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FILENAMING.md

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About

DICOM files tend to have bizarre file names, for example based on the instance UID, e.g. MR.1.3.12.2.1107.5.2.32.35131.2014031013003871821190579. In addition, DICOM images are often 2D slices or 3D volumes that we will combine into a single unified NIfTI file. On the other hand, some enhanced DICOM images save different reconstructions (e.g. phase and magnitude) of the same image that we will want to save as separate NIfTI files. Therefore, dcm2niix attempts to provide a sensible file naming scheme.

Basics

You request the output file name with the -f argument. For example, consider you convert files with dcm2niix -f %s_%p: in this case an image from series 3 with the protocol name T1 will be saved as 3_T1.nii. Here are the available parameters for file names:

  • %a=antenna (coil) name (from Siemens 0051,100F)
  • %b=basename (file name of first DICOM)
  • %c=comments (from 0020,4000)
  • %d=description (from 0008,103E)
  • %e=echo number (from 0018,0086)
  • %f=folder name (name of folder containing first DICOM)
  • %g=accession number (0008,0050)
  • %i=ID of patient (from 0010,0020)
  • %j=series instance UID (from 0020,000E)
  • %k=study instance UID (from 0020,000D)
  • %l=local procedure step description (from 0040,0254)
  • %m=manufacturer short name (from 0008,0070: GE, Ph, Si, To, UI, NA)
  • %n=name of patient (from 0010,0010)
  • %o=mediaObjectInstanceUID (0002,0003)*
  • %p=protocol name (from 0018,1030). If 0018,1030 is empty, the SequenceName (0018,0024) is used.
  • %r=instance number (from 0020,0013)*
  • %s=series number (from 0020,0011)
  • %t=time of study (from 0008,0020 and 0008,0030)
  • %u=acquisition number (from 0020,0012). This option is recommended for DICOM renaming. It is not recommended for DICOM to NIfTI conversion (as BIDS compatible 4D datasets collapses multiple acquisitions to a single file).
  • %v=vendor long name (from 0008,0070: GE, Philips, Siemens, Toshiba, UIH, NA)
  • %x=study ID (from 0020,0010)
  • %y=youth in series: GE RawDataRunNumber (0019,10A2) else TemporalPosition (0020,0100)*
  • %z=sequence name (from 0018,0024)
  • Attributes listed above with an asterisk (*) are likely to vary within a series, and are typically not useful for DICOM to NIfTI conversion (where all images from a series are stacked together). These attributes can be useful for renaming DICOM images

File Name Post-fixes: Image Disambiguation

In general dcm2niix creates images with 3D dimensions, or 4 dimensions when the 4th dimension is time (fMRI) or gradient number (DWI). However, DICOM images can include additional dimensions, e.g. a multiple-echo sequence would generate separate images for each echo. By default dcm2niix will use the following extensions to the file names in order to disambiguate additional dimensions from the same series:

  • _cNx.._cNz where C* refers to the coil name (typically only seen for uncombined data, where a separate image is generated for each antenna)
  • _e1..eN echo number for multi-echo sequences
  • _Eq is commonly seen in CT scans. For example, CT scans of the brain often have many slices closely packed near the brain stem and only a few slices spread far apart near the top of the head. Variable between-slice spacing is rarer in MRI, and if you see this from a MRI sequence you should ensure that all of the acquired slices have been provided to dcm2niix. NIfTI assumes all 2D slices that form a 3D stack are equidistant. Therefore, dcm2niix reslices the input data to generate an equidistant volume.
  • _i1..N appended image number for non-parallel slices
  • _imaginary imaginary component of complex image
  • _MoCo is appended to the ProtocolName if Image Type (0008,0008) includes the term 'MOCO'. This helps disambiguate Siemens fMRI runs where both motion corrected and raw data is stored for a single session.
  • _ph phase map
  • _phMag rare case where phase and magnitude are saved as the 4th dimension
  • _r1..rN repetition number for sequences with multiple repetition times
  • _real real component of complex image
  • _t If the trigger delay time (0020,9153) or trigger time (0018,1060) is non-zero, it will be recorded in the file name. For example, the files "T1_t178.nii" and "T1_t511" suggests that the T1 scan was acquired with two cardiac trigger delays (178 and 511ms after the last R-peak).
  • _Tilt is specific to CT scans. These scans can be acquired with a gantry tilt that causes a skew that can not be stored in a NIfTI qForm. Therefore, the slices are resampled to remove the effect of tilt.

