From 489b8ee8e9956ae4b908c0365288a22c879375e0 Mon Sep 17 00:00:00 2001 From: Teal Hobson-Lowther Date: Wed, 29 Aug 2018 14:08:21 -0700 Subject: [PATCH 1/2] each phasediff should be accompanied by a magnitude1 file --- utils/issues/list.js | 6 ++++++ validators/bids.js | 22 ++++++++++++++++++++++ 2 files changed, 28 insertions(+) diff --git a/utils/issues/list.js b/utils/issues/list.js index 9aa324682..2c176ab88 100644 --- a/utils/issues/list.js +++ b/utils/issues/list.js @@ -503,4 +503,10 @@ module.exports = { reason: '_fieldmap.nii[.gz] file does not have accompanying _magnitude.nii[.gz] file. ', }, + 92: { + key: 'MISSING_MAGNITUDE1_FILE', + severity: 'warning', + reason: + 'Each _phasediff.nii[.gz] file should be associated with a _magnitude1.nii[.gz] file.', + }, } diff --git a/validators/bids.js b/validators/bids.js index 45131899b..08ec903e6 100644 --- a/validators/bids.js +++ b/validators/bids.js @@ -596,6 +596,28 @@ BIDS = { }) // End fieldmap check + // check to see if each phasediff is associated with magnitude1 + const phaseDiffNiftis = niftiNames.filter( + nifti => nifti.indexOf('phasediff') > -1, + ) + const magnitude1Niftis = niftiNames.filter( + nifti => nifti.indexOf('magnitude1') > -1, + ) + phaseDiffNiftis.map(nifti => { + const associatedMagnitudeFile = nifti.replace( + 'phasediff', + 'magnitude1', + ) + if (magnitude1Niftis.indexOf(associatedMagnitudeFile) === -1) { + self.issues.push( + new Issue({ + code: 92, + file: niftis.find(niftiFile => niftiFile.name == nifti), + }), + ) + } + }) + async.eachOfLimit( niftis, 200, From 95a066c12783129e8a3a94597e72716de78c8de5 Mon Sep 17 00:00:00 2001 From: Teal Hobson-Lowther Date: Tue, 4 Sep 2018 09:53:10 -0700 Subject: [PATCH 2/2] add test for phasediff without magnitude1 warning --- tests/bids.spec.js | 22 +++++ .../dataset_description.json | 4 + .../participants.tsv | 2 + .../ses-1/anat/sub-01_ses-1_T1map.nii.gz | 0 .../sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz | 0 .../fmap/sub-01_ses-1_run-1_fieldmap.nii.gz | 0 .../fmap/sub-01_ses-1_run-1_magnitude2.nii.gz | 0 .../fmap/sub-01_ses-1_run-1_phasediff.json | 5 ++ .../fmap/sub-01_ses-1_run-1_phasediff.nii.gz | 0 .../fmap/sub-01_ses-1_run-2_magnitude1.nii.gz | 0 .../fmap/sub-01_ses-1_run-2_magnitude2.nii.gz | 0 .../fmap/sub-01_ses-1_run-2_phasediff.json | 5 ++ .../fmap/sub-01_ses-1_run-2_phasediff.nii.gz | 0 ..._task-rest_acq-fullbrain_run-1_bold.nii.gz | 0 ...ask-rest_acq-fullbrain_run-1_physio.tsv.gz | 0 ..._task-rest_acq-fullbrain_run-2_bold.nii.gz | 0 ...ask-rest_acq-fullbrain_run-2_physio.tsv.gz | 0 ...ses-1_task-rest_acq-prefrontal_bold.nii.gz | 0 ...s-1_task-rest_acq-prefrontal_physio.tsv.gz | 0 .../sub-01/ses-1/sub-01_ses-1_scans.tsv | 4 + .../fmap/sub-01_ses-2_run-1_magnitude1.nii.gz | 0 .../fmap/sub-01_ses-2_run-1_magnitude2.nii.gz | 0 .../fmap/sub-01_ses-2_run-1_phasediff.json | 5 ++ .../fmap/sub-01_ses-2_run-1_phasediff.nii.gz | 0 .../fmap/sub-01_ses-2_run-2_magnitude1.nii.gz | 0 .../fmap/sub-01_ses-2_run-2_magnitude2.nii.gz | 0 .../fmap/sub-01_ses-2_run-2_phasediff.json | 5 ++ .../fmap/sub-01_ses-2_run-2_phasediff.nii.gz | 0 ..._task-rest_acq-fullbrain_run-1_bold.nii.gz | 0 ...ask-rest_acq-fullbrain_run-1_physio.tsv.gz | 0 ..._task-rest_acq-fullbrain_run-2_bold.nii.gz | 0 ...ask-rest_acq-fullbrain_run-2_physio.tsv.gz | 0 ...ses-2_task-rest_acq-prefrontal_bold.nii.gz | 0 ...s-2_task-rest_acq-prefrontal_physio.tsv.gz | 0 .../sub-01/ses-2/sub-01_ses-2_scans.tsv | 4 + .../sub-01/sub-01_sessions.tsv | 3 + .../task-rest_acq-fullbrain_bold.json | 81 +++++++++++++++++++ .../task-rest_acq-fullbrain_run-1_physio.json | 5 ++ .../task-rest_acq-fullbrain_run-2_physio.json | 5 ++ .../task-rest_acq-prefrontal_bold.json | 51 ++++++++++++ .../task-rest_acq-prefrontal_physio.json | 5 ++ 41 files changed, 206 insertions(+) create mode 100644 tests/data/phasediff_without_magnitude1/dataset_description.json create mode 100644 tests/data/phasediff_without_magnitude1/participants.tsv create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/anat/sub-01_ses-1_T1map.