The NeuroVault database (https://neurovault.org/) is a:
place where researchers can publicly store and share unthresholded statistical maps, parcellations, and atlases produced by MRI and PET studies.
This allows researchers to compare results from multiple studies.
The NeuroVault API (https://neurovault.org/api-docs) allows users to access this data with some calls to a RESTful API.
The neurovault package wraps these commands using httr. Here we will look
library(neurovault)
res = nv_collection_images(id = 77)
#> GET command is:
#> Response [https://neurovault.org/api/collections/77/images/]
#> Date: 2020-03-18 16:22
#> Status: 200
#> Content-Type: application/json; charset=utf-8
#> Size: 6.95 kB
df = results_to_df(res$content$results)
head(df)
#> url id
#> 1 https://neurovault.org/images/330/ 330
#> 2 https://neurovault.org/images/331/ 331
#> 3 https://neurovault.org/images/332/ 332
#> 4 https://neurovault.org/images/333/ 333
#> file
#> 1 https://neurovault.org/media/images/77/zstat-young.nii.gz
#> 2 https://neurovault.org/media/images/77/zstat-old.nii.gz
#> 3 https://neurovault.org/media/images/77/zstat-young-old.nii.gz
#> 4 https://neurovault.org/media/images/77/zstat-old-young.nii.gz
#> collection collection_id file_size
#> 1 https://neurovault.org/collections/77/ 77 537724
#> 2 https://neurovault.org/collections/77/ 77 534984
#> 3 https://neurovault.org/collections/77/ 77 538597
#> 4 https://neurovault.org/collections/77/ 77 538602
#> cognitive_paradigm_cogatlas cognitive_paradigm_cogatlas_id
#> 1 color-word stroop with task switching trm_5542841f3dcd5
#> 2 color-word stroop with task switching trm_5542841f3dcd5
#> 3 color-word stroop with task switching trm_5542841f3dcd5
#> 4 color-word stroop with task switching trm_5542841f3dcd5
#> cognitive_contrast_cogatlas cognitive_contrast_cogatlas_id map_type
#> 1 NA NA Z map
#> 2 NA NA Z map
#> 3 NA NA Z map
#> 4 NA NA Z map
#> analysis_level name description add_date
#> 1 NA zstat-young.nii.gz FSL4.1 2016-01-21T17:22:27.296097Z
#> 2 NA zstat-old.nii.gz FSL4.1 2016-01-21T17:23:08.244431Z
#> 3 NA zstat-young-old.nii.gz FSL4.1 2016-01-21T17:21:38.899847Z
#> 4 NA zstat-old-young.nii.gz FSL4.1 2016-01-21T17:21:38.923925Z
#> modify_date is_valid
#> 1 2018-06-30T04:32:22.968402Z TRUE
#> 2 2018-06-30T04:32:23.153311Z TRUE
#> 3 2018-06-30T04:32:18.768310Z TRUE
#> 4 2018-06-30T04:32:18.935690Z TRUE
#> surface_left_file
#> 1 https://neurovault.org/media/images/77/330.L.func.gii
#> 2 https://neurovault.org/media/images/77/331.L.func.gii
#> 3 https://neurovault.org/media/images/77/332.L.func.gii
#> 4 https://neurovault.org/media/images/77/333.L.func.gii
#> surface_right_file data_origin
#> 1 https://neurovault.org/media/images/77/330.R.func.gii volume
#> 2 https://neurovault.org/media/images/77/331.R.func.gii volume
#> 3 https://neurovault.org/media/images/77/332.R.func.gii volume
#> 4 https://neurovault.org/media/images/77/333.R.func.gii volume
#> target_template_image subject_species figure handedness age gender race
#> 1 GenericMNI homo sapiens NA NA NA NA
#> 2 GenericMNI homo sapiens NA NA NA NA
#> 3 GenericMNI homo sapiens NA NA NA NA
#> 4 GenericMNI homo sapiens NA NA NA NA
#> ethnicity BMI fat_percentage waist_hip_ratio mean_PDS_score tanner_stage
#> 1 NA NA NA NA NA NA
