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Siemens Csa headers #80

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kasbohm opened this issue Sep 13, 2017 · 3 comments
Closed

Siemens Csa headers #80

kasbohm opened this issue Sep 13, 2017 · 3 comments

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@kasbohm
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kasbohm commented Sep 13, 2017

Hi, running heudiconv on Siemens (Avanto/Skyra/Prisma) data, I get:
Ignoring xxxx.IMA since not quite a «normal» DICOM: Dataset does not have attribute ‘ProtocolName’.

I guess this is caused by the attribute not being present at the normal location (0018 1030) in our Siemens DICOMS, but exists as tProtocolName in the private Csa header. Did I miss a switch when calling heudiconv, or does some logic need to be added? nibabel.nicom.csareader?

Cheers!
neurolabusc added a commit to rordenlab/dcm2niix that referenced this issue Oct 3, 2017
@neurolabusc
Get ProtocolName from CSA header if it is not in DICOM header nipy/he…
167dbe6 
…udiconv#80
@neurolabusc
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I updated dcm2niix so if ProtocolName is not in the DICOM header it use the ProtocolName in the CSA header for the BIDS sidecar. This is a hail mary, and only influences the BIDS sidecar: the protocol name will still be empty with regards to the output filename (e.g. -f %p). Whether this helps you depends on whether heudiconv uses dcmstack or dcm2niix to determine the protocol name.

@satra
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satra commented Oct 4, 2017

@neurolabusc - thanks. at this point we would probably have to make this change on our side inside our grouping function. but eventually we should consider where the metadata get extracted.

@satra
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satra commented Oct 4, 2017

@mgxd - can you add this as part of your refactor?

@mgxd mgxd mentioned this issue Oct 12, 2017
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yarikoptic added a commit to neurodebian/dcm2niix that referenced this issue Jan 24, 2018
@yarikoptic
Merge commit 'v1.0.20171017-3-g9ccc4c0' into debian
d164ee0 
* commit 'v1.0.20171017-3-g9ccc4c0':
  Detect SMS using 0051,1011 if MosaicRefAcqTimes missing rordenlab#141
  Hide NIfTI sliceOrder if protocolSliceNumber1 > 1
  SliceTiming for reversed image numbering https://github.com/neurolabusc/dcm2niix/issues/40
  Update dcm_qa submodule.
  New version (v1.0.20171017)
  Added link rordenlab#138
  Store mulbiband factor in NIfTI descrip field (e.g. "mb=2") https://www.nitrc.org/forum/message.php?msg_id=22593
  Add patient sex, weight, etc, https://www.nitrc.org/forum/message.php?msg_id=22567
  Add ImageOrientationPatientDICOM and InPlanePhaseEncodingDirectionDICOM for 3D undistortion
  Compiling with CentOS 7: rordenlab#137
  BIDS 1.0.2 DelayTime field for sparse fMRI
  Add InstitutionalDepartmentName
  Get ProtocolName from CSA header if it is not in DICOM header nipy/heudiconv#80
  Change name of output tag of two variables to match DICOM
  Group PixelBandwidth with DwellTime in output json
  Vanquish compiler warnings.
  Report lower order shims prior to higher order (requested by mharms)
  Handle Siemens product gradient offsets?
  More Siemens information saved to BIDS
  BIDS: Do not set multiband factor for 3D EPI, report as "MRAcquisitionType": "3D",
@kasbohm kasbohm mentioned this issue Aug 31, 2018
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@mgxd mgxd mentioned this issue Nov 8, 2018
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@mgxd mgxd closed this as completed in #271 Nov 9, 2018
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@satra @kasbohm @neurolabusc