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_fieldmap.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_magnitude2.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.json create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_magnitude1.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_magnitude2.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_phasediff.json create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_phasediff.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-1_bold.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-1_physio.tsv.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-2_bold.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-2_physio.tsv.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-prefrontal_bold.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-prefrontal_physio.tsv.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-1/sub-01_ses-1_scans.tsv create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_magnitude1.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_magnitude2.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_phasediff.json create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_phasediff.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_magnitude1.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_magnitude2.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_phasediff.json create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_phasediff.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-1_bold.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-1_physio.tsv.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-2_bold.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-2_physio.tsv.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-prefrontal_bold.nii.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-prefrontal_physio.tsv.gz create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/ses-2/sub-01_ses-2_scans.tsv create mode 100644 tests/data/phasediff_without_magnitude1/sub-01/sub-01_sessions.tsv create mode 100644 tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_bold.json create mode 100644 tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_run-1_physio.json create mode 100644 tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_run-2_physio.json create mode 100644 tests/data/phasediff_without_magnitude1/task-rest_acq-prefrontal_bold.json create mode 100644 tests/data/phasediff_without_magnitude1/task-rest_acq-prefrontal_physio.json diff --git a/tests/bids.spec.js b/tests/bids.spec.js index fa35729a2..4dc454924 100644 --- a/tests/bids.spec.js +++ b/tests/bids.spec.js @@ -245,4 +245,26 @@ var suite = describe('BIDS example datasets ', function() { isdone() }) }) + + it('should not throw a warning if all _phasediff.nii are associated with _magnitude1.nii', function(isdone) { + var options = { ignoreNiftiHeaders: true } + validate.BIDS( + 'tests/data/BIDS-examples-' + test_version + '/hcp_example_bids', + options, + function(issues) { + assert.deepEqual(issues.errors, []) + isdone() + }, + ) + }) + + it('should throw a warning if there are _phasediff.nii without an associated _magnitude1.nii', function(isdone) { + var options = { ignoreNiftiHeaders: true } + validate.BIDS('tests/data/phasediff_without_magnitude1', options, function( + issues, + ) { + assert(issues.warnings.length == 2 && issues.warnings[1].code === '92') + isdone() + }) + }) }) diff --git a/tests/data/phasediff_without_magnitude1/dataset_description.json b/tests/data/phasediff_without_magnitude1/dataset_description.json new file mode 100644 index 000000000..cce76c7f5 --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/dataset_description.json @@ -0,0 +1,4 @@ +{ + "BIDSVersion": "1.0.0rc3", + "Name": "7t_trt" +} diff --git a/tests/data/phasediff_without_magnitude1/participants.tsv b/tests/data/phasediff_without_magnitude1/participants.tsv new file mode 100644 index 000000000..0c9cc6617 --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/participants.tsv @@ -0,0 +1,2 @@ +participant_id sex age_at_first_scan_years number_of_scans_before handedness +sub-01 F 29 17 100 diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/anat/sub-01_ses-1_T1map.