10.5.10. Post-preproc, IV: Tracking

Overview

under construction

Probabilistic tracking and 3dTrackID

under construction

Proc: This is an example of fully probabilistic tracking through the set of “inflated” GM regions from the previous 3dROIMaker step. Of the two output FS aseg+aparc atlases, this uses the “2000” one:

# for I/O, same path variable as above
set path_P_ss = data_proc/SUBJ_001

# for variable simplicity, just go to the dir with the ROI maps
cd $path_P_ss/dwi_05

set gm_netw = sel_indt_aparc+aseg_REN_gm_GMI.nii.gz

3dTrackID                             \
    -mode PROB                        \
    -dti_in   dt                      \
    -netrois  $gm_netw                \
    -uncert   dt_UNC.nii.gz           \
    -prefix   o.pr00                  \
    -nifti                            \
    -no_indipair_out                  \
    -dump_rois AFNI                   \
    -alg_Thresh_FA      0.2           \
    -alg_Thresh_Frac    0.1           \
    -alg_Nseed_Vox      5             \
    -alg_Nmonte      1000             \
    -echo_edu                         \
    -overwrite

-> produces output in the same directory ‘data_proc/SUBJ_001/dwi_05/’, since all volume files occupy the same space/grid…

under construction

Visualizing WM connections and fat_proc_connec_vis

Proc: This is an example of viewing several WMCs together in one image that can be viewed in SUMA. Each WMC is surfaceized and colored individually. In this case all AND-logic WMCs that were found through the “Right-Thalamus-Proper” target are viewed:

fat_proc_connec_vis                                            \
    -in_rois o.pr00/NET_000_ROI_*Right-Thalamus-Proper*nii.gz  \
    -prefix  o.pr00_Right-Thalamus-Proper                      \
    -trackid_no_or

-> produces output in the same directory ‘data_proc/SUBJ_001/dwi_05/’, since all volume files occupy the same space/grid…

under construction

under construction

(just axi and cor views)

../../_images/autorecord.A.171219_191503.265.jpg ../../_images/autorecord.A.171219_191508.798.jpg
../../_images/autorecord.A.171219_191622.585.jpg ../../_images/autorecord.A.171219_191637.369.jpg

Visualizing matrices of structural properties and fat_proc_connec_vis

under construction

Proc: This is an example of viewing several WMCs together in one image that can be viewed in SUMA. Each WMC is surfaceized and colored individually. In this case all AND-logic WMCs that were found through the “Right-Thalamus-Proper” target are viewed:

fat_proc_connec_vis                                            \
    -in_rois o.pr00/NET_000_ROI_*Right-Thalamus-Proper*nii.gz  \
    -prefix  o.pr00_Right-Thalamus-Proper                      \
    -trackid_no_or

-> produces output in the same directory ‘data_proc/SUBJ_001/dwi_05/’, since all volume files occupy the same space/grid…