Include and use data subset within the repository

Author: vijayi

BrainMRIAgeClassificationUsingDeepLearning.mlx

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+1.1.0 2019-05-15
+  - Renamed preprocessed data folder to make clear that data were not preprocessed through fmriprep, but rather were preprocessed in SPM8. Clarified timing of reverse correlation events, and provided timings for modeling conditions based on these events, accounting for the hemodynamic lag. Updated paper reference/acknowledgements.
+
+1.0.0	2019-04-03
+
+	- Initial snapshot

README.md

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+Experiment Details
+Participants watched Disney Pixar’s “Partly Cloudy” while lying in the scanner. There was no task; participants were simply instructed to lie still and watch the movie. The movie began after 10s of rest (black screen; TRs 1-5). The first 10s of the movie are the opening credits (disney castle, pixar logo; TRs 6-10). 
+
+IPS = 168 TRs
+TR = 2s
+Experiment length: 5.6 minutes
+
+Pixar Movie Reverse Correlation Events
+Events defined by conducting reverse correlation analysis in two separate adult samples, using the average response in ToM brain regions (ToM events) and in the pain matrix (Pain events). Events listed are those that replicated across the two samples.  Onsets and Durations are noted in TRs (1 TR = 2s); scanner trigger = TR 1.
+
+Event types: Theory of Mind (ToM), Physical Sensation/Pain (Pain)
+TRs identified by RC analysis, as reported in Richardson et al. 2018
+ToM Event Onsets; Durations 
+46; 2
+52; 3
+63; 2
+91; 8
+122; 3
+129; 4
+153; 3
+
+Pain Event Onsets; Durations
+38; 2
+49; 1
+56; 2
+71; 5
+100; 2
+108; 6
+117; 3
+134; 3
+159; 2
+
+
+TIMING OF EVENTS FOR MODELING (taking into account hemodynamic lag (4s), scanner trigger = 0):
+All timings assume 10s from trigger until movie begins to play.
+
+In seconds:
+Mental Event Onsets; Durations
+86; 4
+98; 6
+120; 4
+176; 16
+238; 6
+252; 8
+300; 6
+
+Pain Event Onsets; Durations
+70; 4
+92; 2
+106; 4
+136; 10
+194; 4
+210; 12
+228; 6
+262; 6
+312; 4
+
+In TRs when TR=2:
+Mental Event Onsets; Durations
+43; 2
+49; 3
+60; 2
+88; 8
+119; 3
+126; 4
+150; 3
+
+Pain Event Onsets; Durations
+35; 2
+46; 1
+53; 2
+68; 5
+97; 2
+105; 6
+114; 3
+131; 3
+156; 2

ds000228-1.1.0-subset/CHANGES

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+{
+    "Name": "MRI data of 3-12 year old children and adults during viewing of a short animated film",
+    "BIDSVersion": "1.0.1",
+    "License": "PDDL",
+    "Authors": [
+        "Richardson, Hilary",
+        "Lisandrelli, Grace",
+        "Riobueno-Naylor, Alexa",
+        "Saxe, Rebecca"
+    ],
+    "Acknowledgements": "We thank the Athinoula A. Martinos Imaging Center at the McGovern Institute for Brain Research at MIT, Jorie Koster-Hale, Natalia Velez-Alicea, Mika Asaba, and Nir Jacoby for help with data collection. We thank Todd Thompson for his work making this dataset publicly available.",
+    "HowToAcknowledge": "Richardson, H., Lisandrelli, G., Riobueno-Naylor, A., & Saxe, R. (2018). Development of the social brain from age three to twelve years. Nature communications, 9(1), 1027.",
+    "Funding": [
+        "This project was supported by a NSF Graduate Research Fellowship (#1122374 to HR), and an NSF CAREER award (#095518 to RS), NIH R01-MH096914-05, a Middleton Chair grant (RS), and support from the David and Lucile Packard Foundation (to RS)"
+    ],
+    "ReferencesAndLinks": [
+        "Richardson, H., Lisandrelli, G., Riobueno-Naylor, A., & Saxe, R. (2018). Development of the social brain from age three to twelve years. Nature communications, 9(1), 1027.",
+        "https://www.nature.com/articles/s41467-018-03399-2"
+    ],
+    "DatasetDOI": ""
+}

