News: Announcing the 2012 FSL & FreeSurfer Course, May 14-18, Auckland, New Zealand

2011 FSL & FreeSurfer Course - Lectures & Practicals

All material copyright © 2000-2011, FMRIB Analysis Group & MGH, Boston.

Lectures and Practicals

• Introduction to Imaging, FSL & FreeSurfer   lecture / practical
• Brain Extraction, Registration, Motion Correction and EPI Distortion   (BET, FLIRT, MCFLIRT, PRELUDE & FUGUE)   lecture / practical
• FMRI Preprocessing and Model-Based Analysis  (FEAT)
  1. Preprocesing and Simple Single-Session Stats   lecture part 1, part 2 / practical
  2. Permutation Testing (Randomise) and Multi-Subject Stats    lecture part 1, part 2 / practical
  3. Advanced FMRI Analysis    lecture / practical
• Segmentation & Structural Statistics  (FAST, FIRST, SIENA, FSL-VBM) lecture / practical
• Model-Free FMRI Analysis  (MELODIC)  lecture / practical
• Analysis of Diffusion-Weighted MR Data  (FDT, TBSS)  lecture / practical
• Scripting  lecture & practical. This is not a formal part of the course, but can be carried out on your own during the course if you have time to spare. Within the lecture web pages, to find the interleaved practical instructions, click on the e symbols when they appear in the lecture slides, or go to the lecture index (via the up arrow in the bottom right) and find the green links.

People with no previous experience of UNIX would benefit greatly from spending a few hours working through at least the first 5 sections of A Basic UNIX Tutorial.

Data Files

The data for the course is divided into 5 parts due to the size of the data and can be downloaded using the links below, or using wget [Linux] or curl [Mac OS X]. If you are working at the FMRIB Centre then please see these instructions for information on following the course inside FMRIB.

• File 1 - intro, registration, structural/segmentation and scripting
• File 2 - melodic, diffusion (fdt + tbss)
• File 3 - fmri (excluding one 3 level example)
• File 4 - fmri (3 level controls)
• File 5 - fmri (3 level patients)

Once you have downloaded the files they need to be uncompressed before you can begin the course. To do this, open a terminal, change into the folder where you downloaded the course files to and run the following commands:

      tar zxf fsl_course_data1.tar.gz; tar zxf fsl_course_data2.tar.gz
      tar zxf fsl_course_data3.tar.gz; tar zxf fsl_course_data4.tar.gz
      tar zxf fsl_course_data5.tar.gz
    

NB If you downloaded the files using Safari on Mac OS X, then they may already have been uncompressed, ie missing the .gz extension. In this case, change the tar commands above to 'tar xf'.

2011 Physics

• Karla Miller: MRI Physics Lectures

2010 Physics

• Karla Miller: MRI Physics Lectures

2007 Physics / Applications

• Kate Watkins: Experimental Design
• Richard Wise: FMRI Acquisition
• Andreas Bartsch: Advanced Clinial (F)MRI Applications of FSL

2006 Physics / Applications

• Mark Cohen: MRI Basics
• Susan Bookheimer: FMRI Experimental Design
• Susan Bookheimer: Clinical Applications of FMRI
• Andreas Bartsch: Clinical Applications of FSL
• Nicola De Stefano: Clinical Applications of Structural MRI

All material copyright © 2006-2011 held by talk/practical authors

Using wget to download the course data

As the course data files are large, Linux users may find that using the wget command to download the course data files is more reliable. In a terminal, change to the folder you wish to download the data to and issue the following commands:

      wget -c http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data1.tar.gz
      wget -c http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data2.tar.gz
      wget -c http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data3.tar.gz
      wget -c http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data4.tar.gz
      wget -c http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data5.tar.gz
    

If, for some reason your wget downloads are interrupted, you can restart any incomplete downloads by running that wget command again.

Using curl to download the course data

As the course data files are large, Mac users may find that using the curl command to download the course data files is more reliable. In a terminal, change to the folder you wish to download the data to and issue the following commands:

      curl -# -O -C - http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data1.tar.gz
      curl -# -O -C - http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data2.tar.gz
      curl -# -O -C - http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data3.tar.gz
      curl -# -O -C - http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data4.tar.gz
      curl -# -O -C - http://www.fmrib.ox.ac.uk/fslcourse/fsl_course_data5.tar.gz
    

If, for some reason your curl downloads are interrupted, you can restart any incomplete downloads by running that curl command again.