TRACULA: Troubleshooting, visualization, and group analysis
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1 TRACULA: Troubleshooting, visualization, and group analysis Anastasia Yendiki HMS/MGH/MIT Athinoula A. Martinos Center for Biomedical Imaging 18/11/13 TRACULA: troubleshooting, visualization, group analysis 0/19
2 Directory structure Each subject has a TRACULA output directory, $dtroot/$subj/ Under this directory: dmri/ : Raw diffusion images, outputs of tensor fit dmri.bedpostx/ : Outputs of ball-and stick model fit dlabel/ : Files that aid the tractography (from subject s own anatomical, e.g. aparc+aseg, or from tract atlas, e.g. anatomical priors, initialization) dpath/ : Outputs of tractography scripts/ : Log files 18/11/13 TRACULA: troubleshooting, visualization, group analysis 1/19
3 Ball-and-stick model fit Multiple diffusion compartments in each voxel: Anisotropic compartments that model fibers (1, 2, ) Behrens et al., MRM 03 Jbabdi et al., NeuroImage 07 One isotropic compartment that models everything left over (0) FSL/bedpostX infers from the data: Orientation angles of anisotropic compartments Volumes of all compartments Overall diffusivity in the voxel Multiple fibers only if they are supported by data 18/11/13 TRACULA: troubleshooting, visualization, group analysis 2/19
4 Troubleshooting: Gradient vectors Check that orientation of tensors follows corpus callosum, cingulum, corticospinal tract WRONG! WRONG! 18/11/13 TRACULA: troubleshooting, visualization, group analysis 3/19
5 Troubleshooting: Registration to T 1 Check aparc+aseg transformed to diffusion space, overlay on FA freeview dmri/dtifit_fa.nii.gz\ dlabel/diff/aparc+aseg.bbr.nii.gz Also good for checking quality of aparc+aseg (perhaps recon-all brain mask includes too much or too little?) 18/11/13 TRACULA: troubleshooting, visualization, group analysis 4/19
6 Troubleshooting: Initialization If path has not moved away from its initial position (reconstructed path looks like a 1D curve), there was something wrong with this initial position (maybe goes off white matter?) freeview dmri/dtifit_fa.nii.gz \ dlabel/diff/rh.slfp_pp_avg33_mni_bbr_cpts_5.nii.gz 18/11/13 TRACULA: troubleshooting, visualization, group analysis 5/19
7 Troubleshooting: Initialization If initialization has failed for a specific pathway and subject, choose another initialization and repeat reconstruction (only repeat this particular pathway/subject) In configuration file: set reinit = 1 Limit subjlist to this subject only Limit pathlist to this pathway only Repeat: trac-all -prior -c dmrirc trac-all -path -c dmrirc Make sure to remove set reinit = 1 when done with this! 18/11/13 TRACULA: troubleshooting, visualization, group analysis 6/19
8 Visualization with freeview There is a 4D volume where all the pathway distributions that were estimated have been merged Opening this file in freeview will display all distributions as isosurfaces, thresholded at 20% of their maximum value. 18/11/13 TRACULA: troubleshooting, visualization, group analysis 7/19
9 Visualization: 3D view freeview dmri/dtifit_fa.nii.gz \ -tv dpath/merged_avg33_mni_bbr.mgz Change threshold for display 18/11/13 TRACULA: troubleshooting, visualization, group analysis 8/19
10 Visualization: 3D view freeview dmri/dtifit_fa.nii.gz \ -tv dpath/merged_avg33_mni_bbr.mgz Change threshold for display 18/11/13 TRACULA: troubleshooting, visualization, group analysis 9/19
11 Visualization: Slice view freeview dmri/dtifit_fa.nii.gz \ -tv dpath/merged_avg33_mni_bbr.mgz Change threshold for display 18/11/13 TRACULA: troubleshooting, visualization, group analysis 10/19
12 Tract-based measures Reconstruction outputs Posterior probability distribution of pathway given data (3D): paths.pd.nii.gz Maximum a posteriori pathway (1D): path.map.nii.gz Tract-based diffusion measures (FA, MD, RD, AD) Averaged over the entire pathway distribution: pathstats.overall.txt As a function of position along the pathway: pathstats.byvoxel.txt 18/11/13 TRACULA: troubleshooting, visualization, group analysis 11/19
13 Path stats (average values) pathstats.overall.txt *_Avg: Average values of every voxel with probability > 20% of the maximum *_Avg_Weight: Multiply value at voxel with the probability at that voxel, sum over every voxel with probability > 20% of the maximum This is closest to the notion of mean/expected value *_Center: Average values only on the 1-D path with the highest probability 18/11/13 TRACULA: troubleshooting, visualization, group analysis 12/19
14 Path stats (values along the path) pathstats.byvoxel.txt AD_Avg RD_Avg At each position along the path Value on 1-D path with the highest probability *_Avg: Average value over nearest points from all sampled paths Coordinates are given in native diffusion space Paths from different subjects generally have different number of positions along path 18/11/13 TRACULA: troubleshooting, visualization, group analysis 13/19
15 Example: Huntington s disease (HD) Data courtesy of Dr. Diana Rosas, MGH Healthy HD stage 1 HD stage 2 HD stage 3 18/11/13 TRACULA: troubleshooting, visualization, group analysis 14/19
16 Plot measures along the pathway Want to combine FA/MD/ along the path from multiple subjects, plot mean FA/MD/ for each group 18/11/13 TRACULA: troubleshooting, visualization, group analysis 15/19
17 Plot measures along the pathway Want to display P-values for T-test on differences in mean FA/MD/ between groups CST 0.1 Cingulum /11/13 TRACULA: troubleshooting, visualization, group analysis 16/19
18 New: Assemble group stats trac-all -stat -c dmrirc Combine files of stats along the path from multiple subjects: Find median path, set its mid-point to the origin (zero arc length along the path) For every other path, find the closest point on this path to the midpoint of the median path, set this point to the origin Now every point on every path is assigned an arc length Interpolate values of FA/MD/ at the same arc lengths for all paths Outputs are saved under $dtroot/stats/ and can be used for group studies on FA, MD, RD, AD along the pathway One text file per pathway per measure (FA, MD, RD, AD) Also produces average coordinates for each pathway in the template space (MNI or CVS) for visualization purposes Log file shows which subjects are outliers (different shape-wise) 18/11/13 TRACULA: troubleshooting, visualization, group analysis 17/19
19 Display mean paths Use waypoint (-w) functionality of freeview freeview $mnitemp \ -w $dtroot/stats/*.path.mean.txt 18/11/13 TRACULA: troubleshooting, visualization, group analysis 18/19
20 Paint p-values on mean paths Save p-values in a simple text file, load it as a scalar map 18/11/13 TRACULA: troubleshooting, visualization, group analysis 19/19
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