Merge pull request #534 from olgn/phasediff-magnitude1

each phasediff should be accompanied by a magnitude1 file

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()
+    })
+  })
 })

tests/data/phasediff_without_magnitude1/dataset_description.json

@@ -0,0 +1,4 @@
+{
+  "BIDSVersion": "1.0.0rc3",
+  "Name": "7t_trt"
+}

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

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"
+}

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"
+}

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

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"
+}

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"
+}

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

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

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"
+}

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"]
+}

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"]
+}

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"
+}

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"]
+}

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.',
+  },
 }

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,