mrVista

mrVista Scripts

Scripts contained within this folder can be used to automate the process of setting up a mrVista environment to analyse data. Some user input is required for selecting which scans should be used, and to check the alignment, but on the whole as many elements as possible are automated.

All of the stages that require user input are performed for all subjects first, before the more time-consuming parts (such as motion-correction) are carried out, so that you can leave the script running once you've dealt with the input for each subject.

Step 1:

• Create a project-specific folder, i.e. this is the folder that will contain all your analysis files (data and Anatomy), for example: fMRImyExperiment

Step 2:

• Run script setupAnalysisFolderStruct.m
• You will be prompted to enter the subject ID, and to select which scan sessions you want to setup as part of this project (follow the dialog prompts). Do this for each subject you want to set up a folder for.

Step 3:

• Run the recon on your structural data with fsl (if not already done), this should be within a folder called FS_SUBJECTS in your Project folder. (I will soon add a script for automating this too).

Step 4:

• Run setupAnatomyFiles.m
• This uses the output of the fsl recon, so you need to have already done this. Will prompt for subject ID, and the location of their FS_SUBJECTs folder.

Step 5:

• Run runInit_To_GrayView.m by calling the following in matlab: logProcessing = runInit_To_GrayView([optional Input to project folder path])
• For all subjects in the project folder (created in Step 2), this script will setup the mrVista sessions and do all the steps including creating the gray view.
• User input is required to check the alignment of the inplane to structural for each subject/session, and then once this is done it requires no further input while motion correction etc is performed.
• It does not automatically setup any coherance params, so if this is needed you may need to modify the script (or create another to do this after the session is created).
• N.B. slice timing correction is not included in this step - if using multiband I would not advise doing the correction in mrVista, as far as I can tell it is not set up to appropriately deal with this type of correction. If TRs are quite short then slice timing correction would likely have a minimal effect anyway.

Once these steps are done you can open mrVista sessions from each session folder as normal to work with the data (i.e. when in the session directory call mrVista 3).

TODO - scripts to follow for automating processes such as pRF analysis.