Dataset content overview ======================== This is an overview of the dataset content. There is a short description for each data item, and the name and approximate size of the openfmri.org tarball containing it is given. Note, accessing invidual files possible via openfmri's XNAT server. More information and updates are available at http://www.studyforrest.org Stimulus material, participant demographics and protocol descriptions --------------------------------------------------------------------- [study_description.tar ~200KB] ./acquisition_protocols/04-sT1W_3D_TFE_TR2300_TI900_0_7iso_FS.txt ./acquisition_protocols/05-sT2W_3D_TSE_32chSHC_0_7iso.txt ./acquisition_protocols/06-VEN_BOLD_HR_32chSHC.txt ./acquisition_protocols/07-DTI_high_2iso.txt ./acquisition_protocols/08-field_map.txt Philips-specific MRI acquisition parameters dumps (plain text) for structural MRI (T1w, T2w, SWI, DTI, fieldmap -- in this order) ./acquisition_protocols/task001_fmri_session1.pdf ./acquisition_protocols/task001_fmri_session2.pdf ./acquisition_protocols/angio_session.pdf Siemens-specific MRI acquisition parameters dumps (PDF format) for functional MRI and angiography. ./demographics.csv Participant questionnaire A plain text, comma-separated-value table with all participants' responses to a questionnaire on demographic information, musical preference and background, as well as familiarity with the "Forrest Gump" movie. ./stimulus/task001/annotations/german_audio_description.csv Audio-description transcript This transcript contains all information on the audio-movie content that cannot be inferred from the DVD release — in a plain text, comma-separated-value table. Start and end time stamp, as well as the spoken text are provided for each continuous audio description segment. ./stimulus/task001/annotations/scenes.csv Movie scenes A plain text, comma-separated-value table with start and end time for all 198 scenes in the presented movie cut. In addition, each table row contains whether a scene takes place indoors or outdoors. ./stimulus/task001/generate/generate_melt_cmds.py Python script to generate commands for stimulus generation ./stimulus/task001/psychopy/buttons.csv ./stimulus/task001/psychopy/forrest_gump.psyexp ./stimulus/task001/psychopy/segment_cfg.csv Source code of the stimulus presentation in PsychoPy ./study_key.txt ./task_key.txt ./model_key.txt ./references.txt ./release_history.txt ./scan_key.txt Openfmri.org specific files for encoding study meta data. See openfmri.org documentation for details. Functional imaging ------------------ Prolonged quasi-natural auditory stimulation (Forrest Gump audio movie) Eight approximately 15 min long recording runs, together comprising the entire duration of a two-hour presentation of an audio-only version of the Hollywood feature film "Forrest Gump" made for a visually impaired audience (German dubbing). For each run, there are 4D volumetric images (160x160x36)in NIfTI format , one volume recorded every 2 s, obtain from a Siemens MR scanner at 7 Tesla using a T2*-weighted gradient-echo EPI sequence (1.4 mm isotropic voxel size). These images have partial brain coverage — centered on the auditory cortices in both brain hemispheres and include frontal and posterior portions of the brain. There is no coverage for the upper portion of the brain (e.g. large parts of motor and somato-sensory cortices). Several flavors of raw and preprocessed data are available: Raw BOLD functional MRI ~~~~~~~~~~~~~~~~~~~~~~~ [bold_raw.tar ~80GB] These raw data suffer from severe geometric distortions. Filename examples for subject 001 and run 001 ./sub001/BOLD/task001_run001/bold.nii.gz BOLD data ./sub001/BOLD/task001_run001/bold_dicominfo.txt Image property dump from DICOM conversion Raw BOLD functional MRI (with applied distortion