn_data/adhd/data/0027011/0027011_rest_tshift_RPI_voreg_mni.nii.gz',
  '/home/ubuntu/nilearn_data/adhd/data/0027018/0027018_rest_tshift_RPI_voreg_mni.nii.gz',
  '/home/ubuntu/nilearn_data/adhd/data/0027034/0027034_rest_tshift_RPI_voreg_mni.nii.gz',
  '/home/ubuntu/nilearn_data/adhd/data/0027037/0027037_rest_tshift_RPI_voreg_mni.nii.gz'], target_shape=None, target_affine=None, n_jobs=1, verbose=9, memory=Memory(cachedir='nilearn_cache/joblib'))
[Memory]    0.0s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/b785208af5f14f9f91e9d4537330cafc
________________________________________compute_mean cache loaded - 0.0s, 0.0min
[Memory]    0.0s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/68ce9977a4220d4f8a70c5922748f1c8
________________________________________compute_mean cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/77fdee659db557ad9fbe9ac84a705e65
________________________________________compute_mean cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/c5856518b066b897e831140af867e2e0
________________________________________compute_mean cache loaded - 0.0s, 0.0min
[Memory]    0.2s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/94218a51e1e68bd78e038fe65a7fda2c
________________________________________compute_mean cache loaded - 0.0s, 0.0min
[Memory]    0.2s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/94b844838e6675bd02af98245e7792cc
________________________________________compute_mean cache loaded - 0.0s, 0.0min
[Memory]    0.2s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/8c3ea7072eeaf11d8785d37ccca52dfa
________________________________________compute_mean cache loaded - 0.0s, 0.0min
[Memory]    0.3s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/6e0a548f36e89657613a97883a5410a1
________________________________________compute_mean cache loaded - 0.0s, 0.0min
[Memory]    0.3s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/80e56232a939cb082324ebdd11da35d5
________________________________________compute_mean cache loaded - 0.0s, 0.0min
[Memory]    0.3s, 0.0min: Loading _compute_mean from nilearn_cache/joblib/nilearn/image/image/_compute_mean/b32f181d7a916ec25c5f9431cceb90e6
________________________________________compute_mean cache loaded - 0.0s, 0.0min
___________________________________________compute_multi_epi_mask - 0.4s, 0.0min
[MultiNiftiMasker.transform] Resampling mask
________________________________________________________________________________
[Memory] Calling nilearn.image.resampling.resample_img...
resample_img(<nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, target_shape=None, target_affine=None, copy=False, interpolation='nearest')
_____________________________________________________resample_img - 0.0s, 0.0min
[PCAMultiNiftiMasker.fit] Loading data from None
[PCAMultiNiftiMasker.transform] Resampling mask
________________________________________________________________________________
[Memory] Calling nilearn.image.resampling.resample_img...
resample_img(<nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, target_shape=None, target_affine=None, copy=False, interpolation='nearest')
_____________________________________________________resample_img - 0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd650>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0010042/0010042_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 5054.95166 , ...,  1704.839355],
       ...,
       [ 5000.154297, ...,  1614.666138]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.3s, 0.0min
______________________________________________________session_pca - 5.0s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e20d44d0>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0010064/0010064_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 3108.793213, ...,  4420.460449],
       ...,
       [ 3235.209473, ...,  4447.233398]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.3s, 0.0min
______________________________________________________session_pca - 5.0s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e20d4350>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0010128/0010128_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 5095.173828, ...,  6103.737793],
       ...,
       [ 4955.463379, ...,  5860.027344]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.3s, 0.0min
______________________________________________________session_pca - 5.0s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e20d4810>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0021019/0021019_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 4652.310547, ...,  3347.146973],
       ...,
       [ 4590.550781, ...,  3319.336426]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.3s, 0.0min
______________________________________________________session_pca - 5.1s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e20d4290>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0023008/0023008_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 2000.134766, ...,  2557.731689],
       ...,
       [ 2052.483887, ...,  2543.822754]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.1s, 0.0min
______________________________________________________session_pca - 2.1s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e20d4e50>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0023012/0023012_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 3140.754883, ...,  4101.07959 ],
       ...,
       [ 3147.880615, ...,  4082.906982]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.1s, 0.0min
______________________________________________________session_pca - 2.1s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e20d4b90>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0027011/0027011_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 3304.0625  , ...,  6856.559082],
       ...,
       [ 3356.984375, ...,  6811.176758]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.4s, 0.0min
______________________________________________________session_pca - 9.2s, 0.2min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e20d43d0>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0027018/0027018_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 4153.876953, ...,  4641.816895],
       ...,
