Dear experts,
I am working on the dHCP dMRI data (3rd release). I find that the voxel size of the preprocessed dMRI data is 1.171875 x 1.171875 x 1.5, which is not 1.5 mm isotropic as described in the document.
(e.g. the DWI data: XXX_desc-preproc_dwi.nii.gz)
I tried AFNI, FSL, and also image viewers (ITKsnap, MRIcro) to check the voxel dimension, and all the results are the same.
Do I miss any key information or misunderstand the description?
Thanks!
Sheng-Min
Can you insert the JSON sidecar for the file in question. The standard Prisma HCP dMRI should be 1.25mm isotropic.
The HCP-Aging Prisma protocol shoud be 1.5mm isotropic.
I think the HCP dMRI acquired on the Connectom scanner is higher resolution than for HCP data from the Prisma. So that might explain your discrepancy.
Thanks for the response. I think the dHCP (developing HCP, the neonatal dataset) were acquired on 3T Philips scanner, so that may be different.
The JSON file for the preprocessed DWI data is appended below:
{
"SpatialReference": "orig",
"SkullStripped": false,
"PhaseEncodingDirection": [
"i+",
"j-",
"j+",
"i-",
"i+",
"j-",
"j+",
.........(too many, skip these lines)
"i-",
"i+",
"j-",
"j+",
"i-"
],
"TotalReadoutTime": 0.0852171497584,
"MotionCompensation": 1,
"EddyCurrentCorrection": 1,
"Denoising": "None",
"IntensityNormalization": 0,
"NonLinearCorrections": 1
}
There is also a QC description JSON for each dataset, for example:
{
"data_eddy_para": [
0.0,
1.0,
0.0,
0.055,
0.0,
-1.0,
0.0,
0.055,
1.0,
0.0,
0.0,
0.055,
-1.0,
0.0,
0.0,
0.055
],
"data_file_bvals": "/vols/Data/baby/saad/CC01234BN14/ses-155230/raw/bvals",
"data_file_eddy": "/vols/Data/baby/saad/CC01234BN14/ses-155230/PreProcessed/eddy/eddy_corrected.nii.gz",
"data_file_mask": "/vols/Data/baby/saad/CC01234BN14/ses-155230/PreProcessed/topup/nodif_brain_mask.nii.gz",
"data_no_PE_dirs": 4,
"data_no_b0_vols": 20,
"data_no_dw_vols": 280,
"data_no_shells": 3,
"data_protocol": [
5,
16,
22,
32,
5,
16,
22,
32,
5,
16,
22,
32,
5,
16,
22,
32
],
"data_unique_bvals": [
400,
1000,
2600
],
"data_unique_pes": [
1,
2,
3,
4
],
"data_vox_size": [
1.171875,
1.171875,
1.5
],
"eddy_input": {
"acqp": "/vols/Data/baby/saad/CC01234BN14/ses-155230/PreProcessed/eddy/acqparamsUnwarp.txt",
"b0_flm": "movement",
"b0_only": "False",
"b0_peas": "False",
"b0_slm": "none",
"bvals": "/vols/Data/baby/saad/CC01234BN14/ses-155230/raw/bvals",
"bvecs": "/vols/Data/baby/saad/CC01234BN14/ses-155230/raw/bvecs",
"cnr_maps": "True",
"covfunc": "spheri",
"data_is_shelled": "True",
"dbgindx": "",
"debug": "0",
"dfields": "False",
"dont_mask_output": "True",
"dont_peas": "False",
"dont_sep_offs_move": "False",
"dwi_only": "False",
"epvalid": "False",
"estimate_move_by_susceptibility": "True",
"extrap": "periodic",
"fep": "False",
"ff": "10",
"field": "",
"field_mat": "",
"fields": "False",
"flm": "quadratic",
"fwhm": "10,5,0,0,0",
"history": "False",
"hpcf": "CV",
"hypar": "",
"imain": "/vols/Data/baby/saad/CC01234BN14/ses-155230/raw/data",
"index": "/vols/Data/baby/saad/CC01234BN14/ses-155230/raw/eddyIndex.txt",
"init": "",
"init_mbs": "",
"init_s2v": "",
"initrand": "0",
"interp": "spline",
"json": "",
"log_timings": "False",
"lsr_lambda": "0.01",
