# DICOM handling¶

MRtrix3 includes its own fast DICOM handling backend, allowing all MRtrix3 applications to seamlessly support DICOM images as input. While this works well in most cases, it can fail in some circumstances. Issues specific to this format are outlined below.

## How MRtrix3 handles DICOM data¶

When interpreting the argument provided for an input image to any MRtrix3 command, the image handling backend will assume that the data are in DICOM format if the argument corresponds to a folder, or ends with the .dcm suffix. The DICOM handling backend will then quickly scan through the files (recursively through the entire folder if one was provided), and build a table of contents. This consists of a tree, containing one or more patients, each containing one or more studies, each of which consists of one of more image series. When multiple choices are possible (e.g. multiple series are available), the application will present a menu to select the data of interest. For example:

$mrinfo "Siemens Trio/" mrinfo: [done] scanning DICOM folder "Siemens Trio/" Select series ('q' to abort): 0 - 9 MR images 10:20:52 localizer_sf (*fl2d1) [1] 1 - 21 MR images 10:24:39 diff 20DW 2NEX ALL (*ep_b1000#17) [2] 2 - 54 MR images 10:24:40 diff 20DW 2NEX ALL_ADC (*ep_b0_1000) [3] 3 - 54 MR images 10:24:40 diff 20DW 2NEX ALL_TRACEW (*ep_b1000t) [4] 4 - 54 MR images 10:24:40 diff 20DW 2NEX ALL_FA (*ep_b0_1000) [5] 5 - 21 MR images 10:28:52 ep2d_diff_MDDW_AT_WIP (ep_b1000#2) [7] 6 - 54 MR images 10:28:53 ep2d_diff_MDDW_AT_WIP_ADC (ep_b0_1000) [8] 7 - 54 MR images 10:28:53 ep2d_diff_MDDW_AT_WIP_TRACEW (ep_b1000t) [9] 8 - 54 MR images 10:28:54 ep2d_diff_MDDW_AT_WIP_FA (ep_b0_1000) [10] ?  The user should then enter the integer corresponding to the study of interest, for example (following from the above): ... ? 5 mrinfo: [100%] reading DICOM series "ep2d_diff_MDDW_AT_WIP" ************************************************ Image: "TOURNIER DONALD (1) [MR] ep2d_diff_MDDW_AT_WIP" ************************************************ Dimensions: 84 x 84 x 54 x 21 Voxel size: 2.5 x 2.5 x 2.5 x ? Data strides: [ -1 -2 3 4 ] Format: DICOM Data type: unsigned 16 bit integer (little endian) Intensity scaling: offset = 0, multiplier = 1 Transform: 0.9986 4.186e-08 -0.05229 -99.76 -0.002193 0.9991 -0.04188 -83.83 0.05224 0.04193 0.9978 -43.07 EchoTime: 0.08 PhaseEncodingDirection: j- TotalReadoutTime: 0.0252 comments: TOURNIER DONALD (1) [MR] ep2d_diff_MDDW_AT_WIP study: Head Brain_basic DOS: 11/05/2007 10:28:52 dw_scheme: 0,0,0,0 [21 entries] -0.99949686000000004,-0.0050327100000000001,-0.0050327100000000001,1000 ... -0.11020774999999999,0.27551937999999998,0.95513387000000005,1000 -0.031670320000000002,0.79175793999999999,0.57006572,1000  What happens at this stage is a deeper scan through those files that relate specifically to the data selected, to gather all the information required to read the data correctly. This two-stage process allows MRtrix3 to scan through large datasets rapidly to allow the user to quickly select just those datasets of interest. ### Selecting multiple matching series as a single dataset¶ It is also possible to load multiple series as a single dataset, when the image dimensions and other paramaters match. This is done by using Number sequences to specify the series of interest. For example: $ mrinfo "Siemens Trio/"
mrinfo: [done] scanning DICOM folder "Siemens Trio/"
Select series ('q' to abort):
0 -    9 MR images 10:20:52 localizer_sf (*fl2d1) [1]
1 -   21 MR images 10:24:39 diff 20DW 2NEX ALL (*ep_b1000#17) [2]
2 -   54 MR images 10:24:40 diff 20DW 2NEX ALL_ADC (*ep_b0_1000) [3]
3 -   54 MR images 10:24:40 diff 20DW 2NEX ALL_TRACEW (*ep_b1000t) [4]
4 -   54 MR images 10:24:40 diff 20DW 2NEX ALL_FA (*ep_b0_1000) [5]
5 -   21 MR images 10:28:52 ep2d_diff_MDDW_AT_WIP (ep_b1000#2) [7]
6 -   54 MR images 10:28:53 ep2d_diff_MDDW_AT_WIP_ADC (ep_b0_1000) [8]
7 -   54 MR images 10:28:53 ep2d_diff_MDDW_AT_WIP_TRACEW (ep_b1000t) [9]
8 -   54 MR images 10:28:54 ep2d_diff_MDDW_AT_WIP_FA (ep_b0_1000) [10]
9 -   21 MR images 10:35:01 diff 20DW 2NEX AT TE110 (*ep_b1000#1) [12]
10 -   54 MR images 10:35:01 diff 20DW 2NEX AT TE110_ADC (*ep_b0_1000) [13]
11 -   54 MR images 10:35:02 diff 20DW 2NEX AT TE110_TRACEW (*ep_b1000t) [14]
12 -   54 MR images 10:35:02 diff 20DW 2NEX AT TE110_FA (*ep_b0_1000) [15]
13 -   21 MR images 10:39:39 diff 20DW 2NEX AT TE80 (*ep_b1000#4) [17]
14 -   54 MR images 10:39:51 diff 20DW 2NEX AT TE80_ADC (*ep_b0_1000) [18]
15 -   54 MR images 10:39:51 diff 20DW 2NEX AT TE80_TRACEW (*ep_b1000t) [19]
16 -   54 MR images 10:39:51 diff 20DW 2NEX AT TE80_FA (*ep_b0_1000) [20]
? 4,12,16
mrinfo: [100%] reading DICOM series "diff 20DW 2NEX ALL_FA"
mrinfo: [100%] reading DICOM series "diff 20DW 2NEX AT TE110_FA"
mrinfo: [100%] reading DICOM series "diff 20DW 2NEX AT TE80_FA"
************************************************
Image:               "TOURNIER DONALD (1) [MR] diff 20DW 2NEX ALL FA"
************************************************
Dimensions:        84 x 84 x 54 x 3
Voxel size:        2.5 x 2.5 x 2.5 x ?
Data strides:      [ -1 -2 3 4 ]
Format:            DICOM
Data type:         unsigned 16 bit integer (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform:               0.9986   4.186e-08    -0.05229      -99.76
-0.002193      0.9991    -0.04188      -83.83
0.05224     0.04193      0.9978      -43.07
EchoTime:          0.08
PhaseEncodingDirection: j-
comments:          TOURNIER DONALD (1) [MR] diff 20DW 2NEX ALL FA
DOB: 09/03/1977
DOS: 11/05/2007 10:24:40


