Differential Tractography

Before practicum on Friday, please complete following:

Review Paper

• Read through Differential Tractography.

Differential tractography tutorial

• Documentation.

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During practicum on Friday:

Diffusion MRI analysis methods

Conventional versus Differential Tractography

	Conventional fiber tracking	Differential fiber traacking
seed point	start at any white matter location	start at any white matter location
propagation	propagate along fiber orientation	propagate along fiber orientation
termination criteria	anisotropy threshold, angular threshold	anisotropy threshold, angular threshold, threshold for the anisotropy decrease

Differential Tractography

Variants

1. Longitudinal versus cross-sectional analysis
2. native space versus template space

Type 1: Longitudinal comparison in the native space

summary: comparing patients’ baseline scans with follow-up scans in the native space.

data: SCA patient’s preprocess SRC files, including the baseline scans and the follow up scans.

For each patient, run the following:

1. Run GQI reconstructions on baseline and follow-up SRC files.
2. Export FA maps from the follow-up scans.
3. Open the FIB file of the baseline scan and [Slices][Inser Other Images]=the exported FA maps of the second scan.
4. Specify metrics at [Step T3c: Options][Tracking Parameters][Differential Tracking] and run differential fiber tracking.

dsi_studio --action=rec --source=*.src.gz
dsi_studio --action=exp --source=*02_dwi*.fib.gz --export=dti_fa
dsi_studio --action=trk --source=*_ses-01_dwi.src.gz.gqi.1.25.fib.gz --other_slices=*_ses-02_dwi.src.gz.gqi.1.25.fib.gz.dti_fa.nii.gz --dt_metric1=dti_fa --dt_metric2=*_ses-02_dwi --dt_threshold=0.2 --seed_count=10000000 --min_length=30 --output=*.tt.gz

Type 2: Longitudinal comparison in the template space

summary: comparing patients’ baseline scans with follow-up scans in the template space.

• normalization partly handles deformation
• use template as the tracking framework.

For each patient, run the following:

1. Run QSDR reconstructions on baseline and followup SRC files.
2. Export FA maps from all scans.
3. Open the template FIB file and [Slices][Inser Other Images]=the exported FA maps of the first and second scan.
4. Specify metrics at [Step T3c: Options][Tracking Parameters][Differential Tracking] and run differential fiber tracking.

dsi_studio --action=rec --source=*.src.gz --method=7 --output=*.qsdr.fib.gz
dsi_studio --action=exp --source=*.fib.gz --export=dti_fa
dsi_studio --action=trk --source=0 --other_slices=sub-SCA201_ses-01_dwi.qsdr.fib.gz.dti_fa.nii.gz,sub-SCA201_ses-02_dwi.qsdr.fib.gz.dti_fa.nii.gz --dt_metric1=sub-SCA201_ses-01_dwi --dt_metric2=sub-SCA201_ses-02_dwi --dt_threshold=0.2 --seed_count=10000000 --min_length=30 --output=sub-SCA201.tt.gz

dsi_studio --action=trk --loop=*_ses-01_dwi.qsdr.fib.gz --source=0 --other_slices=*_ses-01_dwi.qsdr.fib.gz.dti_fa.nii.gz,*_ses-02_dwi.qsdr.fib.gz.dti_fa.nii.gz --dt_metric1=*_ses-01_dwi --dt_metric2=*_ses-02_dwi --dt_threshold=0.2 --seed_count=10000000 --min_length=30 --output=*.tt.gz

Type 3: cross-sectional comparison in the native space

summary: compare patients’ scans with their age-sex-matched scan regressed from the control subjects.

data: SCA control subject’s connectometry database (dti_fa).

for each patient, run the following:

1. Open the GQI-FIB file of the baseline scan and [Slices][Inser Other Images]=sub-control_only.dti_fa.db.fib.gz
2. Input subject’s age and sex for generating age-sex-matched data.
3. Specify metrics at [Step T3c: Options][Tracking Parameters][Differential Tracking] and run differential fiber tracking.

dsi_studio --action=trk --source=*_ses-01_dwi.src.gz.gqi.1.25.fib.gz --other_slices=sub-control_only.dti_fa.db.fib.gz --dt_metric1=sub-control_only --dt_metric2=dti_fa --subject_demo=patient_age_sex.txt --dt_threshold=0.2 --seed_count=10000000 --min_length=30 --tip_iteration=16 --output=*.cross_sectional.tt.gz

Type 4: cross-sectional comparison in the template space

summary: compare patients’ scans with their age-sex-matched scan regressed from the control subjects.

for each patient, run the following:

1. Open the QSDR-FIB file of the baseline scan and [Export] dti_fa
2. Open the template FIB file
3. [Slices][Inser Other Images]=the exported FA maps of the baseline scan.
4. [Slices][Inser Other Images]=sub-control_only.dti_fa.db.fib.gz and input subject’s age and sex for generating age-sex-matched data.
5. Specify metrics at [Step T3c: Options][Tracking Parameters][Differential Tracking] and run differential fiber tracking.

dsi_studio --action=trk --loop=*_ses-01_dwi.qsdr.fib.gz.dti_fa.nii.gz --source=0 --other_slices=*_ses-01_dwi.qsdr.fib.gz.dti_fa.nii.gz,sub-control_only.dti_fa.db.fib.gz --dt_metric1=sub-control_only --dt_metric2=*_ses-01_dwi --subject_demo=patient_age_sex.txt --dt_threshold=0.2 --seed_count=10000000 --min_length=30 --tip_iteration=16 --output=*.cross_sectional.tt.gz

Testing the Results

Practicum assignment: false discovery rate (FDR) estimation for differential tractography

longitudinal study

1. run longitudinal differential tractography on all subjects, including controls and patients
2. calculate the averaged volume of findings in the cerebellum from controls –> expected volume of false positives
3. calculate the averaged volume of findings in the cerebellum from patients –> expected volume of true positives+false positives
4. FDR = false positive/(true positive+false positives) = (volume from controls)/(volume from patients)

cross-sectional study

1. run cross-sectional differential tractography on SCA2 controls, including controls and patients
2. same as above
3. same as above
4. same as above