FSL based DTI Processing

DTI (pre)processing is an opinionated process with many opinions on exactly what to do. Here are some ideas.

Preprocessing with FSL

Certainly look to the FDT user guide.

If you're using eddy_correct and dtifit to correct and generate your tensor, we have a simple script to do the appropriate steps for an image: dtifit.sh

Rotate your bvecs?

When you run eddy_correct on your image, you end up rotating your volumes to align them in some way. It's an open question as to whether you should also then rotate the associated bvecs. See our discussion on the topics. FSL comes with a script to do this rotation based on the log files that eddy_correct makes: fdt_rotate_bvecs.

FSL dtifit and ENIGMA DTI as they currrently exist on our file system

Here is an example of the scripts that are run to do a simple FSL DTI preprocessing stream than run the ENIGMA DTI ROI extraction for the TIGRlab data.

on the SCC (as we now do it)

export PROJECTDIR=/external/rprshnas01/tigrlab/archive/data-2.0/<project_name>
module load /KIMEL/quarantine/modules/quarantine
module load datman/latest

  module load FSL/5.0.9 R/3.2.5 ENIGMA-DTI/2015.01
  dm-proc-dtifit.py \
    --inputdir ${PROJECTDIR}/data/nii \
    --outputdir ${PROJECTDIR}/pipelines/dtifit

  dtifit-qc.py \
    ${PROJECTDIR}/pipelines/dtifit/

  dm-proc-enigmadti.py \
    --calc-all \
    --QC-transfer ${PROJECTDIR}/metadata/checklist.csv \
    ${PROJECTDIR}/pipelines/dtifit \
    ${PROJECTDIR}/pipelines/enigmaDTI

on the kimel lab system you SHOULD only need to change some of the modules..

export PROJECTDIR=/archive/data-2.0/<project_name>
module load /archive/code/datman.module

  module load FSL/5.0.7 R/3.1.1 ENIGMA-DTI/2015.01
  dm-proc-dtifit.py \
    --inputdir ${PROJECTDIR}/data/nii \
    --outputdir ${PROJECTDIR}/pipelines/dtifit

  dtifit-qc.py \
    ${PROJECTDIR}/pipelines/dtifit/

  dm-proc-enigmadti.py \
    --calc-all \
    --QC-transfer ${PROJECTDIR}/metadata/checklist.csv \
    ${PROJECTDIR}/pipelines/dtifit \
    ${PROJECTDIR}/pipelines/enigmaDTI

Here is what those pieces do...

dm-proc-dtifit.py

Looks for DTI files in the input folder structure. When it finds them, it runs dtifit.sh on that DWI input. [dtifit.sh] does all the real work of:

1. Running FSL's BET on DWI file
2. Running eddy_current correction
3. Running FSL's dtifit, which calculated FA MD and all those eigenvectors and things.

For more into on this little script. Read what Jon Piptone wrote here. And read FSL's documentation here. dtifit.sh is sitting in the assets folder of the datman project...or can be downloaded from here.

Note: dm-proc-dtifit.py's magik DTI file finding powers really on two rules...

1. The DWI images are sitting in a nested folder structure inside a subject/session
2. The DWI images are nifti images with "DTI" in their file names..

For example:

${PROJECTDIR}/data/nii
├── subject_01
│   ├── subject_01_DTI60-1000_04_Ax-DTI60plus5-20iso.bval
│   ├── subject_01_DTI60-1000_04_Ax-DTI60plus5-20iso.bvec
│   ├── subject_01_DTI60-1000_04_Ax-DTI60plus5-20iso.nii.gz
│   └── subject_01_T1_02_SagT1Bravo-09mm.nii.gz
├── subject_02
│   ├── subject_02_DTI60-1000_04_Ax-DTI60plus5-20iso.bval
│   ├── subject_02_DTI60-1000_04_Ax-DTI60plus5-20iso.bvec
│   ├── subject_02_DTI60-1000_04_Ax-DTI60plus5-20iso.nii.gz
│   └── subject_02_T1_02_SagT1Bravo-09mm.nii.gz
...
└── subject_n
    ├── subject_n_DTI60-1000_04_Ax-DTI60plus5-20iso.bval
    ├── subject_n_DTI60-1000_04_Ax-DTI60plus5-20iso.bvec
    ├── subject_n_DTI60-1000_04_Ax-DTI60plus5-20iso.nii.gz
    └── subject_n_T1_02_SagT1Bravo-09mm.nii.gz

dtifit-qc.py

dtifit-qc.py is a little script that loops over the dtifit outputs and generates two type of snaps-shots.

