Reorienting can also disrupt analysis of the DTI data (as the diffusion directions are not adjusted for the change in image orientation).While I hope it is generally robust and useful, active development has moved to dcm2niix.In general, dcm2niix is typically better suited for modern DICOM images.
On the other hand, dcm2nii is useful for archival studies with legacy proprietary format that predated DICOM. Dicom Converter Mac OSX PPCMRIcron. It is natively compiled for Windows, Linux x86, Mac OSX PPC. Dicom Converter Software That CanNIfTI software that can read the spatial information (MRIcron and SPM5). If 1 then files will be compressed using the parallel pigz compressor (allowing pigz to select the number of threads). You can also specify a value of greater than 1 to explicitly set the number of threads - for example 3 will set pigz to use 3 threads. These are identical to positive values except that dcm2nii does not wait for pigz to complete before continuing to process files. For example -2 will have pigz compress the current image with 2 threads while simultaneously allowing dcm2nii to convert other images. Not that with negative values pigz may be compressing multiple files simultaneously which may cause disk thrashing or thread contention. Therefore, negative values should be used with caution and a provided for evaluation purposes only. If 0, output will be saved to same folder as source (this will cause problems if you try to convert a read-only media, such as a CD-ROM). If 2, the data will be saved to the folder OutDir (see below). SingleNIIFile to 0. If you want to save images a single.nii files, set. LastClip8 then the last 8 volumes of every 4-dimensional dataset. To see your options for running dcm2nii from the command line, simply. The NIfTI format stores spatial transforms so that software can determine the oreintation of the image. ![]() However, many programs ignore these transforms, and display the images as they are saved to disk (e.g. FSLview, MRIcro) - this means that a sagittally acquired scan appears very differently from an axially acquired scan. In fact, the three spatial dimensions (left-right, anterior-posterior, superior-inferior) can be saved in 48 different orthogonal orientations. The drawing below shows just three of these possible orientations. This means programs like FSLview and MRIcro will display the images in a sensible orientation, regardless of the acquisition. The NIfTI transform codes the residual oblique orientations, so no information is lost in this tranformation. However, you will only want to orient anatomical scans to canonical space - reorienting fMRI data can disrupt slice timing correction (as the software assumes that the slice order of the stored data is correlated with the time of acquisition).
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