Data collection

Imaging Protocol

Twenty healthy adults (mean age 36 years, age range 29-46 y.o.(SD = 4.7), 4 men and 16 women) were scanned at the Centre Hospitalier Universitaire of Sherbrooke (CHUS) using a clinical 3T MRI scanner (Ingenia, Philips Healthcare, Best, Netherlands) with a 32-channel head coil. For each participant, images were acquired at approximately the same time of day to avoid potential diurnal effects (i.e., a morning participant had all sessions in the morning, with a tolerated 2–3-hour variation). The study was approved by the local ethics committee (Comité d’éthique de la recherche du CHUS) and all participants gave written informed consent.

3DT1 - Anatomical 3D T1-weighted, DWI - Diffusion weighted Images, reverse b0 - Reverse phase encoding B0, ihMT - inhomogeneous magnetization transfer.

MRI acquisition parameters

All MRI data acquisitions were aligned on the anterior commissure-posterior commissure plan (AC-PC). The imaging protocol included the following sequences:

Parameters / Sequences	T1	DWI	Reverse B0	ihMT	T1 ihMT
Phase-encoding direction*	RL	PA	AP	RL	RL
Technique - Fast imaging method	FFE - TFE	SE - EPI	SE - EPI	FFE - EPI	FFE - EPI
Total scan duration	4 min 20s	9 min 20s	14s	6 min 04 s	13 s
Repetition time (TR, ms)	7.9	4800	4800	112	20
Echo Time (TE, ms)	3.5	92	92	3.6 (Δ = 6)	3.6 (Δ = 6)
Inversion Time (TI, ms)	950
Flip Angle (degree)	8	90	90	15	30
Field of View (FOV, mm)	224 x 224	224 x 224	224 x 224	224 x 224	224 x 224
Slices (n)	150	66	66	65	65
Voxel size (mm)	1 x 1 x 1	2 x 2 x 2	2 x 2 x 2	2 x 2 x 2	2 x 2 x 2
n b0, b-value (n directions)		7, 300 (8), 1000 (32), 2000 (60)
MT stauration pulse				10 Hann pulses of 0.9 ms duration with 1.5 ms interval
Frequency offset of +/-				7000 Hz
n Echoes - Echo spacing					3 - 6 ms

*The directions are specified in coordinates of the patient (LPH).

An example of bvec and bval file for DWI can be downloaded here:

bval bvec files

Data conversion: DICOM to BIDS

To convert data, we use BIDS. An example of the data structure for one subject is shown below:

data-subject
├── dataset_description.json
├── participants.json
├── participants.tsv
├── sub-001_ses-1
├── sub-001_ses-2
├── sub-001_ses-3
├── sub-001_ses-4
├── sub-001_ses-5
├── ...
├── sub-003_ses-1
    │
    ├── anat
    │   ├── sub-003-1_T1w.json
    │   ├── sub-003-1_T1w.nii.gz
    │   ├── sub-003-1_acq-pos_ihmt.json
    │   ├── sub-003-1_acq-pos_ihmt.nii.gz
    │   ├── sub-003-1_acq-neg_ihmt.json
    │   ├── sub-003-1_acq-neg_ihmt.nii.gz
    │   ├── sub-003-1_acq-altnp_ihmt.json
    │   ├── sub-003-1_acq-altnp_ihmt.nii.gz
    │   ├── sub-003-1_acq-altpn_ihmt.json
    │   ├── sub-003-1_acq-altpn_ihmt.nii.gz
    │   ├── sub-003-1_acq-T1w_ihmt.json
    │   └── sub-003-1_acq-T1w_ihmt.nii.gz
    │
    └── dwi
        ├── sub-003-1_dwi.bval
        ├── sub-003-1_dwi.bvec
        ├── sub-003-1_dwi.json
        ├── sub-003-1_dwi.nii.gz
        ├── sub-003-1_rev-b0.json
        └── sub-003-1_rev-b0.nii.gz

To convert our DICOM data folder to the compatible BIDS structure, we used dcm2bids.

dcm2bids -d DICOM_folder -p id_subject -c config.txt -o sub-id

Quality Control raw data

Quality control of raw data was performed using DMRI QC Flow.

Example of datasets for one subject

• Anatomical image

3D-T1w

• Diffusion-weighted images

DWI - b0	DWI - b value = 300	DWI - b value = 1000	DWI - b value = 2000	DWI - Reverse B0

• ihMT images

MT-Off	Positive (pos)	Negative (neg)	Alternative pos-neg	Alternative neg-pos	T1w ihMT