MRI Legacy data and HCP pipelines preprocessing

[Estephan Moana]

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:

1. Structural data: The T1w image has a resolution of 1x1x1 mm, and I have a PD and T2 weighted image with resolution 1x1x3mm. Is there any advantage in trying to use the T2w from this sequence for the structural pre-processing?
2. Stimulus-evoked BOLD data: The field maps for the stimulus-evoked bold are Siemens GRE with two magnitude images and one phase-difference map. Do I need to run Fsl_prepare_fieldmap on these data first? Or should I just enter one magnitude image and the phase-difference map using the option "--dcmethod="${SIEMENS_METHOD_OPT}"" in the GenericfMRIVolumeProcessingPipeline.sh script?
3. Resting BOLD: these images have different resolution than the stimulus-evoked BOLD data. I guess I would need to process them and their field maps separately, correct?
4. DWI: this is a cardiac-gated acquisition with 42 directions, and I also have field maps for the DWI data. Is there a way to use these fieldmaps in the diffusion pipeline? Is it worth pursuing this?
   
5. PCASL data: these data are single post-label delay without background supression and no calibration image was collected (need to use the mean of control volumes). Can these data be processed using the HCP pipelines for ASL?

Any other suggestions on how to get these data processing using the HCP pipelines are welcomed. Thank you.

Estephan

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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

 

[Glasser, Matt]

1. I think you should just process T1w only with the legacy flag.  3mm is too coarse for cortical analysis (for the purposes of surface placement). 
2. You can average the magnitude images if you want.  The pipelines run fsl_prepare_fieldmap.
3. Not sure I understand this question.  Initially each fMRI run is processed through fMRIVolume and fMRISurface separately. 
4. The HCP Pipelines would need to be patched to allow this.  If you want to take this on, we’d welcome this improvement. 
5. I am not sure about the ASL question, so I have CCed Michal Chappell who can hopefully comment or direct this question to the appropriate person.

 

The biggest challenge will be temporally cleaning the fMRI data, as it is not high spatial and temporal resolution fMRI.

 

Matt.

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