       [ 4149.219238, ...,  4709.827637]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.4s, 0.0min
______________________________________________________session_pca - 7.8s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e20d44d0>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0027034/0027034_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 3253.797363, ...,  4891.122559],
       ...,
       [ 3312.044922, ...,  4836.447754]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.4s, 0.0min
______________________________________________________session_pca - 7.8s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e20d4350>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0027037/0027037_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
________________________________________________________________________________
[Memory] Calling nilearn.signal.clean...
clean(array([[ 3718.192139, ...,  3427.711182],
       ...,
       [ 3788.522461, ...,  3418.913086]], dtype=float32), standardize=True, detrend=True, confounds=None, low_pass=None, t_r=None, high_pass=None)
____________________________________________________________clean - 0.4s, 0.0min
______________________________________________________session_pca - 7.8s, 0.1min
________________________________________________________________________________
[Memory] Calling sklearn.utils.extmath.randomized_svd...
randomized_svd(array([[-0.001122, ..., -0.001733],
       ...,
       [-0.002737, ..., -0.000659]]), random_state=0, n_components=10)
___________________________________________________randomized_svd - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling sklearn.decomposition.fastica_.fastica...
fastica(array([[-0.002683, ..., -0.000251],
       ...,
       [-0.003684, ..., -0.007944]]), fun='cube', random_state=209652396, whiten=True)
_________________________________________________________fastica - 21.2s, 0.4min
[Example] Dumping results
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([[-0., ..., -0.],
       ...,
       [-0., ..., -0.]]), <nibabel.nifti1.Nifti1Image object at 0x2ac4e0ebd3d0>)
___________________________________________________________unmask - 0.0s, 0.0min
[Example] Learning maps using DictLearning model
[MultiNiftiMasker.fit] Loading data from [/home/ubuntu/nilearn_data/adhd/data/0010042/0010042_rest_tshift_RPI_voreg_mni.nii.gz, /home/ubuntu/nilearn_data/adhd/data/0010064/0010064_rest_tshift_RPI_voreg_mni.nii.gz, /home/ubuntu/nilearn_data/a
[MultiNiftiMasker.fit] Computing mask
[Memory]    0.0s, 0.0min: Loading compute_multi_epi_mask from nilearn_cache/joblib/nilearn/masking/compute_multi_epi_mask/f7f5b9486f842a07eb5111b4c80af701
______________________________compute_multi_epi_mask cache loaded - 0.0s, 0.0min
[MultiNiftiMasker.transform] Resampling mask
[Memory]    0.0s, 0.0min: Loading resample_img from nilearn_cache/joblib/nilearn/image/resampling/resample_img/371845ea4f4318a8a934fb20f64517a9
________________________________________resample_img cache loaded - 0.0s, 0.0min
[DictLearning] Loading data
[PCAMultiNiftiMasker.fit] Loading data from None
[PCAMultiNiftiMasker.transform] Resampling mask
[Memory]    0.0s, 0.0min: Loading resample_img from nilearn_cache/joblib/nilearn/image/resampling/resample_img/6bf62dc8e259f962f805794bacf4e43f
________________________________________resample_img cache loaded - 0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230fe90>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0010042/0010042_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]    4.3s, 0.1min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/467a4dc2e4ee96da05d60a7555aa08a0
_______________________________________________clean cache loaded - 0.0s, 0.0min
______________________________________________________session_pca - 5.3s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230f090>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0010064/0010064_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]    9.6s, 0.2min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/b5962aa6f03c7f8e72a58e0e795769e0
_______________________________________________clean cache loaded - 0.0s, 0.0min
______________________________________________________session_pca - 4.8s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230ff10>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0010128/0010128_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]   14.4s, 0.2min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/b7aef7723245655b911aff46c00c8e90
_______________________________________________clean cache loaded - 0.0s, 0.0min
_____________________________________________________session_pca - 10.7s, 0.2min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230ff90>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0021019/0021019_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]   25.2s, 0.4min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/ff91ee44e25d342d4abd4eabb1f74bc6
_______________________________________________clean cache loaded - 0.0s, 0.0min
______________________________________________________session_pca - 4.8s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230fb90>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0023008/0023008_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]   27.2s, 0.5min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/06379d2f5ce92c942058187bf0a9282a
_______________________________________________clean cache loaded - 0.0s, 0.0min
______________________________________________________session_pca - 1.9s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230ff10>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0023012/0023012_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]   29.1s, 0.5min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/7188f11650134185e5bd18e4c806ae19
_______________________________________________clean cache loaded - 0.0s, 0.0min
______________________________________________________session_pca - 