This README.txt file was generated on 20181129 by Colleen Schneider ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Survival of Retinal Ganglion Cells After Damage to the Occipital Lobe in Humans is Activity-Dependent 2. Author Information First Author Contact Information Name: Colleen L. Schneider Institution: Carnegie Mellon University Address: 5000 Forbes Ave, Pittsburgh, PA 15213 Email: cschnei2@andrew.cmu.edu Second Author Contact Information Name: Emily K. Prentiss Institution: University of Rochester School of Medicine and Dentistry Address: 601 Elmwood Ave, Rochester, NY 14642 Email:emily_prentiss@urmc.rochester.edu Third Author Contact Information Name: Ania Busza Institution: University of Rochester School of Medicine and Dentistry Address: 601 Elmwood Ave, Rochester, NY 14642 Email: ania_busza@urmc.rochester.edu Fourth Author Contact Information Name: Kelly Matmati Institution: Rochester Regional Health Address: 100 Kings Highway South, Rochester, NY 14617 Email: kelly.matmati@rochesterregional.org Fifth Author Contact Information Name: Nabil Matmati Institution: Rochester Regional Health Address: 100 Kings Highway South, Rochester, NY 14617 Email: nabil.matmati@rochesterregional.org Sixth Author Contact Information Name: Zoe R. Williams Institution: University of Rochester School of Medicine and Dentistry Address: 601 Elmwood Ave, Rochester, NY 14642 Email: zoe_williams@urmc.rochester.edu Seventh Author Contact Information Name: Bogachan Sahin Institution: University of Rochester School of Medicine and Dentistry Address: 601 Elmwood Ave, Rochester, NY 14642 Email: bogachan_sahin@urmc.rochester.edu Corresponding Author Contact Information Name: Bradford Z. Mahon Institution: Carnegie Mellon University Address: 5000 Forbes Ave, Pittsburgh, PA 15213 Email: bmahon@andrew.cmu.edu 3. Date of data collection: 2015-01-09 to 2018-07-27 4. Geographic location of data collection: Rochester, NY, USA 5. Funding sources: Data collection is supported by NIH grants R21NS076176 and R01NS089609 to Bradford Z. Mahon, a core NIH grant to the Center for Visual Science (P30EY001319), a grant from the Schmitt Program on Integrative Brain Research (University of Rochester) to Bogachan Sahin and Bradford Z. Mahon, and an unrestricted grant from Research to Prevent Blindness to the Ophthalmology Department at the Flaum Eye Institute to Zoe R. Williams. Preparation of this database was funded, in part, by NIH grant F30EY027988 to Colleen L. Schneider. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC BY 4.0 2. DOI: 10.1184/R1/7403780v1 3. For data usage please cite as follows: Schneider, Colleen L; Prentiss, Emily K; Busza, Ania; Matmati, Kelly; Matmati, Nabil; Williams, Zoe R; Sahin, Bogachan; Mahon, Bradford Z (2018): Survival of Retinal Ganglion Cells After Damage to the Occipital Lobe in Humans is Activity-Dependent. figshare. Dataset. DOI 10.1184/R1/7403780v1. --------------------- DATA & FILE OVERVIEW --------------------- Directory of Files A. Filename: participants.tsv Short description: Participant table and demographics. B. Filename: BIDS_sub_summary.xlsx Short description: Summary of MRI scans for each subject at each session. C. Filename: task-Fullfield_bold.json Short description: MRI parameters of the fullfield flickering checkerboard runs. D. Filename: task-PA_bold.json Short description: MRI parameters of the polar angle runs. E. Filename: OphthalmologyRawData.zip Short description: Ganglion cell thickness from optical coherence tomography of the macula, visual sensitivity values from automated Humphrey perimetry, and performance on a letter detection and identification task for all subjects at all sessions. F. Filename: ProcessedDataTable.xlsx Short description: Contains the values for fMRI voxel counts, ganglion cell complex thickness, visual sensitivity, and visual ability at each wedge location within the visual field for all subjects at all sessions. G. Filename: sub-X_ses-Y.zip Short description: BIDS format MRI data collected in for each subject (X) at each session (Y) Contains anat folder with T1 weighted scan and func folder with BOLD scans and events.tsv files. Clinical sessions (ses-clinical) contain scans collected upon hospital admission for stroke work-up. Anat folder contains T1 weighted and T2 FLAIR scans and dwi folder contains diffusion weighted scan. ---------------------------------------------- DATA DESCRIPTION FOR: participants.tsv ---------------------------------------------- This file contains the demographic and relevant clinical information