Various info you need to collect, manage, and analyse data
Data collection/management
Read the CHN User Manual for details about how data is stored on FlyWheel. Kelly also has a good set of slides. Little quirks you should know 1. Always collect a T2 if you want to segment. It really helps 2. Always collect an anat on each session if you want to run Gears on flywheel
Data Management
One of the things that will save you a lot of headaches later is having a consistent naming scheme for files that is consistent with both BIDS and FLYWHEEL format.
We’d recommend starting by refreshing yourself with the MRI manual (beginning with Overview of the Flywheel Data Management Server).
Example naming systems consistent with this are:
- sub-subID_func_bold_taskname_run_01
- sub-subID_anat-T1w_mprage_run01
(you can add the datestamp/timestamp if you want put it’s saved in the file, and some people don’t like long filenames) We’d recommend using the same naming system for experimental files that describe the conditions you ran, or subject responses. But in this case it’s good to add the datestamp and timestamp. E.g.
- sub-subID_task-taskname_datestamp-timestamp_run-01
- sub-subID_resp-taskname_datestamp-timestamp_run-01
Many people in the Viscog group uses the following way to store condition and resp files, and their code is based on this kind of organization.
Data should be saved in mat file containing the following
conditions.mat is a cell array [ #events x # condition descriptors]. Condition and responses can either be in the same mat file, or in similar mat files, so it’s easy to cat them together later
conditions.Name is a [1 x #condition descriptors] cell array describing of each column. The description can be a cell array. E.g.
conditions.Name{1} = {‘Trial Num’}
conditions.Name{2} = {‘Seq’} {‘Onset’} {‘Random’}
conditions.Name{3} = {‘left’, ‘right’}
conditions.Description is a longer description of each condition.E.g.
conditions.Description{2}{1} = {‘Seq: motion traveling coherently from left to right or vice versa’}