ds000228-1.1.0-subset/README

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+Derivatives
+
+fMRI Prep
+sub-[]_task-pixar_run-001_swrf_bold.nii.gz
+BOLD images collected during movie viewing. FMRI data were analyzed using SPM8 (http://www.fil.ion.ucl.ac.uk/spm) and custom software written in Matlab. Functional images were registered to the first image of the run; that image was registered to each participant’s anatomical image, and each participant’s anatomical image was normalized to the Montreal Neurological Institute (MNI) template. Registration of each individual’s brain to the MNI template was visually inspected, including checking the match of the cortical envelope and internal features like the AC-PC and major sulci. All data were smoothed using a Gaussian filter (5mm kernel).
+
+As participants were initially recruited for different studies, there are small differences in voxel size and slice gaps across participants (3.13 mm isotropic with no slice gap (n=5 adults, n=3 7yos, n=20 8-12yo); 3.13 mm isotropic with 10% slice gap (n=28 adults), 3 mm isotropic with 20% slice gap (n=1 3yo, n=3 4yo, n=2 7yo, n=1 9yo); 3 mm isotropic with 10% slice gap (all remaining participants)); all functional data were subsequently upsampled in normalized space to 2mm isotropic voxels. 
+
+IPS = 168 TRs; 1 TR = 2s
+TR 1-5: Rest (black screen)
+TR 6-10: Pixar and Disney logos
+TR 11-end: Movie
+
+sub-[]_normed_anat.nii.gz
+Individual subject anatomical image, normalized to the Montreal Neurological Institute (MNI) template.
+
+sub-[]_analysis_mask.nii.gz
+Individual subject skull-stripped whole-brain mask. 
+
+sub-[]_CompCor_mask.nii.gz
+Individual subject white matter mask, normalized in MNI space, and eroded by two voxels in every direction (in order to avoid partial voluming with grey matter). This white matter mask was used for creation of CompCor regressors.
+
+sub-[]_task-pixar_run-001_ART_and_CompCor_nuisance_regressors.mat
+Individual subject artifact timepoint regressors and CompCor regressors. 
+
+Artifact timepoint regressors were created using the Artifact Detection Tool (ART; https://www.nitrc.org/projects/artifact_detect/) as timepoints for which there was 1) more than 2mm composite motion relative to the previous timepoint or 2) a fluctuation in global signal that exceeded a threshold of three standard deviations from the mean global signal. 
+
+Compcor regressors are 5 principle component analysis (PCA)-based noise regressors generated using CompCor within individual subject eroded white matter masks. CompCor regressors were defined using scrubbed data (e.g. artifact timepoints were identified and interpolated over prior to running CompCor). 
+
+
+
+ROIs (Regions of Interest)
+Center coordinates are in MNI space; size is in voxels. 
+
+ToM Network 
+RTPJ_9mm_sphere_xyz.mat (center: 48,-60,30; size: 376)
+LTPJ_9mm_sphere_xyz.mat (center: -48,-62,30; size: 368)
+PC_9mm_sphere_xyz.mat (center: 0,-54,34; size: 382)
+DMPFC_9mm_sphere_xyz.mat (center: -6,54,36; size: 217)
+MMPFC_9mm_sphere_xyz.mat (center: -4,58,16; size: 275)
+VMPFC_9mm_sphere_xyz.mat (center: -4,56,-16; size: 198)
+
+Pain Matrix
+RS2_9mm_sphere_xyz.mat (center: 60,-28,38; size: 368)
+LS2_9mm_sphere_xyz.mat (center: -62,-32,34; size: 269)
+RInsula_9mm_sphere_xyz.mat (center: 42,6,-6; size: 309)
+LInsula_9mm_sphere_xyz.mat (center: -42,-2,-4; size: 240)
+RMFG_9mm_sphere_xyz.mat (center: 50,42,12; size: 142)
+LMFG_9mm_sphere_xyz.mat (center: -46,36,14; size: 256)
+AMCC_9mm_sphere_xyz.mat (center: 0,2,42; size: 249)
+
+Face Network
+rSTS_masked.mat
+lSTS.mat
+rOFA.mat
+lOFA.mat
+rFFA.mat
+lFFA.mat   
+
+Place Network
+rRSC.mat                  
+lRSC.mat
+rTOS.mat
+lTOS.mat
+rPPA.mat                  
+lPPA.mat
+
+Primary motor cortex
+right_primotor.mat
+left_primotor.mat
+
+Primary visual cortex
+right_CS.mat                      
+left_CS.mat
+
+
+ToM and pain matrix group ROIs were created in an independent group of adults (n=20), scanned by Evelina Fedorenko and colleagues. These data were preprocessed and analyzed with procedures identical to those used for participants in the current study. Reverse correlation analyses were conducted in this separate group of adults, using 10mm group ROIs surrounding peaks reported in previous publications (ToM regions: Dufour et al., 2013; Pain matrix: Bruneau et al., 2015). Seven ToM and nine pain events were identified (ToM: 60s total, M(SD) length: 8.6(4.6)s, Pain: 66s total, M(SD) length: 7.3(4.4)s). We subsequently used a general-linear model to analyze BOLD activity of these participants as a function of condition, using these events. Second-level random effects analyses were used to examine the group-level response to Mental > Pain and Pain> Mental (p<.001, k=10, uncorrected). We then drew 9mm spheres surrounding the peak activation in each region.
+
+Face and scene parcels are publicly available (http://web.mit.edu/bcs/nklab/GSS.shtml), and described in:
+Julian, J. B., Fedorenko, E., Webster, J. & Kanwisher, N. An algorithmic method for functionally defining regions of interest in the ventral visual pathway. NeuroImage 60, 2357–2364 (2012).
+
+Primary motor and visual cortex ROIs are 10mm spheres drawn around peak coordinates generated with Neurosynth (http://neurosynth.org/; M1: search term: “primary motor,” coordinates: [38,-24,58], [-38,-20,58]; V1: search term: “primary visual,” coordinates: [-10 -86 2], [10 -86 2]. 
+