======================== MRI dataset description ======================== The dataset currently consist of a hanful of participants, being scanned as part of the course. The dataset will increase over the years. Where to find the data on the server ------------------------------------ The dataset is stored in ``/home/lab1user/SHARED_labdata/PSYC724_LAB-DATA/`` This is a shared space available from each machine. That folder contains 4 subfolders - ``01_sourcedata`` contains the files coming directly from the scanner in dicom format. - ``02_rawdata`` contains the files converted in nifti format. This copy of the dataset will serve as a backup in case the files are corrupted during the preprocessing. - ``03_derivatives`` will contain all the files generated by the preprocessing and analyses steps - ``04_scripts`` will contain the matlab script written to perform the analyses. You should start by getting your local copy of the ``03_derivatives`` folder. Open a file explorer and in ``/home/lab1user/STUDENT-DATA/``, create a folder called ``PSYC724_LAB-DATA/`` where you can copy ``03_derivatives``. Do not copy the source and raw data. Data structure -------------- The scanner produces images in a format called dicom (.dcm). This is a standard medical format but statistical packages only deal with a different format, called nifti (.nii). The dataset has a standardized structure: Each subject folder contains an anatomical directory and a functional directory labeled ``anat`` and ``func``, and these in turn contain the anatomical and functional images collected during the experiment. The files are named according to `BIDS `__, or Brain Imaging Data Structure, which makes it easy to organize and analyze and share your data. .. figure:: 02_dataset_structure.png The ``func`` directory contains functional data - in this case, five runs of functional data. The files are in 4D, they contains times series of 3D images. The json file contains information about the image acquisition from the scanner. The files "events.tsv" contain **onsets**, or timestamps of which condition happened at what time. They have been created from the logfiles generated by the stimulus presentation software, contained in ``beh`` You can open these as a text file or as a spreadsheet. We will use these later when we build our General Linear Model. The ``fmap`` directory contains filedmap images that can be used to correct for distortions. Functional image files contain 170 contiguous echo planar imaging (EPI) whole-brainfunctional volumes (Multiband factor=3; TR=1500 ms; TE=30 ms; flip angle=72, 72 slices, matrix=108*108; FOV=216 mm; acquisition voxel size=2x2x2mm) during each of the five task runs. A high-resolution T1-weighted anatomical image was also acquired using a magnetization prepared gradient echo sequence (MPRAGE, TR=2100 ms; TE=2.26 ms; flip angle=8; 176 slices, FOV=256 mm).