diff --git a/docs/source/_static/iqms.json b/docs/source/_static/iqms.json new file mode 100644 index 000000000..4454aef01 --- /dev/null +++ b/docs/source/_static/iqms.json @@ -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": "", + "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 +} diff --git a/mriqc/qc/__init__.py b/mriqc/qc/__init__.py index 7906704bd..75d1c2983 100644 --- a/mriqc/qc/__init__.py +++ b/mriqc/qc/__init__.py @@ -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 `_ under the ``/derivatives/`` +an image are saved in a `JSON file `_ under the ``/derivatives/`` folder. The IQMs can be grouped in four broad categories, providing a vector of 56