"mask": "/vols/Data/baby/saad/CC01234BN14/ses-155230/PreProcessed/topup/nodif_brain_mask.nii.gz",
"mb": "1",
"mb_offs": "0",
"mbs_ksp": "10",
"mbs_lambda": "10",
"mbs_niter": "20",
"mporder": "8",
"niter": "5",
"nvoxhp": "5000",
"offset_model": "linear",
"ol_ec": "1",
"ol_nstd": "3",
"ol_nvox": "250",
"ol_pos": "False",
"ol_sqr": "False",
"ol_type": "both",
"out": "/vols/Data/baby/saad/CC01234BN14/ses-155230/PreProcessed/eddy/eddy_corrected",
"peas": "False",
"pmip": "False",
"pmiv": "False",
"range_cnr_maps": "False",
"rbvde": "False",
"ref_scan_no": "0",
"rep_noise": "False",
"repol": "True",
"resamp": "jac",
"residuals": "True",
"rms": "False",
"s2v_fwhm": "0",
"s2v_interp": "trilinear",
"s2v_lambda": "1",
"s2v_niter": "10",
"sep_offs_move": "False",
"session": "",
"slm": "none",
"slorder": "",
"slspec": "/vols/Scratch/saad/dHCP_prepare_release/dHCP_neo_dMRI_pipeline_release/slorder.txt",
"test_rot": "",
"topup": "/vols/Data/baby/saad/CC01234BN14/ses-155230/PreProcessed/topup/topup_results",
"very_verbose": "True",
"with_outliers": "False",
"write_predictions": "False",
"write_scatter_brain_predictions": "False",
"wss": "False"
},
"eddy_input_flag": true,
"qc_cnr_avg": [
13.300000190734863,
0.4699999988079071,
0.7200000286102295,
0.5899999737739563
],
"qc_cnr_flag": true,
"qc_cnr_std": [
6.139999866485596,
0.3100000023841858,
0.4000000059604645,
0.33000001311302185
],
"qc_field_flag": true,
"qc_mot_abs": 0.9,
"qc_mot_rel": 1.05,
"qc_ol_flag": true,
"qc_outliers_b": [
9.4970703125,
2.610085227272727,
0.67138671875
],
"qc_outliers_pe": [
2.0208333333333335,
3.1666666666666665,
2.25,
4.875
],
"qc_outliers_tot": 3.2979910714285716,
"qc_params_avg": [
-0.0904950934611407,
0.40124125636692215,
0.0934963386815736,
-0.013126569072443896,
-4.03867926963001e-05,
0.002864641002094067,
0.12827385385256362,
0.11735134912879046,
0.09618855354533273
],
"qc_params_flag": true,
"qc_path": "/vols/Data/baby/saad/CC01234BN14/ses-155230/PreProcessed/eddy/eddy_corrected.qc",
"qc_rss_flag": true,
"qc_s2v_params_avg_std": [
0.05044781401292098,
0.055247662385045505,
0.11122891120048162,
0.35263837402916653,
0.17267446701343026,
0.23060880704621736
],
"qc_s2v_params_flag": true,
"qc_vox_displ_std": 1.5787311792373657
}
I suggest you contact the corresponding author for the Developing Human Connectome Project Neonatal Data Release regarding the discrepancy. Perhaps they decided to decrease the field of view due to the smaller size of the participants brains.
Thanks for the suggestion. I am now contacting dHCP about this issue. Will update if any progress.
Hi,
I am part of the dHCP team and I think I can help here. The diffusion MRI data was indeed acquired at an in-plane resolution of 1.5mm. The neonatal data in the FSL-based pipeline was interpolated (upsampled) at an in-plane voxel size of 1.17mm during MRI reconstruction. The SHARD-based pipeline that is also used for the fetal dMRI data processes the data at the original (acquired) resolution.
Best wishes,
Daan
Hi Daan,
Thank you a lot for the confirmation.
Currently I am focusing on the eddy pipeline data. I will consider using the SHARD pipeline data as well.
Best regards,
Sheng-Min
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