12.5.10. 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
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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…
