Skip to content

refactor to use BIDSLayoutIndexer across entire pipeline #58

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 4 commits into from
Jul 1, 2025
Merged

refactor to use BIDSLayoutIndexer across entire pipeline #58

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
5f1a9ee
refactor to use BIDSLayoutIndexer across project
bendhouseart Jun 25, 2025
f194747
added test for excluding subjects
bendhouseart Jul 1, 2025
363d427
added 'second' subject to test exlusions
bendhouseart Jul 1, 2025
88e1fd7
test passes
bendhouseart Jul 1, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions data/participants.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,2 +1,3 @@
participant_id height weight age gender
sub-01 178 58 28 male
sub-02 178 58 28 male
69 changes: 69 additions & 0 deletions data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 123.254,
"Manufacturer": "Siemens",
"ManufacturersModelName": "Prisma_fit",
"InstitutionName": "Rigshospitalet",
"InstitutionalDepartmentName": "Rontgen",
"InstitutionAddress": "Blegdamsvej 9,Kobenhavn,District,DK,DK-2100",
"DeviceSerialNumber": "67006",
"StationName": "MN213418",
"BodyPartExamined": "HEAD",
"PatientPosition": "HFS",
"ProcedureStepDescription": "MR cerebrum",
"SoftwareVersions": "syngo MR D13D",
"MRAcquisitionType": "3D",
"SeriesDescription": "t1_mpr_3d_sag_p2_iso_Siemens",
"ProtocolName": "t1_mpr_3d_sag_p2_iso_Siemens",
"ScanningSequence": "GR\\IR",
"SequenceVariant": "SK\\SP\\MP",
"ScanOptions": "IR",
"SequenceName": "*tfl3d1rs16ns",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS3D", "DIS2D"],
"SeriesNumber": 3,
"AcquisitionTime": "15:31:52.362500",
"AcquisitionNumber": 1,
"SliceThickness": 1,
"SAR": 0.0754335,
"EchoTime": 0.00252,
"RepetitionTime": 1.9,
"InversionTime": 0.9,
"FlipAngle": 9,
"PartialFourier": 1,
"BaseResolution": 256,
"ShimSetting": [
-5020,
-11544,
-9996,
104,
27,
-15,
-3,
-8 ],
"TxRefAmp": 261.958,
"PhaseResolution": 1,
"ReceiveCoilName": "HeadNeck_64",
"ReceiveCoilActiveElements": "HC1-7;NC1,2",
"PulseSequenceDetails": "%SiemensSeq%\\tfl",
"RefLinesPE": 24,
"ConsistencyInfo": "N4_VD13D_LATEST_20130810",
"PercentPhaseFOV": 100,
"PercentSampling": 100,
"PhaseEncodingSteps": 255,
"AcquisitionMatrixPE": 256,
"ReconMatrixPE": 256,
"ParallelReductionFactorInPlane": 2,
"PixelBandwidth": 170,
"DwellTime": 1.15e-05,
"ImageOrientationPatientDICOM": [
0.050593,
0.998719,
5.87093e-08,
-0.0348548,
0.00176573,
-0.999391 ],
"InPlanePhaseEncodingDirectionDICOM": "ROW",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20210317"
}
Binary file added data/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii
View file
Open in desktop
Binary file not shown.
235 changes: 235 additions & 0 deletions data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,235 @@
{
"Manufacturer": "Siemens",
"ManufacturersModelName": "HR+",
"Units": "Bq/mL",
"BodyPart": "Brain",
"TracerName": "DASB",
"TracerRadionuclide": "C11",
"TracerMolecularWeight": 282.39,
"TracerMolecularWeightUnits": "g/mol",
"InjectedRadioactivity": 629.74,
"InjectedRadioactivityUnits": "MBq",
"MolarActivity": 55.5,
"MolarActivityUnits": "MBq/nmol",
"SpecificRadioactivity": 196.53670455752683,
"SpecificRadioactivityUnits": "MBq/ug",
"Purity": 99,
"ModeOfAdministration": "bolus",
"InjectedMass": 3.2041852,
"InjectedMassUnits": "ug",
"AcquisitionMode": "list mode",
"ImageDecayCorrected": true,
"ImageDecayCorrectionTime": 0,
"TimeZero": "17:28:40",
"ScanStart": 0,
"InjectionStart": 0,
"FrameDuration": [
20,
20,
20,
60,
60,
60,
120,
120,
120,
300,
300.066,
600,
600,
600,
600,
600,
600,
600,
600,
600,
600
],
"FrameTimesStart": [
0,
20,
40,
60,
120,
180,
240,
360,
480,
600,
900,
1200.066,
1800.066,
2400.066,
3000.066,
3600.066,
4200.066,
4800.066,
5400.066,
6000.066,
6600.066
],
"ReconMethodParameterLabels": [
"lower_threshold",
"upper_threshold",
"recon_zoom"
],
"ReconMethodParameterUnits": [
"keV",
"keV",
"none"
],
"ReconMethodParameterValues": [
0,
650,
3
],
"ScaleFactor": [
8.548972374455843e-08,
1.7544691388593492e-07,
1.3221580275057931e-07,
1.2703590357432404e-07,
1.1155360368775291e-07,
2.2050951997698576e-07,
2.184752503353593e-07,
1.7056818535365892e-07,
1.6606901453997125e-07,
1.5532630470715958e-07,
2.19175134930083e-07,
2.0248222654117853e-07,
2.277063231304055e-07,
2.425933018912474e-07,
2.3802238047210267e-07,
2.514642005735368e-07,
2.802861729378492e-07,
2.797820570776821e-07,
3.5299004252919985e-07,
4.6313422785715375e-07,
4.904185857412813e-07
],
"ScatterFraction": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0
],
"DecayCorrectionFactor": [
1.0056782960891724,
1.0171427726745605,
1.0287377834320068,
1.0522810220718384,
1.0886797904968262,
1.1263376474380493,
1.1851094961166382,
1.2685142755508423,
1.3577889204025269,
1.5278561115264893,
1.811025857925415,
2.328737735748291,
3.271937131881714,
4.597157001495361,
6.459125518798828,
9.075239181518555,
12.750947952270508,
17.915414810180664,
25.1716251373291,
35.36678695678711,
49.69125747680664
],
"PromptRate": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0
],
"RandomRate": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0
],
"SinglesRate": [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0
],
"ReconMethodName": "Vendor",
"ReconFilterType": [
"Shepp 0.5",
"All-pass 0.4"
],
"ReconFilterSize": [
2.5,
2
],
"AttenuationCorrection": "transmission scan"
}
Binary file added data/sub-02/ses-baseline/pet/sub-02_ses-baseline_pet.nii.gz
View file
Open in desktop
Binary file not shown.
Loading