IntendedFor field in json files

mainux commented 6 years ago

Hi! I am not able to find the IntendedFor field to specify in the fmaps which run is intended to be used with which functional or diffusion scan. Should it be added by hand?

Our case corresponds to the Case 4: Multiple phase encoded directions (topup) specified in the BIDS_spec.

Below I paste an example of the Json file of the fieldmaps corresponding to a task fMRI file.

Best,

Maite

{
  "AcquisitionNumber": 1,
  "AcquisitionTime": "14:40:22.670000",
  "BandwidthPerPixelPhaseEncode": 22.282,
  "BodyPartExamined": "BRAIN",
  "ConversionSoftware": "dcm2niix",
  "ConversionSoftwareVersion": "v1.0.20170724 GCC4.4.7",
  "DeviceSerialNumber": "167004",
  "EchoTime": 0.035,
  "EchoTrainLength": 88,
  "EffectiveEchoSpacing": 0.000509992,
  "FlipAngle": 56,
  "ImageType": [
    "ORIGINAL",
    "PRIMARY",
    "M",
    "MB",
    "ND",
    "MOSAIC"
],
  "InstitutionAddress": "Mikeletegi_69_San_Sebastian_District_ES_20009",
  "InstitutionName": "BCBL",
  "MagneticFieldStrength": 3,
  "Manufacturer": "Siemens",
  "ManufacturersModelName": "Prisma_fit",
  "PhaseEncodingDirection": "j-",
  "PhaseEncodingLines": 88,
  "ProcedureStepDescription": "CRANEO_FUNCIONAL",
  "ProtocolName": "petit_nicolas_1_AP",
  "RepetitionTime": 0.85,
  "ScanningSequence": "EP",
  "SequenceName": "epfid2d1_88",
  "SequenceVariant": "SK_SS",
  "SeriesDescription": "petit_nicolas_1_AP",
  "SliceTiming": [0, 0.4525, 0.075, 0.5275, 0.15, 0.6025, 0.225, 0.6775, 0.3025, 0.755, 0.3775, 0, 0.4525, 0.075, 0.5275, 0.15, 0.6025, 0.225, 0.6775, 0.3025, 0.755, 0.3775, 0, 0.4525, 0.075, 0.5275, 0.15, 0.6025, 0.225, 0.6775, 0.3025, 0.755, 0.3775, 0, 0.4525, 0.075, 0.5275, 0.15, 0.6025, 0.225, 0.6775, 0.3025, 0.755, 0.3775, 0, 0.4525, 0.075, 0.5275, 0.15, 0.6025, 0.225, 0.6775, 0.3025, 0.755, 0.3775, 0, 0.4525, 0.075, 0.5275, 0.15, 0.6025, 0.225, 0.6775, 0.3025, 0.755, 0.3775],
  "SoftwareVersions": "syngo_MR_E11",
  "TaskName": "petit",
  "TotalReadoutTime": 0.0443693}

mgxd commented 6 years ago

Hi @mainux - currently you'll have to add the IntendedFor entry yourself, although we plan on autogenerating this in the future

mainux commented 6 years ago

Ok thanks, no problem!

It was driving me crazy ;)

Maite Termenon Postdoctoral Researcher at BCBL Neurobiology of language group www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

From: "Mathias Goncalves" notifications@github.com To: "nipy/heudiconv" heudiconv@noreply.github.com Cc: "mainux" m.termenon@bcbl.eu, "Mention" mention@noreply.github.com Sent: Thursday, January 25, 2018 4:18:52 PM Subject: Re: [nipy/heudiconv] IntendedFor field in json files (#138)

Hi @mainux - currently you'll have to add the IntendedFor entry yourself, although we plan on autogenerating this in the future

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oesteban commented 5 years ago

hi @mgxd, any updates on this?

mgxd commented 5 years ago

@oesteban - I'm hoping to take a look at this next week, in theory it should doable (at least with Siemens) - related to #148

ChristianNSchmitz commented 4 years ago

Hey @mgxd, is there any update on this feature? Thanks a lot!

mirestrepo commented 3 years ago

In case it's helpful, this is our work around, we do it as a post processing step

nipy / heudiconv

IntendedFor field in json files #138