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Import does not work with all MOSAICs #407

@jan-petr

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@jan-petr

EPAD site 110 has some issue with converting DICOMs to NIIs. It doesn't restore correctly the slices and keeps it in the MOSAIC format.

  1. We have to try a new version of dcm2nii - no need to integrate it to xASL yet, but simple download and import of the data should be enough. If it works, we carry on with issue Update dcm2nii version #435 and leave this issue for later when we discover another MOSAIC that doesn't work with dcm2nii.
  2. Most probably the reason is that the information about the MOSAIC was in a private DICOM tag that was removed by the anonymization.
  3. To fix this, we adopt Henk's script - xASL_io_RepairSiemensASL_MOSAIC. We rename it to xASL_io_RepairMosaic - make sure that all calls in ExploreASL and CustomScripts have changed name as well.
  4. Inside this script, we have to update it a bit - write a proper header, load parameters from .json sidecar and not from _parms.mat sidecar. Make sure that all the checks and resolution calculations work fine with the site-110. Redo warning on line 62 - we don't mention Siemens specifically and we should be more specific why we couldn't correct it. Line 76 - the whole set of for-cycles can be probably replaced by a single RESHAPE command - to be checked. If not, it can be at least simplified and pre-allocated.
  5. See if the AcquisitionMatrix field is really there and if this gives us the necessary information about the size of real slices to be used to cut the MOSAIC, otherwise, we would have to find out automatically, but lets avoid this extra work if not needed.
  6. Once this function is revamped, we want to add it to the import script, so that it is automatically run. In ExploreASL_ImportBIDS, after the merging of NIFTIes (line ~1414), we want to run this new script. We can first check if there's indeed only a single large slice (use xASL_io_ReadNifti to read NIFTI header). We can also read the JSON and do a quick pre-check like is done inside this function - if single slice, Siemens, etc, then run this correction function. You want to add the same thing to ExploreASL_Import.m as well.
  7. Once finished - write also to Luigi L.
  8. Concerns this dataset Siemens_PASL_3DGRASE_E11_1
  9. This still doesn't work with dcm2nii_version2022

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