Hello, I have a legacy MRI dataset that I want to process using the HCP pipelines. I attached below the imaging parameters. My questions are:
Equipment
· Siemens 3T Trio scanner
· 12-channel head coil
Imaging sequence
1. Localizer
2. Field map acquisition PCASL (resting ASL)
2.1. Parameters not described in pulse sequence document
3. PCASL (Resting ASL) 1 of 2
3.1. Acquisition time per run = 5m30s; 60 time points
3.2. TR = 5000 ms; TE = 6.7 ms; voxel size = 3.4 x 3.4 x 5.0 mm; Slices = 25; FoV read = 220 mm; Accel. factor PE = 4; Filter: Raw filter, Prescan Normalize; Flip angle = 90 deg; Measurements = 60; Delay in TR = 0 ms; PAT mode = GRAPPA; Multi-slice mode: Interleaved; Series: Ascending; Fat suppr.: Fat sat.; Echo spacing = 0.46 ms; CASL Method: Multi-slice; Label Offset: 90 mm; Post Label Delay: 1,000,000 us
3.3. Information from pre-2022 documents: Pseudocontinuous ASL (pcASL); Tag-control pairs; No background suppression; Labelling duration = 1.5 s
4. Field map for resting BOLD
4.1. Gradient echo field maps for BOLD fMRI: one scan as a pair of magnitude and phase image, acquisition time per run =1m14s
4.2. TR = 561 ms; TE1 = 4.92 ms; TE2 = 7.38 ms; TE difference = 2.46 ms; voxel size = 3.4 x 3.4 x 4.0 mm; Slices = 33; FoV read = 220 mm; Filter: None; Flip angle = 60 deg; Measurements = 1; Multi-slice mode: Interleaved; Series: Interleaved; Fat suppr.: None; Phase enc. Dir. = A >> P (Y-axis)
5. Resting fMRI BOLD 1 of 2
5.1. Acquisition time per run = 5m12s; 154 time points
5.2. TR = 2000 ms; TE = 30 ms; voxel size = 3.4 x 3.4 x 4.0 mm; Slices = 33; FoV read = 220 mm; Filter: Raw filter; Flip angle = 77 deg; Measurements = 154; Delay in TR = 0 ms; PAT mode = None; Multi-slice mode: Interleaved; Series: Ascending; Fat suppr.: Fat sat.; Echo spacing = 0.5 ms
6. Field map for stimulus-evoked BOLD: gradient echo field maps
6.1. Gradient echo field maps for BOLD fMRI: one scan as a pair of magnitude and phase image, acquisition time per run =1m14s
6.2. TR = 561 ms; TE1 = 4.92 ms; TE2 = 7.38 ms; TE difference = 2.46 ms; voxel size = 3.0 mm isotropic; Slices = 49; FoV read = 192 mm; Filter: None; Flip angle = 60 deg; Measurements = 1; Multi-slice mode: Interleaved; Series: Interleaved; Fat suppr.: None; Phase enc. Dir. = A >> P (Y-axis)
7. Stimulus-evoked fMRI BOLD intermingled stimulation (mechanical and auditory)
7.1. Acquisition time per run = 10m33s; 208 time points
7.2. TR = 3,000 ms; TE = 30 ms; voxel size = 3 mm isotropic; Slices = 49; FoV read = 192 mm; Accel. factor PE = 2; Filter: Raw filter; Flip angle = 77 deg; Measurements = 208; Delay in TR = 0 ms; PAT mode = GRAPPA; Multi-slice mode: Interleaved; Series: Ascending; Fat suppr.: Fat sat.; Echo spacing = 0.52 ms
8. Anatomical T1-weighted: One scan, acquisition time per run = 3m16s
8.1. Acquisition time per run = 3m16s; Magnetization prepared rapid gradient echo (MPRAGE)
8.2. TR = 4000 ms; TE = 3.74 ms; voxel size = 1.0 mm isotropic; Slices per slab = 160; FoV read = 256 mm; Phase enc. dir. R >> L; Filter: Prescan Normalize; TI = 900 ms; Flip angle = 8 deg; PAT mode = GRAPPA; Accel. factor PE = 2; Multi-slice mode: Single shot; Series: Interleaved; Fat suppr.: None
9. Stimulus-evoked fMRI BOLD single stimulation (mechanical)
9.1. Same parameters as Stimulus-evoked fMRI BOLD intermingled stimulation
10. Anatomical PD+T2-weighted (proton-density and T2-weighted)
10.1. Acquisition time per run = 5m22s
10.2. TR = 4000 ms; TE1 = 20 ms; TE2 = 92 ms; voxel size = 1.0 x 1.0 x 3.0 mm; Slices = 55; FoV read = 256 mm; Phase enc. dir. R >> L; Filter: Distortion Corr.(2D), Elliptical filter; Flip angle = 120 deg; PAT mode = None; Multi-slice mode: Interleaved; Series: Interleaved; Fat suppr.: None; Turbo factor: 5; Echo trains per slice: 39
11. Stimulus-evoked fMRI BOLD single stimulation (auditory)
11.1. Same parameters as Stimulus-evoked fMRI BOLD intermingled stimulation
12. Field map for DTI
12.1. Gradient echo field maps for DWI: one scan as a pair of magnitude and phase image, acquisition time per run =1m20s
12.2. TR = 800 ms; TE1 = 4.92 ms; TE2 = 7.38 ms; TE difference = 2.46 ms; voxel size = 4.0 x 4.0 x 2.0 mm; Slices = 68; FoV read = 256 mm; Filter: None; Flip angle = 60 deg; Measurements = 1; Multi-slice mode: Interleaved; Series: Interleaved; Fat suppr.: None; Phase enc. Dir. = A >> P (Y-axis)
13. Diffusion MRI
13.1. 42-directions; Acquisition time per run = 6m56s
13.2. TR = 8000 ms; TE = 83 ms; voxel size = 2.0 mm isotropic; Slices = 68; FoV read = 256 mm; Accel. factor PE = 2; Filter: Raw filter, Prescan Normalize; Flip angle = not described; Delay in TR = 0 ms; PAT mode = GRAPPA; Multi-slice mode: Interleaved; Series: Interleaved; Fat suppr.: Fat sat.; Echo spacing = 0.73 ms; b-value 1 = 0 s/mm2; b-value 2 = 1000 s/mm2, b-value 1 and = 1; Diffusion scheme" Monopolar
13.3. Information from pre-2022 documents: Cardiac-gated acquisition; # of volumes = 49 (42 directions, 7 B0)
14. Stimulus-evoked fMRI BOLD simultaneous stimulation (mechanical + auditory)
14.1. Same parameters as Stimulus-evoked fMRI BOLD intermingled stimulation
15. PCASL (Resting ASL) 2 of 2
15.1. Same parameters as PCASL (Resting ASL) 1 of 2
16. Resting fMRI BOLD 2 of 2
16.1. Same parameters as Resting fMRI BOLD 1 of 2