for all participants. Age is age when participant was first scanned. Lesion describes the location of the lesion for all stroke patients. Original_field_cut labeled as RHH = right homonymous hemianopia, LHH = left homonymous hemianopia, RLQ = right lower quadrantanopia, RUQ = right upper quadrantanopia, LLQ = left lower quadrantanopia. ---------------------------------------------- DATA DESCRIPTION FOR: BIDS_sub_summary.xlsx ---------------------------------------------- This file contains the subject ID (Sub) corresponding to the zip file sub-X_ses-Y.zip that contains all MRI data collected for that subject at that session (Ses). Also included are subject IDs that are internal to our lab (fMRI and Behav), the date the scans were collected (ScanDate), and the run numbers of T1, T2FLAIR, DWI, PolarAngle BOLD, and Fullfield BOLD scans that were collected in that session. ---------------------------------------------- DATA DESCRIPTION FOR: OphthalmologyRawData.zip ---------------------------------------------- This file contains all raw data from Humphrey visual field testing, the letter test, and the ganglion cell thickness analysis from spectral-domain optical coherence tomography of the macula. Subfolders: 1. Humphrey PDF files for right (OS) and left (OD) eyes for each subject and session. MAT files for both (OU) eyes for each subject and session. Mat files contain the raw sensitivity (left.rawd and right.rawd matrices with columns x-coord, y-coord, sensitivity) and total deviation (left.totaldev and right.totaldev matrices with columns x-coord, y-coord, total deviation) for each eye at each test location within the 24-2 test. Also included is the perimetric mean deviation (left.PMD and right.PMD) for each eye, and a map of smoothed sensitivity values (left.smoothed and right.smoothed) obtained with linear interpolation between test locations using a 0.25 kernel (left.kernel and right.kernel). The raw sensitivity and total deviation values for each eye are also combined by taking the average over the two eyes at each test location (combinedavg.rawd and combinedavg.totaldev matrices with columns x-coord, y-coord, sensitivity or total deviation) or the winner of the two test locations (combinedwinner.rawd and combinedwinner.totaldev matrices with columns x-coord, y-coord, sensitivity or total deviation). The average and winner sensitivity values also have a corresponding smoothed map of sensitivity values (combinedavg.smoothed and combinedwinner.smoothed) created with linear interpolation between test locations using a 0.25 kernel (combinedavg.kernel and combinedwinner.kernel). File naming convention: sub-X_ses-Y_Humphrey where eye = OD or OS or OU for example: sub-01_ses-01_HumphreyOD is the right eye of subject 1 at the first time point. 2. LetterTest JPG files showing the results of the letter detection and identification task. (See SI materials and methods and figure S6. MAT files containing the testing parameters and results. The results are stored in the variable FieldTest.VisField.responses in a 6 x 12 cell. Rows refer to the eccentricities tested (FieldTest.startingValues.actualradiiNumber2use in degrees visual angle, row 1 is most foveal, row 6 is most peripheral) and columns refer to the wedges tested (centered on the clock hours, column 1 is 4 o’clock and columns proceed clockwise). An entry of 0 means the subject made no response, an entry of 999 means the subject detected the letter but incorrectly identified it, an entry of 1 means the subject correctly identified the letter. File naming convention: sub-X_ses-Y_LetterTest for example: sub-01_ses-01_LetterTest is the letter test results from subject 1 at the first time point. 3. GanglionCellThickness Ganglion Cell PDF files containing the ganglion cell analysis for right (OS) and left (OD) eyes for each subject and session. This is the print out generated by the OCT machine. Thickness EPS files containing a heatmap of the thickness of the ganglion cell complex centered on the fovea. Fovea, IPL, and MRNFL TXT files: _fovea.txt contains the x and y coordinates of the fovea for each eye _MRNFL.txt contains the outer boundary of the retinal nerve fiber layer (512 data points for each of 128 B-scans) _IPL.txt contains the outer boundary of the inner plexiform layer (512 data points for each of 128 B-scans) File naming convention: sub_X_ses-Y__ where eye = OD or OS or OU and filetype = fovea, IPL, MRNFL, Thickness, or GanglionCell OCT_GCCthickness.m: matlab script to extract the ganglion cell complex thickness