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/anat/sub-01_ses-1_T1map.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/anat/sub-01_ses-1_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_fieldmap.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_fieldmap.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_magnitude2.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_magnitude2.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.json b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.json new file mode 100644 index 000000000..2fba548bf --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.json @@ -0,0 +1,5 @@ +{ + "EchoTime2": 0.00702, + "EchoTime1": 0.006, + "IntendedFor": "ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-1_bold.nii.gz" +} diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-1_phasediff.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_magnitude1.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_magnitude1.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_magnitude2.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_magnitude2.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_phasediff.json b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_phasediff.json new file mode 100644 index 000000000..e1364865a --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_phasediff.json @@ -0,0 +1,5 @@ +{ + "EchoTime2": 0.00702, + "EchoTime1": 0.006, + "IntendedFor": "ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-2_bold.nii.gz" +} diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_phasediff.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/fmap/sub-01_ses-1_run-2_phasediff.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-1_bold.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-1_bold.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-1_physio.tsv.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-1_physio.tsv.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-2_bold.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-2_bold.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-2_physio.tsv.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-fullbrain_run-2_physio.tsv.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-prefrontal_bold.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-prefrontal_bold.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-prefrontal_physio.tsv.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/func/sub-01_ses-1_task-rest_acq-prefrontal_physio.tsv.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-1/sub-01_ses-1_scans.tsv b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/sub-01_ses-1_scans.tsv new file mode 100644 index 000000000..76ab17c6f --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/sub-01/ses-1/sub-01_ses-1_scans.tsv @@ -0,0 +1,4 @@ +filename positive negative future past myself people surroundings vigilance images words specific_vague intrusive +func/sub-01_ses-1_task-rest_acq-fullbrain_run-1_bold.nii.gz 90 0 100 100 80 100 100 95 0 100 90 30 +func/sub-01_ses-1_task-rest_acq-fullbrain_run-2_bold.nii.gz 85 0 90 100 100 100 20 100 0 100 100 30 +func/sub-01_ses-1_task-rest_acq-prefrontal_bold.nii.gz 75 0 75 100 100 85 15 100 0 100 95 35 diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_magnitude1.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_magnitude1.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_magnitude2.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_magnitude2.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_phasediff.json b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_phasediff.json new file mode 100644 index 000000000..5545d84fb --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_phasediff.json @@ -0,0 +1,5 @@ +{ + "EchoTime2": 0.00702, + "EchoTime1": 0.006, + "IntendedFor": "ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-1_bold.nii.gz" +} diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_phasediff.