MRI Acquisition Protocols for DTI

The quality of the raw data sets the ceiling on what preprocessing can achieve; no amount of correction fixes a flawed acquisition.

Required Scans

A complete DTI acquisition for the preprocessing pipeline described in this tutorial requires four scan types:

Scan	Purpose	Typical Duration
T1-weighted structural	High-resolution anatomical reference for skull stripping and registration	5–7 min
DWI (main diffusion run)	Diffusion-weighted images with multiple gradient directions and b-values	8–20 min
Fieldmap AP	B0 field map with anterior-to-posterior phase encoding	30 sec – 1 min
Fieldmap PA	B0 field map with posterior-to-anterior phase encoding	30 sec – 1 min

Without fieldmaps, you cannot run TOPUP to correct susceptibility distortions. Skipping TOPUP means your frontal and temporal lobe data will be geometrically distorted, which biases FA measurements and degrades registration accuracy. Always acquire fieldmaps with opposite phase encoding directions.

T1-Weighted Structural

The T1 provides high-resolution anatomy for:

• Skull stripping (brain extraction)
• Registering diffusion space to structural space
• Bridging from structural to standard space (MNI)

Common sequences: MPRAGE (Siemens), BRAVO (GE), 3D TFE (Philips). Typical resolution: 1 mm isotropic.

DWI — The Main Diffusion Acquisition

This is your primary data. Key parameters to consider:

Parameter	Recommendation	Why
b-values	0, 1000 for basic DTI; 0, 1000, 2000, 3000 for multi-shell	Higher shells enable CSD/NODDI; single shell is sufficient for FA/MD
Number of directions	30 minimum, 60+ preferred	More directions = more robust tensor fit and better angular resolution
Number of b=0 images	6–10 scattered throughout the run	More b=0 images improve SNR for brain masking and normalization
Resolution	1.5–2.5 mm isotropic	Smaller voxels resolve finer anatomy but have lower SNR
Multiband factor	2–4 (if available)	Acquires multiple slices simultaneously, reducing scan time

Number of Directions

Analysis	Minimum Directions	Recommended
Basic DTI (FA, MD)	6 (absolute minimum)	30+
Robust DTI with reliable statistics	20	30–64
HARDI / CSD (crossing fibers)	45	60–90 per shell
NODDI	30 per shell	60+ per shell

More directions are almost always better. The main constraint is scan time — each additional direction adds a few seconds.

Fieldmaps (Reverse Phase-Encoded B0s)

Fieldmaps correct susceptibility distortions — geometric warping that occurs near air-tissue interfaces (sinuses, ear canals). These distortions are strongest in the frontal and temporal lobes.

The method used in this pipeline (TOPUP) requires B0 images acquired with opposite phase encoding directions:

• AP (anterior-to-posterior): Distortions push the frontal lobe posteriorly
• PA (posterior-to-anterior): Distortions push the frontal lobe anteriorly

By comparing the two distortion patterns, TOPUP can estimate and correct the underlying field inhomogeneity.

What to acquire: A short spin-echo EPI sequence with the same geometry (resolution, FOV, slice thickness) as your main DWI, but acquired once with AP and once with PA phase encoding. Each takes about 30 seconds.

Vendor-Specific Naming

Different scanner vendors use different names for the same things:

Concept	Siemens	GE	Philips
T1 structural	MPRAGE	BRAVO / IR-FSPGR	3D TFE
DWI sequence	ep2d_diff	DTI / DW-EPI	DWI / dMRI
Multiband	SMS (CMRR)	HyperBand	MultiBand SENSE
Phase encoding direction	In DICOM header	In DICOM header	In .PAR file
DICOM output	One file per slice or enhanced DICOM	One file per series	Classic DICOM or PAR/REC

Before running dcm2niix, understand how your scanner exports DICOMs. Some scanners produce one DICOM file per slice (thousands of files per scan), while others produce one enhanced DICOM file per series. Both work with dcm2niix, but the directory organization will look very different.