correction) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [bold_dico_task001.tar ~74GB] Identical to raw BOLD data, but with a scanner-side correction for geometric distortions applied (also include correction for participant motion). These data are most suitable for analysis of individual brains. Filename examples for subject 001 and run 001 ./sub001/BOLD/task001_run001/bold_dico.nii.gz BOLD data ./sub001/BOLD/task001_run001/moco_ref.nii.gz Reference volume used for motion correction. Only runs 1 and 5 (first runs in each session) ./sub001/BOLD/task001_run001/bold_dico_dicominfo.txt Image property dump from DICOM conversion Raw BOLD functional MRI (linear anatomical alignment) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [bold_algnd_grpbold7Tad_lin_task001.tar ~85GB] These images are motion and distortion corrected and have been anatomically aligned to a BOLD group template image that was generated from the entire group of participants. Alignment procedure was linear (image projection using an affine transformation). These data are most suitable for group-analyses and inter-individual comparisons. Filename examples for subject 001 and run 001 ./sub001/BOLD/task001_run001/bold_dico_dico7Tad2grpbold7Tad.nii.gz BOLD data ./sub001/BOLD/task001_run001/bold_dico_brainmask_dico7Tad2grpbold7Tad.nii.gz Matching brain mask volume ./sub001/BOLD/task001_run001/bold_dico_xfm_dico7Tad2grpbold7Tad.mat 4x4 affine transformation matrix (plain text format) Raw BOLD functional MRI (non-linear anatomical alignment) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [bold_algnd_grpbold7Tad_nonlin_task001.tar ~91GB] These images are motion and distortion corrected and have been anatomically aligned to a BOLD group template image that was generated from the entire group of participants. Alignment procedure was non-linear (image projection using an affine transformation with additional transformation by non-linear warpfields). These data are most suitable for group-analyses and inter-individual comparisons. Filename examples for subject 001 and run 001 ./sub001/BOLD/task001_run001/bold_dico_dico7Tad2grpbold7Tad_nl.nii.gz BOLD data ./sub001/BOLD/task001_run001/bold_dico_brainmask_dico7Tad2grpbold7Tad_nl.nii.gz Matching brain mask volume ./sub001/BOLD/task001_run001/bold_dico_warp_dico7Tad2grpbold7Tad_nl.nii.gz Warpfield (associated affine transformation is identical with "linear" alignment Structural MRI data (T1w, T2w, SWI) ----------------------------------- [structural.tar ~3GB] T1-weighted images (gray-white contrast) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Full-brain volumetric images (384x384x274) in NIfTI format recorded with a Philips MR scanner at 3 Tesla using a 3D TFE sequence (0.67 mm isotropic voxel size). Facial features have been removed from these images for de-identification. ./sub001/anatomy/highres001.nii.gz Data ./sub001/anatomy/highres001_dicominfo.txt Image property dump from DICOM conversion ./sub001/anatomy/highres001_defacemask.nii.gz Binary mask indicating voxels modified during de-facing T2-weighted images (fluid-tissue contrast) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Full-brain volumetric images (384x384x274) in NIfTI format recorded with a Philips MR scanner at 3 Tesla using a 3D TSE sequence (0.67 mm isotropic voxel size). Facial features have been removed from these images for de-identification. ./sub001/anatomy/other/t2w001.nii.gz Data ./sub001/anatomy/other/t2w001_defacemask.nii.gz Binary mask indicating voxels modified during de-facing ./sub001/anatomy/other/t2w001_dicominfo.txt Image property dump from DICOM conversion Susceptibility-weighted images (venography) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Full-brain volumetric images (512x512x500) in NIfTI format recorded with a Philips MR scanner at 3 Tesla using a 3D Presto FFE sequence (0.43x0.43x0.35 mm voxel size). Facial