1. Snapshots of the BET brainmask outline on the DWI images
2. Some colorful views of all DTI directions

This should just work on any ditfit output folder structure..

dm-proc-enigma.py

dm-proc-enigmadti.py looks for dtifit output directories and extracts ROI values following the ENIGMA-JHU atlas protocol (check out the ENIGMA protocols site for more into about that) - (Also cite this paper is you use this method)..

dm-proc-enigmadti.py does not actually run the enigma-dti pipeline itself but instead writes smaller scripts to run three other functions:

1. doInd-enigma-dti.py : runs enigma-DTI for one person
2. dm-proc-enigma-concat.py : concatenates all the ROI values into one csv file
3. dm-qc-enigma.py: creates qc snapshots of the skeleton for visual inspection.

The ENIGMA / JHU White Matter ROIs

Read more about the ENIGMA Protocol from their website

The ENIGMA Protocol Paper

Acheson, A., Wijtenburg, S. A., Rowland, L. M., Winkler, A., Mathias, C. W., Hong, L. E., … Dougherty, D. M. (2017). Reproducibility of tract‐based white matter microstructural measures using the ENIGMA‐DTI protocol. Brain and Behavior, 7(2), e00615. http://doi.org/10.1002/brb3.615 PMC Full Text

Open the atlas in NeuroVault

Integer	Label	Tract Name
3	GCC	Genu of corpus callosum
4	BCC	Body of corpus callosum
5	SCC	Splenium of corpus callosum
6	FX	Fornix (column and body of fornix)
7	CST-R	Corticospinal tract right
8	CST-L	Corticospinal tract left
9	ML-R	Medial lemniscus right
10	ML-L	Medial lemniscus left
11	ICP-R	Inferior cerebellar peduncle right
12	ICP-L	Inferior cerebellar peduncle left
13	SCP-R	Superior cerebellar peduncle right
14	SCP-L	Superior cerebellar peduncle left
15	CP-R	Cerebral peduncle right
16	CP-L	Cerebral peduncle left
17	ALIC-R	Anterior limb of internal capsule right
18	ALIC-L	Anterior limb of internal capsule left
19	PLIC-R	Posterior limb of internal capsule right
20	PLIC-L	Posterior limb of internal capsule left
21	RLIC-R	Retrolenticular part of internal capsule right
22	RLIC-L	Retrolenticular part of internal capsule left
23	ACR-R	Anterior corona radiata right
24	ACR-L	Anterior corona radiata left
25	SCR-R	Superior corona radiata right
26	SCR-L	Superior corona radiata left
27	PCR-R	Posterior corona radiata right
28	PCR-L	Posterior corona radiata left
29	PTR-R	Posterior thalamic radiation (include optic radiation) right
30	PTR-L	Posterior thalamic radiation (include optic radiation) left
31	SS-R	Sagittal stratum (include inferior longitidinal fasciculus and inferior fronto-occipital fasciculus) right
32	SS-L	Sagittal stratum (include inferior longitidinal fasciculus and inferior fronto-occipital fasciculus) left
33	EC-R	External capsule right
34	EC-L	External capsule left
35	CGC-R	Cingulum (cingulate gyrus) right
36	CGC-L	Cingulum (cingulate gyrus) left
37	CGH-R	Cingulum (hippocampus) right
38	CGH-L	Cingulum (hippocampus) left
39	FX/ST-R	Fornix (cres) / Stria terminalis (can not be resolved with current resolution) right
40	FX/ST-L	Fornix (cres) / Stria terminalis (can not be resolved with current resolution) left
41	SLF-R	Superior longitudinal fasciculus right
42	SLF-L	Superior longitudinal fasciculus left
43	SFO-R	Superior fronto-occipital fasciculus (could be a part of anterior internal capsule) right
44	SFO-L	Superior fronto-occipital fasciculus (could be a part of anterior internal capsule) left
45	IFO-R	Inferior fronto-occipital fasciculus right
46	IFO-L	Inferior fronto-occipital fasciculus left
47	UNC-R	Uncinate fasciculus right
48	UNC-L	Uncinate fasciculus left