#> 2 NA NA NA NA NA NA
#> 3 NA NA NA NA NA NA
#> 4 NA NA NA NA NA NA
#> days_since_menstruation hours_since_last_meal bis_bas_score spsrq_score
#> 1 NA NA NA NA
#> 2 NA NA NA NA
#> 3 NA NA NA NA
#> 4 NA NA NA NA
#> bis11_score thumbnail
#> 1 NA https://neurovault.org/media/images/77/glass_brain_330.jpg
#> 2 NA https://neurovault.org/media/images/77/glass_brain_331.jpg
#> 3 NA https://neurovault.org/media/images/77/glass_brain_332_1.jpg
#> 4 NA https://neurovault.org/media/images/77/glass_brain_333_1.jpg
#> reduced_representation is_thresholded
#> 1 https://neurovault.org/media/images/77/transform_4mm_330.npy FALSE
#> 2 https://neurovault.org/media/images/77/transform_4mm_331.npy FALSE
#> 3 https://neurovault.org/media/images/77/transform_4mm_332.npy FALSE
#> 4 https://neurovault.org/media/images/77/transform_4mm_333.npy FALSE
#> perc_bad_voxels not_mni brain_coverage perc_voxels_outside number_of_subjects
#> 1 84.39691 FALSE 55.60851 9.785711 64
#> 2 84.39691 FALSE 55.60851 9.785711 64
#> 3 84.39691 FALSE 55.60851 9.785711 64
#> 4 84.39691 FALSE 55.60851 9.785711 64
#> modality statistic_parameters smoothness_fwhm
#> 1 fMRI-BOLD NA NA
#> 2 fMRI-BOLD NA NA
#> 3 fMRI-BOLD NA NA
#> 4 fMRI-BOLD NA NA
#> contrast_definition contrast_definition_cogatlas
#> 1 stroop inference versus color naming
#> 2 stroop inference versus color naming
#> 3 stroop inference versus color naming
#> 4 stroop inference versus color naming
#> cognitive_paradigm_description_url image_type
#> 1 NA statistic_map
#> 2 NA statistic_map
#> 3 NA statistic_map
#> 4 NA statistic_mapAtlases
We can download and view a labeled atlas for the results:
library(neurobase)
#> Loading required package: oro.nifti
#> oro.nifti 0.10.1
res = download_nv_atlas(id = 1408)
#> GET command is:
#> Response [https://neurovault.org/api/atlases/1408/]
#> Date: 2020-03-18 16:22
#> Status: 200
#> Content-Type: application/json; charset=utf-8
#> Size: 1.11 kB
#>
#>
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#>
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atlas = readnii(res$outfile[1])
ortho2(atlas)
NIDM Results
You can access the neuroimaging data model (NIDM) (http://nidm.nidash.org/) information using:
nidm = nv_nidm_results()
#> GET command is:
#> Response [https://neurovault.org/api/nidm_results/]
#> Date: 2020-03-18 16:22
#> Status: 200
#> Content-Type: application/json; charset=utf-8
#> Size: 324 kB
#> Multiple pages must be called - more results than 1 call
#> GET command is:
#> Response [https://neurovault.org/api/nidm_results/?limit=100&offset=100]
#> Date: 2020-03-18 16:22
#> Status: 200
#> Content-Type: application/json; charset=utf-8
#> Size: 365 kB
#> GET command is:
#> Response [https://neurovault.org/api/nidm_results/?limit=100&offset=200]
#> Date: 2020-03-18 16:22
#> Status: 200
#> Content-Type: application/json; charset=utf-8
#> Size: 385 kB
#> GET command is:
#> Response [https://neurovault.org/api/nidm_results/?limit=100&offset=300]
#> Date: 2020-03-18 16:23
#> Status: 200
#> Content-Type: application/json; charset=utf-8
#> Size: 492 kB
#> GET command is:
#> Response [https://neurovault.org/api/nidm_results/?limit=100&offset=400]
#> Date: 2020-03-18 16:23
#> Status: 200
#> Content-Type: application/json; charset=utf-8
#> Size: 271 kB