Multiband (Simultaneous Multi-Slice) Acceleration

Multiband acceleration acquires multiple slices simultaneously, dramatically reducing scan time. A multiband factor of 3 (MB3) means 3 slices are acquired at once, reducing the time for each volume by roughly 3x.

This technology was developed by the CMRR group at the University of Minnesota and is now available on most modern scanners (Siemens, GE, Philips).

Practical considerations:

• MB2–MB3 is standard and well-tested
• MB4+ can introduce artifacts (slice leakage) — use with caution
• In-plane acceleration (GRAPPA/SENSE) is often combined with multiband
• The combination of multiband and GRAPPA dramatically reduces scan time, enabling high-quality multi-shell acquisitions in under 15 minutes

Phase Encoding Direction and Readout Time

Two parameters from your acquisition are critical for configuring TOPUP and eddy:

Phase Encoding Direction

This determines which direction susceptibility distortions occur in the image. For most DTI acquisitions:

• AP (anterior-to-posterior): Phase encoding runs from front to back. In the acqp.txt file, this is typically 0 -1 0 readout_time
• PA (posterior-to-anterior): Phase encoding runs from back to front. This is typically 0 1 0 readout_time

The mapping between AP/PA and the numeric encoding in acqp.txt depends on your scanner and how the DICOM images were reconstructed. Always verify using the JSON sidecar from dcm2niix — look for the PhaseEncodingDirection field. See Configuration Files for details.

Total Readout Time

The total readout time (in seconds) is needed for the acqp.txt file. It can be found in the JSON sidecar from dcm2niix:

{
  "PhaseEncodingDirection": "j-",
  "TotalReadoutTime": 0.0959097,
  "EffectiveEchoSpacing": 0.000689998
}

If TotalReadoutTime is not directly available, it can be calculated from other parameters. See the dcm2niix documentation for details.

Example Protocols

Basic DTI (Single Shell, ~10 minutes)

Suitable for studies focused on FA and MD:

• 1 mm isotropic T1 MPRAGE (~6 min)
• 64 directions at b=1000, 8 b=0 images, 2 mm isotropic (~8 min)
• AP and PA fieldmaps (~1 min total)
• Total: ~15 minutes

Multi-Shell DTI (~20 minutes)

Suitable for CSD, NODDI, and DKI:

• 1 mm isotropic T1 MPRAGE (~6 min)
• 10 b=0 + 64 at b=1000 + 64 at b=2000 + 64 at b=3000, 1.5 mm isotropic, MB3 (~15 min)
• AP and PA fieldmaps (~1 min total)
• Total: ~22 minutes

Minimal DTI (~7 minutes)

Suitable for clinical settings with limited scan time:

• 1 mm isotropic T1 MPRAGE (~6 min)
• 30 directions at b=1000, 5 b=0 images, 2.5 mm isotropic (~4 min)
• AP and PA fieldmaps (~1 min total)
• Total: ~11 minutes

Before Leaving the Scanner

Always verify your data before the participant leaves:

1. Check volume counts: Does the DWI have the expected number of volumes? (directions + b=0 images)
2. Quick visual check: Open the DWI on the scanner console — is the brain fully in the FOV? Any obvious artifacts?
3. Fieldmaps acquired: Confirm both AP and PA fieldmaps are in the export queue
4. DICOM export: Start the DICOM transfer before the participant leaves — if something went wrong, you can re-scan

References

• Jones DK, Knosche TR, Turner R (2013). White matter integrity, fiber count, and other fallacies: The do's and don'ts of diffusion MRI. NeuroImage, 73, 239-254.
• Tournier JD, Mori S, Leemans A (2011). Diffusion tensor imaging and beyond. Magnetic Resonance in Medicine, 65(6), 1532-1556.
• Sotiropoulos SN, Jbabdi S, Xu J, et al. (2013). Advances in diffusion MRI acquisition and processing in the Human Connectome Project. NeuroImage, 80, 125-143.
• Setsompop K, Gagoski BA, Polimeni JR, et al. (2012). Blipped-controlled aliasing in parallel imaging for simultaneous multislice echo planar imaging with reduced g-factor penalty. Magnetic Resonance in Medicine, 67(5), 1210-1224.