If 2, the data will be saved to the folder "OutDir" (see below). If 1, the user will be prompted to find an output folder. 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). Images with a larger matrix size than this value will be reoriented to canonical space (see below). Therefore, negative values should be used with caution and a provided for evaluation purposes only. Not that with negative values pigz may be compressing multiple files simultaneously which may cause 'disk thrashing' or thread contention. For example -2 will have pigz compress the current image with 2 threads while simultaneously allowing dcm2nii to convert other images. These are identical to positive values except that dcm2nii does not wait for pigz to complete before continuing to process files.
The software also allows you to specify negative values. 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. In general, pigz is faster than the inbuilt compressor. If 1 then files will be compressed using the parallel pigz compressor (allowing pigz to select the number of threads). If 0 then files are compressed using the (single threaded) internal gzip compression routine. fMRI scanningĬontinued after behavioral paradigm ended). To be removed from the end of a 4D acquisition (e.g. Specifies number of volumes to be removed from the beginning of a 4D acquisition (e.g. par/.rec files in the source folder will be converted, otherwise only the file specified will be converted If '=1' then output filename will include source filename. If '=1' then output filename will include patient name. If '=1' then output filename will include protocol name. If '=1' then output filename will include acquisition number. If '=1' then output filename will include date of study. If '=1' then dcm2nii will create Analyze images (SPM2 style), otherwise headers will be in NIfTI (SPM5/FSL). If '=1' then dcm2nii will create compressed. hdr/.img pairs will be created (SPM style) If '=1' then patient name will not be copied to NIfTI header. If '=1' then dcm2nii will generate 4D files (FSL style), otherwise output will be 3D (SPM style). Otherwise, subformat will be based on $D, Prompt user to describe output subformat for every NIfTI image dragged You will be able to adjust the settings:Ĭreate anonymized copies of DICOM images (remove name, DOB, patient ID, (optional) Open dcm2nii.ini with a text editor (double click on the file).This file is created in your home directory. If you are using Windows, this file is in Double click on dcm2nii.exe - a file namedĭcm2nii.ini will be created.
It is natively compiled for Windows, Linux x86, Mac OSX PPC
DCM2NII is a stand-alone program that is distributed with NIfTI is a modern incarnation of the Analyzeįormat, but includes important information like the orientation of the Scanner format to the NIfTI format used by FSL, SPM5, MRIcron and many This software is provided under the BSD 2-Clause license.ĭCM2NII attempts to convert images from the proprietary On the other hand, dcm2nii is useful for archival studies with legacy proprietary format that predated DICOM. In general, dcm2niix is typically better suited for modern DICOM images. While I hope it is generally robust and useful, active development has moved to dcm2niix.