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-1_phasediff.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_magnitude1.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_magnitude1.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_magnitude2.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_magnitude2.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_phasediff.json b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_phasediff.json new file mode 100644 index 000000000..e60f834bb --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_phasediff.json @@ -0,0 +1,5 @@ +{ + "EchoTime2": 0.00702, + "EchoTime1": 0.006, + "IntendedFor": "ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-2_bold.nii.gz" +} diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_phasediff.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/fmap/sub-01_ses-2_run-2_phasediff.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-1_bold.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-1_bold.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-1_physio.tsv.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-1_physio.tsv.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-2_bold.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-2_bold.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-2_physio.tsv.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-fullbrain_run-2_physio.tsv.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-prefrontal_bold.nii.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-prefrontal_bold.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-prefrontal_physio.tsv.gz b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/func/sub-01_ses-2_task-rest_acq-prefrontal_physio.tsv.gz new file mode 100644 index 000000000..e69de29bb diff --git a/tests/data/phasediff_without_magnitude1/sub-01/ses-2/sub-01_ses-2_scans.tsv b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/sub-01_ses-2_scans.tsv new file mode 100644 index 000000000..d23e770a0 --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/sub-01/ses-2/sub-01_ses-2_scans.tsv @@ -0,0 +1,4 @@ +filename positive negative future past myself people surroundings vigilance images words specific_vague intrusive +func/sub-01_ses-2_task-rest_acq-fullbrain_run-1_bold.nii.gz 95 0 100 0 90 100 75 100 20 100 100 60 +func/sub-01_ses-2_task-rest_acq-fullbrain_run-2_bold.nii.gz 70 25 100 0 100 100 80 75 0 100 100 65 +func/sub-01_ses-2_task-rest_acq-prefrontal_bold.nii.gz 100 0 100 100 100 100 20 70 0 100 80 65 diff --git a/tests/data/phasediff_without_magnitude1/sub-01/sub-01_sessions.tsv b/tests/data/phasediff_without_magnitude1/sub-01/sub-01_sessions.tsv new file mode 100644 index 000000000..b047cfb7d --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/sub-01/sub-01_sessions.tsv @@ -0,0 +1,3 @@ +session CCPT_avg_succ_RT CCPT_avg_FP_RT CCPT_avg_FN_RT CCPT_succ_count CCPT_FP_count CCPT_FN_count subject_id panas_cheerful panas_disgusted panas_attentive panas_bashful panas_sluggish panas_daring panas_surprised panas_strong panas_scornful panas_relaxed panas_irritable panas_delighted panas_inspired panas_fearless panas_disgusted_with_self panas_sad panas_calm panas_afraid panas_tired panas_amazed panas_shaky panas_happy panas_timid panas_alone panas_alert panas_upset panas_angry panas_bold panas_blue panas_shy panas_active panas_guilty panas_joyful panas_nervous panas_lonely panas_sleepy panas_excited panas_hostile panas_proud panas_jittery panas_lively panas_ashamed panas_at_ease panas_scared panas_drowsy panas_angry_at_self panas_enthusiastic panas_downhearted panas_sheepish panas_distressed panas_blameworthy panas_determined panas_frightened panas_astonished panas_interested panas_loathing panas_confident panas_energetic panas_concentrating panas_dissatisfied_with_self hours_of_sleep_ussually hours_of_sleep_last_night vigilance quality_of_sleep thirst liters_of_water_daily relative_water_intake caffeine_daily relative_caffeine_intake systolic_blood_pressure_left diastolic_blood_pressure_left