from the TXT files and generate the EPS files and the summary CSV files. The thickness of the ganglion cell complex in micrometers is equal to (IPL - RNFL)*(2/1024)*1000 (there are 1024 pixels per 2mm of thickness). Summary csv files: average ganglion cell complex thickness for each of 12 wedges centered on the clock hours (numbered in retinal coordinates) for the right eye (RightEyeThickness.csv), left eye (LeftEyeThickness.csv) and the average of both eyes (AvgEyeThickness.csv). In the case where thickness values could only be used from the scan of one eye and not the other, the average thickness is just the thickness of the usable eye (subs 6, 7, 8, 15). Columns with the labels ‘one’ - ‘twelve’ correspond to the 12 wedges centered on the clock hours (numbered in retinal coordinates). ---------------------------------------------- DATA DESCRIPTION FOR: ProcessedDataTable.xlsx ---------------------------------------------- This file contains all of the data that was used to perform statistical analyses including the number of significantly active voxels (nVoxTC_contra), the thickness of the ganglion cell complex in micrometers (MacularT), visual sensitivity in decibels (sensitivity), and visual ability (Letter Test) at each wedge location within the visual field for all patients at all time points. Key for the variable names in this file can be found in the README tab of the spreadsheet. ------------------------------------- DATA DESCRIPTION FOR: sub-X_ses-Y.zip ------------------------------------- These files contain all of the MRI data (in BIDS format v1.0.1) acquired for a given subject (sub-X) during a given session (ses-Y). File naming convention follows the brain imaging data structure (BIDS) format (Gorgolewski et al., 2016) The tsv file named sub-X_ses-Y_scans.tsv lists all of the scans contained within the sub-X_ses-Y.zip file. Subfolders: 1. anat nifti file containing T1 weighted scan data (and T2 FLAIR scan data for clinical sessions) json file containing scanner parameters 2. func nifti file containing BOLD scan 3D time-series data json file containing scanner parameters tsv file containing timestamps for stimulus onset and duration *the stimulus presented during the BOLD scans was either a fullfield flickering checkerboard (task-Fullfield) or a checkerboard wedge (task-PA) presented in 12 non-overlapping locations in a random order. During both tasks, subjects were instructed to fixate on a central fixation point. 3. dwi (only for ses-clinical zip files) nifti file containing the diffusion weighted scan data json file containing scanner parameters -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Software-specific information: Generic software Name: MATLAB Version: 2015b Product URL: https://www.mathworks.com/products/matlab.html Software for stimulus presentation Name: Psychtoolbox Version: 3.0.11 Product URL: http://psychtoolbox.org/download.html Additional Notes: Used on Windows 10 Software for data acquisition Name: ViewPoint Eyetracker System Requirements: Windows 7 or greater Developer: Arrington Research Product URL: http://www.arringtonresearch.com/viewpoint.html Additional Notes: software controlled with MATLAB toolbox Software for data analysis Name: Brainvoyager Version: 2.8.2 Developer: Rainer Goebel Product URL: http://www.brainvoyager.com Name: BVQXtools Version: v08d Developer: Jochen Weber Product URL: http://neuroelf.net/ Name: Freesurfer Version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Product URL: http://surfer.nmr.mgh.harvard.edu Name: Clusterize toolbox for SPM Version: SPM version 12 Product URL: http://www.medizin.uni-tuebingen.de/kinder/en/research/neuroimaging/software/?download=clusterize-toolbox Name: R studio Version: 1.1.442 Product URL: https://www.rstudio.com 2. Equipment-specific information: MRIs Manufacturer: GE Model: 750W (3T) Head coil: 8 channel Manufacturer: Seimens Model: Prisma (3T) Head coil: 20 channel Manufacturer: Seimens Model: Trim Trio (3T) Head coil: 12 channel MRI stimulus presentation Manufacturer: Nordic Neuro Model: Visual System Additional Notes: contains infrared camera for eye tracking Spectral-domain optical coherence tomography Manufacturer: Zeiss Model: Cirrus HD-OCT 5000 Additional Notes: Macular cube (512 x 128) Humphrey perimetry Manufacturer: Zeiss Model: HFAIIi Embedded Software: SITA Additional Notes: 24-2 field, size III white target, fixation enforced, corrected for near vision Eye tracker Manufacturer: Eyelink Model: 1000 Additional Notes: desktop mode, controlled through MATLAB