dicom2nii
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— | dicom2nii [2011/04/14 18:15] (current) – created jochen | ||
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+ | ====== dicom2nii (import DICOM or PAR/REC images) ====== | ||
+ | ===== Motivation ===== | ||
+ | Neuroimaging data is usually acquired in a format unsuitable for data processing (e.g. missing or incomplete support for data manipulation in existing files), such as DICOM or PAR/REC (Philips proprietary). For those who do not have SPM available but still want to be able to convert DICOM or PAR/REC images, NeuroElf also offers an experimental function that converts from those formats into 3D/4D NIftI files. | ||
+ | |||
+ | ===== Requirements ===== | ||
+ | You simply need the list of files (or the single file in case of a PAR file) to import. | ||
+ | |||
+ | ===== Function reference ('help dicom2nii' | ||
+ | < | ||
+ | |||
+ | FORMAT: | ||
+ | |||
+ | Input fields: | ||
+ | |||
+ | imafiles | ||
+ | multiple-slice files must be sorted correctly | ||
+ | flags | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | Output fields: | ||
+ | |||
+ | nii NIftI object</ | ||
+ | |||
+ | ===== Options ===== | ||
+ | |||
+ | ==== .disdaqs ==== | ||
+ | This option can be used to remove the first few images from the scan, which is important if the scanner has not already discarded the data from the very beginning of the scan that lacks proper T2* contrast stabilization. In that case, typical values would be between 3 and 6, depending on the TR. | ||
+ | |||
+ | ==== .dtype ==== | ||
+ | Can be used to override the default datatype (single), so that images will be stored as int16. While this is clearly enough to store the data (in most cases, both DICOM and PAR/REC will only ever have up to 16-bit integer data), subsequent processing of the data requires additional precision to avoid rounding error build-up! It is thus advised to use single precision values for any data that is to be processed! | ||
+ | |||
+ | ==== .flip ==== | ||
+ | String flag. If it contains an ''' | ||
+ | |||
+ | ==== .mosaic ==== | ||
+ | Boolean flag to force interpreting the data as mosaic. | ||
+ | |||
+ | ==== .misdimord ==== | ||
+ | Order of slices for mosaic' | ||
+ | |||
+ | ==== .nslices ==== | ||
+ | Option to set the number of slices for a DICOM images in a one-file-per-slice series. | ||
+ | |||
+ | ==== .xyres ==== | ||
+ | Functional x/y resolution used to detect the number of slices in a mosaic image (defaults to [64, 64]). If your data is stored as mosaic' | ||
+ | |||
+ | ===== Usage notes ===== | ||
+ | Other than the [[dcm2nii]] function, this will *not* create a file by itself. The resulting output ([[xff|xff object]]) needs to be saved using the '' |
dicom2nii.txt · Last modified: 2011/04/14 18:15 by jochen