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140 changes: 140 additions & 0 deletions docs/source/_static/iqms.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,140 @@
{
"aor": 0.0037614999999999997,
"aqi": 0.023297618900000004,
"bids_meta": {
"AcquisitionMatrixPE": 95,
"AcquisitionNumber": 8,
"AcquisitionTime": "10:15:56.720000",
"B0FieldSource": "pepolar_fmap0",
"BodyPartExamined": "BRAIN",
"CoilString": "MULTI COIL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20211006",
"DeviceSerialNumber": "17057",
"EchoTime": 0.039,
"EchoTrainLength": 95,
"EffectiveEchoSpacing": 0.000608401,
"EstimatedEffectiveEchoSpacing": 0.000608401,
"EstimatedTotalReadoutTime": 0.0577981,
"FileSize": 0.14147014450281858,
"FileSizeUnits": "GB",
"FlipAngle": 65,
"ImageOrientationPatientDICOM": [
0.998569,
0.00766079,
0.0529228,
-0.00367802,
0.997181,
-0.0749475
],
"ImageType": [
"ORIGINAL",
"PRIMARY",
"M",
"FFE",
"M",
"FFE"
],
"ImagingFrequency": 127.804,
"InPlanePhaseEncodingDirectionDICOM": "COL",
"InstitutionName": "SPMMRC Nottingham",
"InstitutionalDepartmentName": "MRI",
"MRAcquisitionType": "2D",
"MTState": false,
"MagneticFieldStrength": 3,
"Manufacturer": "Philips",
"ManufacturersModelName": "Achieva",
"Modality": "MR",
"NumberOfVolumes": 400,
"ParallelAcquisitionTechnique": "SENSE",
"PartialFourierDirection": "PHASE",
"PartialFourierEnabled": "YES",
"PatientPosition": "HFS",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"PhaseEncodingAxis": "j",
"PhaseEncodingDirection": "j",
"PhaseEncodingStepsNoPartialFourier": 95,
"PhilipsRescaleIntercept": 0,
"PhilipsRescaleSlope": 0.818071,
"PhilipsScaleSlope": 0.00153639,
"PixelBandwidth": 2328,
"ProcedureStepDescription": "H1408201447",
"ProtocolName": "WIP rs-fmri_singleMB4_HF0.8",
"ReconMatrixPE": 96,
"RepetitionTime": 1.15,
"SAR": 0.0227829,
"ScanOptions": "FS",
"ScanningSequence": "GR",
"SequenceVariant": "SK",
"SeriesDescription": "rs-fmri_singleMB4_HF0.8",
"SeriesNumber": 801,
"SliceThickness": 2.4,
"SoftwareVersions": "5.3.0\\5.3.0.3",
"SpacingBetweenSlices": 2.4,
"StationName": "PHILIPS-T6O3EHP",
"TaskName": "rest",
"TotalReadoutTime": 0.0577981,
"UsePhilipsFloatNotDisplayScaling": 1,
"WaterFatShift": 25.3797,
"dataset": "<unset>",
"datatype": "func",
"extension": ".nii.gz",
"modality": "bold",
"session": "NOT1ACH001",
"subject": "03286",
"suffix": "bold",
"task": "rest"
},
"dummy_trs": 0,
"dvars_nstd": 44.00571358506266,
"dvars_std": 1.1092985154385975,
"dvars_vstd": 0.9788209838095238,
"efc": 0.4504,
"fber": 553307.625,
"fd_mean": 0.2239716689042766,
"fd_num": 215,
"fd_perc": 53.75,
"fwhm_avg": 2.3961225784666915,
"fwhm_x": 2.4589816467849612,
"fwhm_y": 2.401594514446574,
"fwhm_z": 2.32779157416854,
"gcor": 0.00260741,
"gsr_x": -0.018688196316361427,
"gsr_y": 0.006971913389861584,
"provenance": {
"md5sum": "6462858509954133c8448a10b04757e5",
"settings": {
"fd_thres": 0.2,
"testing": false
},
"software": "mriqc",
"version": "24.1.0.dev0+gd5b13cb5.d20240826"
},
"size_t": 400,
"size_x": 96,
"size_y": 96,
"size_z": 48,
"snr": 2.602224857820378,
"spacing_tr": 1.1500004529953003,
"spacing_x": 2.3958332538604736,
"spacing_y": 2.3958332538604736,
"spacing_z": 2.4000000953674316,
"summary_bg_k": 93.4153,
"summary_bg_mad": 959.2436,
"summary_bg_mean": 17223.3027,
"summary_bg_median": 647.0,
"summary_bg_n": 339609.0,
"summary_bg_p05": 0.0,
"summary_bg_p95": 76174.0,
"summary_bg_stdv": 61176.0266,
"summary_fg_k": 2.1816,
"summary_fg_mad": 142208.0543,
"summary_fg_mean": 500750.8674,
"summary_fg_median": 481252.0,
"summary_fg_n": 102759.0,
"summary_fg_p05": 206803.0,
"summary_fg_p95": 833312.0,
"summary_fg_stdv": 184937.7685,
"tsnr": 25.0640248588752
}
2 changes: 1 addition & 1 deletion mriqc/qc/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@
of the actual image which cannot be compared to a reference value for the metric
since there is no ground-truth about what this number should be.
All the computed :abbr:`IQMs (image quality metrics)` corresponding to
an image are saved in a `JSON file <iqm_json>`_ under the ``<output-dir>/derivatives/``
an image are saved in a `JSON file <https://mriqc.readthedocs.io/en/latest/_static/iqms.json>`_ under the ``<output-dir>/derivatives/``
folder.

The IQMs can be grouped in four broad categories, providing a vector of 56
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