Or How To Handle Large Amounts Of Data Efficiently

This is for neuroscientists who need to process documents from a large number of people. An extended example of an ideal batch script is developed below. It belongs to the typical image data analysis software, but it mainly uses the Python scripting language and is therefore quite general.


For a multi-subject experiment, the same analysis programs are typically used for each data set in each discipline. This is the perfect application for looking for a simple script program capable of passing multiple sets of data to the same set of parsers. To take full advantage of the wonders of modern computing, batch scripting is required for content creation.

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This tutorial creates a typical and useful batch script. Once most people have gone through this, you can create your own analysis program by simply copying the parts you want and changing a few lines to pass the current data.enrolled in the program of your choice. I tried to shift the “computer to programming” workload to “cut and paste”.

Is an

This is an example of an FSL program that uses a “fast” program that precisely segments an MRI image into multiple tissue components (gray matter, white matter, cerebrospinal fluid) and then tries to reanimate the heterogeneity artifact, i.e. pixels. the same type of tissue have the same values ‚Äč‚Äčthroughout the brain.

Recursive Parsing

The easiest way to start a cycle of the same type of scans is to force each command by clicking on the shell, press “return”, wait for completion, and then enter a new command: < /p>

>fast – and even /fullpath/fn_1.img
quickly > -or /fullpath/fn_2.img
> quickly /fullpath/fn_3 -ou.img

Usually the only change you need to make is a few filenames. However, this has several drawbacks:

  • You must be physically behind the keyboard.
  • You must wait for one process before you can prepare for the nextto him. This can be depressing, as each process usually takes several minutes, so it’s easy to get distracted.
  • Operator for misprints and misrepresentations
  • You must make sure that the program has created the correct processing files.
  • You should check the result to make sure it is acceptable.
  • A significant improvement in efficiency would probably be to enter commands in your own text editor, save them as an executable text file, and run from the command line. The most common way to do this is to use a simple bash file. For this to work, our instruction file line must first contain a command environment that will eventually be used for execution commands. For them, put the party environment up to about this text on the first line:

    The Smash environment is very useful and can be found on most Unix, Linux, and later Macintosh computers. Your company may be working on fairly complex bash scripts, but sooner or later (probably sooner) you may run intobash syntax. Therefore, I recommend that families start with a slightly more complete programming language – the Python programming language. this sleep uses the Python example.

    Example 1:

    To start scanning “almost” all three files, create the following file:

    How? ‘Or’ What

    res is equal to os.system(‘fast -or /fullpath/fn_1.img’)
    Ers = os.system(‘fast -or /fullpath/fn_2.img’)
    Ers = os.system(‘fast -or /fullpath/fn_3.img’)

    The first line tells the computer how to run the python script from the text archive. In the individual lab Href=”http://brainimaging jumped edu/~jjo/”>John with A clever way to link a Python Exe program to the Python interpreter.

    The second line imports the entire “os” library. Most of the incredibly useful parts of Python are included, down to libraries that are only loaded on demand to make the methods as simple as possible. The “os” library contains routines that the operating system interacts with.


    Three quick lines, call us once for each input file. In Python, subroutines or directory entries are identified. in the format “library.subroutine”. In this case, the set (text brackets) between them is transmitted to the entire operating system in the same way as when entering a command from the keyboard. This means that you can type the name of a text file type (script) on the command line, return popular and output data, and three files will be fully processed. Previously, when smoking was allowed inside, this would have been the ideal time, equivalent to a 10-minute break for a cigarette. Currently, the device is a cafe.


    As a scientist, or at least an aspiring craftsman, we usually ask you, “How can we do this better?” Here are some problems with this script:

  • You need to edit the file each time the owners want to scan a new set of files.
  • You still need to check each of our results both in terms of the final viability of the program (creating files) and in terms of the quality of the results.
  • If there is a possibility of a data entry problem, the main stagenarium will not work. This annoying problem occurs when the script crashes at least 5 times after you leave Friday night and then come back to this lab on Sunday morning hoping to start again with your amazing results…
  • Example 2: Adding A Loop

    One thing we can use is that the same thing happens for every input file. We can then create a “loop” that goes through each file to find the analysis. This result has two advantages:

    1. The code has become more compact and easier to understand.
    2. The number of files can, of course, vary.


    We create a callable list (also an array) of filenames. The “loop adds” to each filename in the list one by one, a good solid body creates a string (command) that passes that filename “quickly” and the command is executed. Pink shows the text has changed from the old example.