FSL-TBSS Processing Guide - Blackford Lab

1 Vanderbilt University Institute of Imaging Science FSL-TBSS Processing Guide Suzanne Avery 2010. Suzanne Avery FSL-TBSS Analysis Guide 09/2010. Software Versions Used: MATLAB R2009a vuTools downloaded 9/14/09. FSL running in VMware virtual machine VMware Player version build-156735 (centOS, GNOME file mgmt). WinZip MRIcro version build 1. DTIstudio version Software Downloads: MRIcro: MRIcron: DCM2 NII: DTIstudio: FSL: VMware Player: Data Set Used: WS data set: 20 subjs Philips format DTI -- 32 direction 2x2x2. Important tbss Articles: Pubmed link to NeuroImage tbss article: Pubmed link to Nature Protocols tbss article: Important Processing Links: FSL-TBSS Guide : FMRIB- tbss webpage: FSL-Email Archives: NeuroWiki: Processing DTI (FSL): :Processing_DTI_(FSL).

2 Fiber Tract-based Atlas of Human White Matter Anatomy: FSL-FDT Diffusion Toolbox Guide : VUIIS Wiki: Matlab Image Processing Tools: 2. Suzanne Avery FSL-TBSS Analysis Guide 09/2010. This Guide is written for Vanderbilt Philips users who are beginners at preprocessing DTI data in FSL. FSL. provides a set of toolboxes which can be used exclusively for tbss preprocessing (see FSL-TBSS Guide for the basic recommended preprocessing steps). However, vuTools scripts and custom Matlab scripts are supplementally used throughout this Guide to address specific Processing problems. vuTools scripts may be downloaded from the VUIIS wiki, and custom scripts will be provided with this Guide .

3 This Guide is meant to supplement the FSL Processing information pages by providing a walkthrough of the basic FSL- recommended steps plus additional troubleshooting steps proven on Philips DTI data. Outline of Basic Processing Steps: Step 1: Establish initial file structure Step 2: Check PAR files for important header information Step 3: Check images for visible quality issues Step 4: Reformat image files (Matlab, DTIstudio, or dcm2nii). Step 5: Move/Rename Nifti image files Step 6: Eddy Current Correction (FSL). Step 8: Extract b=0 image (Matlab). Step 9: Brain Extraction (Matlab). Step 11: DTIfit (FSL). Step 12: Check FA images using fslview (FSL).

4 Step 13: Create tbss skeleton and perform group statistics (FSL). Outline of Optional Processing Steps: Step 7: Distortion Correction (Matlab optional for data with problematic distortions). Step 10: Automated Outlier Rejection (DTIstudio optional for high motion data). 3. Suzanne Avery FSL-TBSS Analysis Guide 09/2010. Step 1: Establish initial file structure o Changes to the file structure become difficult later in Processing , so it is important to design an intuitive file structure from the beginning. In this recommended design, raw files are stored separately from preprocessing folders so that the raw data aren't accidentally modified.

5 Recommended initial file structure: Create one raw data directory per subject, place all raw PAR/REC files here for safekeeping /DTI/RawData/subj#/rawdatafiles Create one preprocessing directory per subject /DTI/Preproc/subj#. o If running FSL through a virtual machine (VM), your analysis folder on your hard drive should be shared' with your VM. This allows you to write FSL Processing files directly to your hard drive folder and eliminates the need to constantly copy and paste files between the two machines, which can result in overwritten data and confusion. This also allows data to be accessed through MRIcro, DTIstudio, or Matlab without opening the VM.

6 Depending on the version of VMware you are using, these steps may need to be done in VMware either prior to or after opening the FSL virtual machine: Select VMware Player Shared Folders . Set host path 4. Suzanne Avery FSL-TBSS Analysis Guide 09/2010. To navigate to this shared folder, open a new Terminal window in the VM and use a change directory (cd) command (ie. cd /mnt/hgfs/DTI) prior to opening FSL. Step 2: Check PAR files for important header information o Open DTI PAR file using notepad or another text editor that does not word wrap o From upper panel, note: Software version #. # of slices FOV. Water Fat Shift 5.

7 Suzanne Avery FSL-TBSS Analysis Guide 09/2010. o From lower panel, note: Reconstruction size (scan resolution). Slice thickness Diffusion value Diffusion gradient (it's not necessary at this point to note the exact diffusion gradient values, just note where these columns are in the par file for later). ** ** **. **dotted lines indicate break points in screenshot 6. Suzanne Avery FSL-TBSS Analysis Guide 09/2010. Step 3: Check images for visible quality issues o It is very common to have image quality problems such as ghosting (phase error due to finite motion), complete disappearance of images (due to severe motion), zebra patterns (spikes in k-space), and missing data (upload, download, or conversion error).

8 These images must be identified by visual inspection. Images may be checked in any image viewer (ie. Matlab, fslview, MRIcro, or DTIstudio); however, DTIstudio is superior for detailed visual analysis. PAR/REC. images can be opened and viewed directly in DTIstudio or Matlab. However, PAR/REC images must first be converted to Nifti or Analyze format to be viewed in MRIcro or fslview (see image conversion steps below). Ghosting EPI distortion artifact Vitamin E. Motion artifact marker artifact o For 4D DTI series: There should be 1 DTI volume per direction + one non-diffusion image (T2. weighted, or b=0) + (usually) one average DTI image.

9 The b=0 and avg DTI images should be located at either the beginning or end of the 4D sequence. Note whether the b=0 and avg DTI. image are first or last in the 4D sequence o DTIstudio viewing: Open DTIstudio Select File DTI Mapping Select image file type (Philips REC). Enter correct Image Parameters for data (these values are in the PAR file). Set b_Value (usually 1000 or greater). Click Add a File, select appropriate DTI REC file Create a Gradient Table file using your bvecs file (see DTIfit step below for explanation of bvecs file and how to extract this from the PAR file if necessary). Each row of the DTIstudio Gradient Table should begin with a row number and colon.

10 B-values in the first and second columns should be followed by a comma. Save each Gradient Table file as a text document in the subject folder and copy and paste into DTIstudio. Example of a Gradient Table: 0: , , 1: , , 2: , , 3: . 7. Suzanne Avery FSL-TBSS Analysis Guide 09/2010. 32: 0, 0, 0. 33: 100, 100, 100. Click OK. An image such as the one below should be displayed. Select the DtiMap tab on the bottom right panel. Click the Original ADC Mean STD' button on the right-hand tool bar 8. Suzanne Avery FSL-TBSS Analysis Guide 09/2010. This window displays all image gradient blocks side-by-side at the same slice level.