pulse_left systolic_blood_pressure_right diastolic_blood_pressure_right pulse_right positive negative future past myself people surroundings vigilance_nyc-q images words specific_vague intrusive +ses-1 500.7708333333333 507.0 n/a 96.0 1.0 0.0 1 6 4 6 2 4 4 2 5 4 6 3 5 6 6 2 1 5 2 2 4 2 7 4 1 5 1 2 4 4 1 7 1 7 2 1 5 6 1 4 2 6 2 1 1 4 2 6 1 1 1 4 5 1 5 6 1 4 6 3 5 8.0 9.5 9 5 9 1.0 7 0.5 1 108 64 66 109 69 70 0 0 75 15 5 70 0 100 0 100 95 50 +ses-2 503.3333333333333 595.0 n/a 96.0 1.0 0.0 1 4 2 6 1 4 5 2 4 5 6 3 5 5 3 2 5 7 1 5 4 1 7 4 1 6 1 1 4 4 1 6 5 5 3 1 1 6 1 4 2 6 1 1 1 4 1 5 1 4 1 4 4 1 5 7 1 6 6 7 1 8.0 7.5 7 9 9 2.0 5 2.0 3 101 66 70 101 65 76 100 5 80 90 5 80 20 100 0 100 100 50 diff --git a/tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_bold.json b/tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_bold.json new file mode 100644 index 000000000..0d489f210 --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_bold.json @@ -0,0 +1,81 @@ +{ + "CogAtlasID": "trm_4c8a834779883", + "EchoTime": 0.017, + "EffectiveEchoSpacing": 0.0003333262223739227, + "PhaseEncodingDirection": "j-", + "RepetitionTime": 3.0, + "SliceEncodingDirection": "k", + "SliceTiming": [ + 1.508, + 0.0, + 1.55, + 0.043, + 1.592, + 0.087, + 1.635, + 0.13, + 1.677, + 0.173, + 1.722, + 0.215, + 1.765, + 0.26, + 1.808, + 0.302, + 1.85, + 0.345, + 1.893, + 0.388, + 1.938, + 0.43, + 1.98, + 0.475, + 2.022, + 0.518, + 2.065, + 0.56, + 2.11, + 0.603, + 2.152, + 0.645, + 2.195, + 0.69, + 2.238, + 0.733, + 2.28, + 0.775, + 2.325, + 0.818, + 2.367, + 0.86, + 2.41, + 0.905, + 2.453, + 0.948, + 2.495, + 0.99, + 2.54, + 1.032, + 2.583, + 1.075, + 2.625, + 1.12, + 2.668, + 1.163, + 2.71, + 1.205, + 2.755, + 1.248, + 2.798, + 1.293, + 2.84, + 1.335, + 2.883, + 1.378, + 2.925, + 1.42, + 2.97, + 1.462 + ], + "TaskName": "Rest" +} diff --git a/tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_run-1_physio.json b/tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_run-1_physio.json new file mode 100644 index 000000000..ff79e46dd --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_run-1_physio.json @@ -0,0 +1,5 @@ +{ + "StartTime": 0, + "SamplingFrequency": 100, + "Columns": ["cardiac", "respiratory", "trigger", "oxygen saturation"] +} diff --git a/tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_run-2_physio.json b/tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_run-2_physio.json new file mode 100644 index 000000000..ff79e46dd --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/task-rest_acq-fullbrain_run-2_physio.json @@ -0,0 +1,5 @@ +{ + "StartTime": 0, + "SamplingFrequency": 100, + "Columns": ["cardiac", "respiratory", "trigger", "oxygen saturation"] +} diff --git a/tests/data/phasediff_without_magnitude1/task-rest_acq-prefrontal_bold.json b/tests/data/phasediff_without_magnitude1/task-rest_acq-prefrontal_bold.json new file mode 100644 index 000000000..ac2f54e87 --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/task-rest_acq-prefrontal_bold.json @@ -0,0 +1,51 @@ +{ + "CogAtlasID": "trm_4c8a834779883", + "EchoTime": 0.026, + "EffectiveEchoSpacing": 0.00032998944033790924, + "PhaseEncodingDirection": "j-", + "RepetitionTime": 4.0, + "SliceEncodingDirection": "k", + "SliceTiming": [ + 3.915, + 3.815, + 3.715, + 3.615, + 3.515, + 3.413, + 3.312, + 3.212, + 3.112, + 3.013, + 2.913, + 2.81, + 2.71, + 2.61, + 2.51, + 2.41, + 2.31, + 2.21, + 2.108, + 2.008, + 1.908, + 1.808, + 1.707, + 1.608, + 1.505, + 1.405, + 1.305, + 1.205, + 1.105, + 1.005, + 0.902, + 0.802, + 0.703, + 0.603, + 0.502, + 0.402, + 0.302, + 0.2, + 0.1, + 0.0 + ], + "TaskName": "Rest" +} diff --git a/tests/data/phasediff_without_magnitude1/task-rest_acq-prefrontal_physio.json b/tests/data/phasediff_without_magnitude1/task-rest_acq-prefrontal_physio.json new file mode 100644 index 000000000..ff79e46dd --- /dev/null +++ b/tests/data/phasediff_without_magnitude1/task-rest_acq-prefrontal_physio.json @@ -0,0 +1,5 @@ +{ + "StartTime": 0, + "SamplingFrequency": 100, + "Columns": ["cardiac", "respiratory", "trigger", "oxygen saturation"] +}