Data collection =============== Study design ----------------- Twenty healthy adults (mean age 36 years, age range 29-46 y.o.(SD = 4.7), 4 men and 16 women) were scan 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. Each MRI session was repeated 5 times over 5 months and a 4-week interval (+/- 1 week). 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). Study design - 20 healthy subjects .. image:: acquisition_design.png :align: center :width: 700 All MRI data acquisitions were aligned on the anterior commissure-posterior commissure plan (AC-PC) and each MRI session include : * Anatomical 3D T1-weighted (3DT1) * Multi-shell diffusion-weighted images (DWI) * Reverse phase encoding B0 (revb0) * inhomogeneous magnetization transfer (ihMT) MRI acquisition parameters --------------------------- +--------------------------------+-------------+-------------+-------------+----------------+----------------+ | Parameters / Sequences | T1 | DWI | Reverse B0 | ihMT | T1 ihMT | +================================+=============+=============+=============+================+================+ | Phase-encoding direcion* | 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 | +--------------------------------+-------------+-------------+-------------+----------------+----------------+ | | |7, 300 (8), | | | | | n b0, b-value (n directions) | |1000 (32), | | | | | | |2000 (60) | | | | +--------------------------------+-------------+-------------+-------------+----------------+----------------+ | | | | | 10 Hann pulses | | | | | | | of. 0.9 ms | | | MT stauration pulse | | | | duration with | | | | | | | 1.5 ms interval| | +--------------------------------+-------------+-------------+-------------+----------------+----------------+ | Frequency offset of +/- | | | | 7000 Hz | | +--------------------------------+-------------+-------------+-------------+----------------+----------------+ | n Echoes - Echo spacing | | | | | 3 - 6 ms | +--------------------------------+-------------+-------------+-------------+----------------+----------------+ *The directions are specified in the standard way i.e. in coordinates of the patient (LPH). An example of bvec and bval file can be downloaded here: :download:`bval bvec files<../download/bval_bvec_files.zip>` Data conversion: DICOM to BIDS ------------------------------ To convert data we use `BIDS standard `__. An example of the data structure for one subject is shown below: :: data-subject ├── dataset_description.json ├── participants.json ├── participants.tsv ├── sub-001_ses-01 ├── sub-001_ses-02 ├── sub-001_ses-03 ├── sub-001_ses-04 ├── sub-001_ses-04 ├── sub-002_ses-01 ├── ... ├── sub-003_ses-01 │    ├── anat     │   ├── sub-003-01_T1w.json    │   ├── sub-003-01_T1w.nii.gz    │   ├── sub-003-01_acq-pos_ihmt.json     │   ├── sub-003-01_acq-pos_ihmt.nii.gz     │   ├── sub-003-01_acq-neg_ihmt.json    │   ├── sub-003-01_acq-neg_ihmt.nii.gz    │   ├── sub-003-01_acq-altnp_ihmt.json    │   ├── sub-003-01_acq-altnp_ihmt.nii.gz    │   ├── sub-003-01_acq-altpn_ihmt.json    │   ├── sub-003-01_acq-altpn_ihmt.nii.gz    │   ├── sub-003-01_acq-T1w_ihmt.json    │   └── sub-003-01_acq-T1w_ihmt.nii.gz │    └── dwi    ├── sub-003-01_dwi.bval    ├── sub-003-01_dwi.bvec    ├── sub-003-01_dwi.json    ├── sub-003-01_dwi.nii.gz    ├── sub-003-01_b0.json    ├── sub-003-01_b0.nii.gz    ├── sub-003-01_rev-b0.json   └── sub-003-01_rev-b0.nii.gz To convert our DICOM data folder to the compatible BIDS structure, we used `dcm2bids `__. .. code-block:: bash 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 DMRIQC flow `DMRIQC flow `__. Example of datasets for one subject ----------------------------------- * Anatonimal image +---------------------------------+ | 3D-T1w | +=================================+ | .. image:: 3DT1.gif | | :width: 200 | +---------------------------------+ * Diffusion images +----------------------------+----------------------------+----------------------------+----------------------------+----------------------------+ | DWI - b0 | DWI - b value = 300 | DWI - b value = 1000 | DWI - b value = 2000 | DWI - Reverse B0 | +============================+============================+============================+============================+============================+ | .. image:: b0.gif | .. image:: b300.gif | .. image:: b1000.gif | .. image:: b2000.gif | .. image:: epi.gif | | :width: 200 | :width: 200 | :width: 200 | :width: 200 | :width: 200 | +----------------------------+----------------------------+----------------------------+----------------------------+----------------------------+ * ihMT images +--------------------------+-----------------------+-----------------------+-----------------------+-----------------------+----------------------+ | MT-Off | Positive (pos) | Negative (neg) | Alternative pos-neg | Alternative neg-pos | T1w ihMT | +==========================+=======================+=======================+=======================+=======================+======================+ | .. image:: mtoff.gif | .. image:: pos.gif | .. image:: neg.gif | .. image:: altpn.gif | .. image:: altnp.gif | .. image:: T1w.gif | | :width: 200 | :width: 200 | :width: 200 | :width: 200 | :width: 200 | :width: 200 | +--------------------------+-----------------------+-----------------------+-----------------------+-----------------------+----------------------+