1.9s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230fc50>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0027011/0027011_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]   36.5s, 0.6min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/6eafce7dfb26245b1301fbff28174877
_______________________________________________clean cache loaded - 0.0s, 0.0min
______________________________________________________session_pca - 7.8s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230f150>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0027018/0027018_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]   45.5s, 0.8min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/a7b6618686f4ce1911c47f28bcf0b64f
_______________________________________________clean cache loaded - 0.0s, 0.0min
______________________________________________________session_pca - 8.8s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230ff10>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0027034/0027034_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]   52.9s, 0.9min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/4644caaaf857c1cc60465b90d0512af5
_______________________________________________clean cache loaded - 0.0s, 0.0min
______________________________________________________session_pca - 7.5s, 0.1min
________________________________________________________________________________
[Memory] Calling nilearn.decomposition._base.session_pca...
session_pca(<nibabel.nifti1.Nifti1Image object at 0x2ac4e230fc50>, <nibabel.nifti1.Nifti1Image object at 0x2ac4e2060790>, verbose=10, parameters={'detrend': True,
'high_pass': None,
'low_pass': None,
'smoothing_fwhm': 6.0,
'standardize': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=None, memory_level=2, random_state=0, n_components=10, memory=Memory(cachedir='nilearn_cache/joblib'), copy=True)
[PCAMultiNiftiMasker.transform_imgs] Resampling
[PCAMultiNiftiMasker.transform_imgs] Loading data from Nifti1Image('/home/ubuntu/nilearn_data/adhd/data/0027037/0027037_rest_tshift_RPI_voreg_mni.nii.gz')
[PCAMultiNiftiMasker.transform_imgs] Masking and smoothing
[PCAMultiNiftiMasker.transform_imgs] Cleaning signal
[Memory]   60.2s, 1.0min: Loading clean from nilearn_cache/joblib/nilearn/signal/clean/71bacd5b0d41303c3655eb3fd031821d
_______________________________________________clean cache loaded - 0.0s, 0.0min
______________________________________________________session_pca - 8.2s, 0.1min
[DictLearning] Initializating dictionary
[CanICA] Learning mask
[MultiNiftiMasker.fit] Loading data from None
[MultiNiftiMasker.transform] Resampling mask
[Memory]    0.0s, 0.0min: Loading resample_img from nilearn_cache/joblib/nilearn/image/resampling/resample_img/6bf62dc8e259f962f805794bacf4e43f
________________________________________resample_img cache loaded - 0.0s, 0.0min
[PCAMultiNiftiMasker.fit] Loading data from None
[PCAMultiNiftiMasker.transform] Resampling mask
[Memory]    0.0s, 0.0min: Loading resample_img from nilearn_cache/joblib/nilearn/image/resampling/resample_img/6bf62dc8e259f962f805794bacf4e43f
________________________________________resample_img cache loaded - 0.0s, 0.0min
[Memory]    0.0s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/9fe7306aed7e40b6fb0e209b28b0644f
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.0s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/88b1ab741034da7cb8c3b9f7792eff8e
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/e20b7a776ed6c955fdbc49a2cd24c944
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/7ef79d678c69d01a63101c3e58357bc0
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/ea51856ceb234c6c34e0fcf1aff15024
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/6ddaedae4ecd0e5a75067fbc2bf4ef17
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/f90e2060601758f38b4eea7581c29450
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/73d9e69ec5e70c32d14e6ff4d7bead2c
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/6280fe6d252369b2742456f2f70abf0d
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading session_pca from nilearn_cache/joblib/nilearn/decomposition/_base/session_pca/be326fb04d8ecc25b7a286d8269a2ba7
_________________________________________session_pca cache loaded - 0.0s, 0.0min
[Memory]    0.1s, 0.0min: Loading randomized_svd from nilearn_cache/joblib/sklearn/utils/extmath/randomized_svd/96b836010b8ad63d555acdb68a365c27
______________________________________randomized_svd cache loaded - 0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling sklearn.decomposition.fastica_.fastica...
fastica(array([[-0.002683, ..., -0.000251],
       ...,
       [-0.003684, ..., -0.007944]]), fun='cube', random_state=209652396, whiten=True)
_________________________________________________________fastica - 21.2s, 0.4min
[DictLearning] Learning dictionary
________________________________________________________________________________
[Memory] Calling sklearn.decomposition.dict_learning.dict_learning_online...
dict_learning_online(array([[-1.204563, ..., -0.481738],
       ...,
       [-2.939631, ..., -0.183237]]),
10, n_iter=6500, n_jobs=1, shuffle=True, verbose=9, return_code=False, batch_size=10, dict_init=array([[-0.330532, ...,  0.504328],
       ...,
       [-0.335018, ...,  0.078819]]), random_state=0, alpha=6, method='lars')
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____________________________________________dict_learning_online - 28.6s, 0.5min
________________________________________________________________________________
[Memory] Calling sklearn.decomposition.dict_learning.sparse_encode...
sparse_encode(array([[-1.204563, ..., -0.481738],
       ...,
       [-2.939631, ..., -0.183237]]),
array([[-0.195469, ..., -0.010853],
       ...,
       [-0.238024, ..., -0.011437]]), n_jobs=1, algorithm='lasso_cd')
___________________________________________________sparse_encode - 49.1s, 0.8min
[Example] Dumping results
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([[-0., ..., -0.],
       ...,
       [-0., ..., -0.]]), <nibabel.nifti1.Nifti1Image object at 0x2ac4d6dc8d10>)
___________________________________________________________unmask - 0.0s, 0.0min
[Example] Displaying

