Publications by Brandon Whitcher
Remote download and viewing of brain atlas
The dcemriS4 package allows one to easily import and display NIfTI-1 class data sets. The following code takes the MNI152 brain atlas from the WWW and produces an orthographic display using the mid-axial, mid-sagittal and mid-coronal planes. Related To leave a comment for the author, please follow the link and comment on their blog...
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writeNIfTI() is fully compatible with FSLView
With the NIfTI-1 header extensions the world is your oyster. We decided that one use for such a capability is to keep an audit trail of all operations performed on the image data volume. This is a key feature in the dcemriS4 package. There are three main components to a NIfTI-1 header extension: esize, ecode and edata. At firs...
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oro.dicom 0.2.4
The R package oro.dicom is a major revision, and improvement, on the previous package DICOM. New features includeIncreased speedUploading only header information (for restricted memory)Reading implicit value representations (VR’s)Parsing SequenceItem tags (undefined lengths are allowed)Integration with oro.nifti to convert DICOM t...
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oro.nifti 0.1.3
The R package oro.nifti has been released. Medical imaging data, in NIfTI or Analyze formats, may be input, created from scratch, converted from DICOM (using oro.dicom) and output to a file. Related To leave a comment for the author, please follow the link and comment on their blog: Rigorous Analytics. R-bloggers.com offers d...
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DICOM-to-NIfTI Conversion
Now that the two packages oro.dicom and oro.nifti have been released, we can put them together and perform the much sought after conversion from DICOM format to NIfTI format (entirely in R). Why? Because DICOM is the international “standard” for medical imaging data coming off the scanners, but it’s not the easiest thing to ...
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Converting Siemens MOSAIC
Siemens multi-slice EPI data may be collected as a “mosiac” image; i.e., all slices acquired in a single TR (repitition time) of a functional MRI run are stored in a single DICOM file. The images are stored in an MxN array of images. The function create3D() will try to guess the number of images embedded within the single DICO...
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oro.dicom 0.2.5
The latest version of oro.dicom (0.2.5) has been released on CRAN. New features include:Added “mosaic” capability when creating 3D arrays from DICOMdicomTable() now accepts single DICOM fileBetter handling of SequenceItem tags when reading in DICOM files Work is ongoing to provide 4D array creation for both single-file and mosai...
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oro.nifti 0.1.4
The latest release of oro.nifti (0.1.4) has been released on CRAN. New features include:Added text capability in the (unused) fourth pane in orthographic()A vignette is now included (taken from dcemriS4) Related To leave a comment for the author, please follow the link and comment on their blog: Rigorous Analytics. R-bloggers.co...
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Where do you sit? Author position and the h-index
I was recently introduced to the concept of the h-index and was compelled to find out my own h-index via Scopus. Numbers don’t matter, but discussion with my colleagues turned to the issue of author position. We quickly decided that there are three important “positions” in the list of authors for a publication: first, last a...
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oro.dicom 0.2.6
The latest version of oro.dicom (0.2.6) has been released on CRAN. New features/improvements include:33% increase in the speed of DICOM file handlingAutomatic re-orientation/re-slicing of 3D and 4D volumes when converting from DICOM to NIfTI formatWork is underway to incorporate the best features across the different DICOM file-hand...
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