features have been removed from these images for de-identification. Separate phase and magnitude images are provided. ./sub001/anatomy/other/swi001_mag.nii.gz Magnitude image ./sub001/anatomy/other/swi001_mag_defacemask.nii.gz Binary mask indicating voxels modified during de-facing ./sub001/anatomy/other/swi001_mag_dicominfo.txt Image property dump from DICOM conversion ./sub001/anatomy/other/swi001_pha_defacemask.nii.gz ./sub001/anatomy/other/swi001_pha_dicominfo.txt ./sub001/anatomy/other/swi001_pha.nii.gz Corresponding files for the phase image Diffusion tensor imaging data ----------------------------- [dti.tar ~400MB] Full-brain volumetric images (144x144x70) in NIfTI format recorded with a Philips MR scanner at 3 Tesla using a diffusion-weighted single-shot spin-echo EPI sequence (2 mm isotropic voxel size). Facial features have been removed from these images for de-identification. Records of B-values and B-vector orientations are provided, as well as a fieldmap (3 mm isotropic voxel size) for distortion correction ./sub001/dti/dti001.nii.gz DTI data ./sub001/dti/dti001.bvals ./sub001/dti/dti001.bvecs B-values and orientations (plain text) ./sub001/dti/dti001_defacemask.nii.gz Binary mask indicating voxels modified during de-facing ./sub001/fieldmap/fieldmap001_mag_defacemask.nii.gz ./sub001/fieldmap/fieldmap001_mag_dicominfo.txt ./sub001/fieldmap/fieldmap001_mag.nii.gz ./sub001/fieldmap/fieldmap001_pha_defacemask.nii.gz ./sub001/fieldmap/fieldmap001_pha_dicominfo.txt ./sub001/fieldmap/fieldmap001_pha.nii.gz Fieldmap files (analog filename to SWI images) Physiological recordings and fMRI motion estimates -------------------------------------------------- [physio_task001.tar ~100MB] Participant motion estimates ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ These data have been estimated from the raw BOLD images prior to distortion correction. Files are provided in a six-column plain text format for each fMRI scanning run separately. Example filenames for subject 001: ./sub001/BOLD/task001_run001/bold_dico_moco.txt ./sub001/BOLD/task001_run002/bold_dico_moco.txt ./sub001/BOLD/task001_run003/bold_dico_moco.txt ./sub001/BOLD/task001_run004/bold_dico_moco.txt ./sub001/BOLD/task001_run005/bold_dico_moco.txt ./sub001/BOLD/task001_run006/bold_dico_moco.txt ./sub001/BOLD/task001_run007/bold_dico_moco.txt ./sub001/BOLD/task001_run008/bold_dico_moco.txt Cardiac and respiratory trace (physiological confounds) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ These data have been obtain simultaneously to the fMRI recording during auditory stimulation. Files are in plain text format (compressed) for each scanning run separately and includes the MR scanner's volume acquisition trigger signal for precise temporal alignment. These data are useful for de-noising of fMRI time series. Example filenames for subject 001 and run 001: ./sub001/physio/task001_run001/physio.txt.gz Data file ./sub001/physio/task001_run001/conversion.log Conversion log with information on potential anomalies Time-of-flight inflow angiography (arteriography) ------------------------------------------------- [angio.tar ~1GB] Volumetric images (640x480x150) in NIfTI format recorded with a Siemens MR scanner at 7 Tesla using a 3D multi-slab sequence (0.3 mm isotropic voxel size). These images have partial brain coverage — approximately the same volume as the functional MRI scans. ./sub001/angio/angio001_dicominfo.txt ./sub001/angio/angio001.nii.gz Phantom raw BOLD fMRI --------------------- [subphantom.tar ~8GB] Identical imaging set up as the auditory stimulation fMRI, but scanning a gel phantom instead of a human participant. This data is a measurement of the technical noise in the fMRI acquisition pipeline. These data are aslo contained in the respective BOLD data tarballs. Example filenames for run001: ./subphantom/BOLD/task001_run001/bold.nii.gz Raw BOLD data ./subphantom/BOLD/task001_run001/bold_dicominfo.txt Image property dump from DICOM conversion ./subphantom/BOLD/task001_run001/bold_dico.nii.gz Motion and distortion-corrected data ./subphantom/BOLD/task001_run001/bold_dico_dicominfo.txt Image property dump from DICOM conversion ./subphantom/BOLD/task001_run001/bold_dico_moco.txt Motion correction estimates ./subphantom/BOLD/task001_run001/moco_ref.nii.gz Motion correction reference volume (only run 1 and 5) Group template volumes ---------------------- [templates.tar ~1.5GB] Group-template images for anatomical alignment of individual brains into group space. Individual template images are provided for BOLD, T1w, and T2w images. T1w template: ./templates/t1w/head.nii.gz Template image ./templates/t1w/brain.nii.gz Brain extracted template image ./templates/t1w/in_mni/brain_12dof.nii.gz Brain extracted template image projected into MNI space ./templates/t1w/xfm/mni2tmpl_12dof.mat ./templates/t1w/xfm/tmpl2mni_12dof.mat Affine transformation matrices from template into MNI space (and back) ./templates/t1w/from_mni/MNI152_T1_1mm_brain_mask_dil.nii.gz ./templates/t1w/from_mni/MNI152_T1_1mm_brain_mask.nii.gz ./templates/t1w/from_mni/MNI152_T1_1mm.nii.gz ./templates/t1w/from_mni/avg152T1_brain.nii.gz ./templates/t1w/from_mni/avg152T1_csf.nii.gz ./templates/t1w/from_mni/avg152T1_gray.nii.gz ./templates/t1w/from_mni/avg152T1_white.nii.gz MNI152 template images (masks and prior maps) projected into the template space T2w template: ./templates/t2w/brain.nii.gz ./templates/t2w/from_mni/avg152T1_brain.nii.gz ./templates/t2w/from_mni/avg152T1_csf.nii.gz ./templates/t2w/from_mni/avg152T1_gray.nii.gz ./templates/t2w/from_mni/avg152T1_white.nii.gz ./templates/t2w/from_mni/MNI152_T1_1mm_brain_mask_dil.nii.gz ./templates/t2w/from_mni/MNI152_T1_1mm_brain_mask.nii.gz ./templates/t2w/from_mni/MNI152_T1_1mm.nii.gz ./templates/t2w/head.nii.gz ./templates/t2w/in_mni/brain_12dof.nii.gz ./templates/t2w/xfm/mni2tmpl_12dof.mat ./templates/t2w/xfm/tmpl2mni_12dof.mat Files analog to T1w template BOLD template: ./templates/grpbold7Tad/brain.nii.gz ./templates/grpbold7Tad/from_mni/avg152T1_brain.nii.gz ./templates/grpbold7Tad/from_mni/avg152T1_csf.nii.gz ./templates/grpbold7Tad/from_mni/avg152T1_gray.nii.gz ./templates/grpbold7Tad/from_mni/avg152T1_white.nii.gz ./templates/grpbold7Tad/from_mni/MNI152_T1_1mm_brain_mask_dil.nii.gz ./templates/grpbold7Tad/from_mni/MNI152_T1_1mm_brain_mask.nii.gz ./templates/grpbold7Tad/from_mni/MNI152_T1_1mm.nii.gz ./templates/grpbold7Tad/head.nii.gz ./templates/grpbold7Tad/in_mni/brain_12dof.nii.gz ./templates/grpbold7Tad/xfm/mni2tmpl_12dof.mat ./templates/grpbold7Tad/xfm/tmpl2mni_12dof.mat Files analog to T1w template ./templates/grpbold7Tad/qa/dico7Tad2grpbold7Tad/aligned_brain_samples.nii.gz 4D volume with all aligned reference images across runs and participants. For QA. ./templates/grpbold7Tad/qa/dico7Tad2grpbold7Tad/brain_mask_stats.nii.gz Brain mask overlap stats for linear alignment of all individual fMRI runs across participants to the BOLD template. ./templates/grpbold7Tad/qa/dico7Tad2grpbold7Tad/brain_mask_intersection.nii.gz Brain mask intersection across all runs and participants ./templates/grpbold7Tad/qa/dico7Tad2grpbold7Tad_nl/aligned_brain_samples.nii.gz ./templates/grpbold7Tad/qa/dico7Tad2grpbold7Tad_nl/brain_mask_intersection.nii.gz ./templates/grpbold7Tad/qa/dico7Tad2grpbold7Tad_nl/brain_mask_stats.nii.gz Analog files for non-linear alignment All data for a single example participant ----------------------------------------- [sub016.tar ~18GB] These are all files available for sub016. All files are available in tarballs for the respective data modalities also. The purpose of this tarball is to offer a single download providing examples of all data items. Filenames: ./sub016/*