Some post-fixes are specific to Philips DICOMs

  • _ADC Philips specific case. A DWI image where derived isotropic, ADC or trace volume was appended to the series. Since this image will disrupt subsequent processing, and because subsequent processing (dwidenoise, topup, eddy) will yield better derived images, dcm2niix will also create an additional image without this volume. Therefore, the _ADC file should typically be discarded. If you want dcm2niix to discard these useless derived images, use the ignore feature ('-i y').
  • _fieldmaphz unwrapped B0 field map (in Hz) generated by a Philips scanner. Suggests Image Type (0008,0008) includes the terms 'B0' and 'MAP'.
  • Raw Philips XX* DICOMs (Raw Data Storage).
  • PS Philips PS* DICOMs (Grayscale Softcopy Presentation State).

If you do not want post-fixes, run dcm2niix in the terse mode (--terse). In this mode, most post-fixes will be omitted. Beware that this mode can have name clashes, and images from a series may over write each other.

Overlays

DICOM images can have up to 16 binary (black or white) overlays as described by the Overlay Plane Module. dcm2niix will save these regions of interest with the post-fix "_ROIn" where N is the overlay number (1..16).

File Name Conflicts

dcm2niix will attempt to write your image using the naming scheme you specify with the '-f' parameter. However, if an image already exists with the specified output name, dcm2niix will append a letter (e.g. 'a') to the end of a file name to avoid overwriting existing images. Consider a situation where dcm2niix is run with '-f %t'. This will name images based on the study time. If a single study has multiple series (for example, a T1 sequence and a fMRI scan, the reulting file names will conflict with each other. In order to avoid overwriting images, dcm2niix will resort to adding the post fix 'a', 'b', etc. There are a few solutions to avoiding these situations. You may want to consider using both of these:

  • Make sure you specify a naming scheme that can discriminate between your images. For example '-f %t' will not disambiguate different series acquired in the same session. However, '-f %t_%s' will discriminate between series.
  • Localizer (scout) images are the first scans acquired for any scanning session, and are used to plan the location for subsequent images. Localizers are not used in subsequent analyses (due to resolution, artefacts, etc). Localizers are often acquired with three orthogonal image planes (sagittal, coronal and axial). The NIfTI format requires that all slices in a volume are co-planar, so these localizers will generate naming conflicts. The solution is to use '-i y' which will ignore (not convert) localizers (it will also ignore derived images and 2D slices). This command helps exclude images that are not required for subsequent analyses.
  • Be aware that if you run dcm2niix twice with the same parameters on the same data, you will encounter file naming conflicts.

Special Characters

Some characters are not permitted in file names. The following characters will be replaced with underscorces (_). Note that the forbidden characters vary between operating systems (Linux only forbids the forward slash, MacOS forbids forward slash and colon, while Windows forbids any of the characters listed below). To ensure that files can be easily copied between file systems, dcm2niix restricts file names to characters allowed by Windows. While technically legal in all filesystems, the semicolon can wreak havoc in Windows and Linux. Likewise, the dollar sign can cause issues.

List of Forbidden Characters

< (less than)
> (greater than)
: (colon - sometimes works, but is actually NTFS Alternate Data Streams)
" (double quote)
/ (forward slash)
\ (backslash)
| (vertical bar or pipe)
? (question mark)
* (asterisk)
; (semicolon)
$ (dollar sign)

Control characters like backspace and tab are also forbidden.

Be warned that dcm2niix will copy all allowed characters verbatim, which can cause problems for some other tools. Consider this sample dataset where the DICOM Protocol Name (0018,1030) is 'Axial_EPI-FMRI_(Interleaved_I_to_S)'. The parentheses ("round brackets") may cause other tools issues. Consider converting this series with the command 'dcm2niix -f %s_%p ~/DICOM' to create the file '4_Axial_EPI-FMRI_(Interleaved_I_to_S).nii'.If you now run the command 'fslhd 4_Axial_EPI-FMRI_(Interleaved_I_to_S).nii' you will get the error '-bash: syntax error near unexpected token `(''. Therefore, it is often a good idea to use double quotes to specify the names of files. In this example 'fslhd "4_Axial_EPI-FMRI_(Interleaved_I_to_S).nii"' will work correctly.