Python source code: plot_dict_learning_resting_state.py

### Load ADHD rest dataset ####################################################
from nilearn import datasets
# For linear assignment (should be moved in non user space...)

adhd_dataset = datasets.fetch_adhd(n_subjects=10)
func_filenames = adhd_dataset.func  # list of 4D nifti files for each subject

# print basic information on the dataset
print('First functional nifti image (4D) is at: %s' %
      adhd_dataset.func[0])  # 4D data

### Apply DictLearning ########################################################
from nilearn.decomposition import DictLearning, CanICA

n_components = 10

dict_learning = DictLearning(n_components=n_components, alpha=6,
                             smoothing_fwhm=6.,
                             memory="nilearn_cache",
                             memory_level=2,
                             verbose=10, random_state=0)
canica = CanICA(n_components=n_components, n_init=1, smoothing_fwhm=6.,
                memory="nilearn_cache",
                memory_level=2,
                verbose=10, random_state=0)

estimators = [canica, dict_learning]

components_imgs = []

for estimator in estimators:
    print('[Example] Learning maps using %s model'
          % type(estimator).__name__)
    estimator.fit(func_filenames)
    print('[Example] Dumping results')
    components_img = estimator.masker_.inverse_transform(estimator.components_)
    components_img.to_filename('%s_resting_state.nii.gz'
                               % type(estimator).__name__)
    components_imgs.append(components_img)

### Visualize the results #####################################################
# Show some interesting components
import matplotlib.pyplot as plt
from nilearn.plotting import plot_prob_atlas, find_xyz_cut_coords
from nilearn.image import index_img

print('[Example] Displaying')

fig, axes = plt.subplots(nrows=2)
cut_coords = find_xyz_cut_coords(index_img(components_imgs[1], 6))
for estimator, cur_img, ax in zip(estimators, components_imgs, axes):
    plot_prob_atlas(cur_img, title="%s" % estimator.__class__.__name__,
                    axes=ax,
                    cut_coords=cut_coords, colorbar=False)

plt.show()

Total running time of the example: 242.70 seconds ( 4 minutes 2.70 seconds)