In the above example, the application accessed 3 FA maps produced with different echo times as a single 4D dataset, consisting of DICOM series 4,12,16.

It is good practice to write scripts to perform the full analysis from the raw data, so that the analysis can be performed afresh if required, and so that the exact steps taken at every stage of the analysis are recorded. However, access to DICOM data requires user interaction to select the right series for each subject. There are two ways this can be done within MRtrix3:

#### 1. Piping known selections to the command¶

The first time the data are inspected, the relevant selections can be recorded and piped as input to the commands, allowing their use in scripts. For example, assuming we have a data folder containing lots of data, and we are interested in Donald’s T1 scan:

$mrinfo DICOM_folder/ mrinfo: [done] scanning DICOM folder "DICOM_folder/" Select patient (q to abort): 1 - WILLATS LISA (000188) 06/04/1981 2 - TOURNIER DONALD (BRI) 09/03/1977 ? 2 patient: TOURNIER DONALD (BRI) 09/03/1977 Select series ('q' to abort): 0 - 9 MR images 15:31:22 localiser (*fl2d1) [1] 1 - 160 MR images 15:37:34 t1_mpr_1mm iso qk (*tfl3d1_ns) [2] 2 - 60 MR images 15:38:33 AX MPR T1 (*tfl3d1_ns) [3] 3 - 60 MR images 15:38:56 COR MPR T1 (*tfl3d1_ns) [4] 4 - 51 MR images 15:39:28 SAG MPR T1 (*tfl3d1_ns) [5] 5 - 8 MR images 15:46:57 svs_se_30 PWM NWS (*tfl3d1_ns) [6] 6 - 8 MR images 15:52:32 svs_se_30 PWM WS 32 ACQ (*tfl3d1_ns) [7] 7 - 167 MR images 15:58:40 diff60_b3000_2.3_iPat2+ADC (*ep_b3000#93) [8] 8 - 54 MR images 16:16:50 diff60_b3000_2.3_iPat2+ADC_ADC (*ep_b0_3000) [9] 9 - 108 MR images 16:16:50 diff60_b3000_2.3_iPat2+ADC_TRACEW (*ep_b3000t) [10] 10 - 54 MR images 16:16:51 diff60_b3000_2.3_iPat2+ADC_FA (*ep_b0_3000) [11] ? 1 mrinfo: [100%] reading DICOM series "t1_mpr_1mm iso qk" ************************************************ Image: "TOURNIER DONALD (BRI) [MR] t1_mpr_1mm iso qk" ************************************************ Dimensions: 160 x 256 x 256 Voxel size: 1 x 1 x 1 Data strides: [ 3 -1 -2 ] Format: DICOM Data type: unsigned 16 bit integer (little endian) Intensity scaling: offset = 0, multiplier = 1 Transform: 0.9987 0.05056 0.003483 -85.68 -0.05056 0.9987 -0.0001763 -106.9 -0.003487 9.906e-09 1 -130.2 EchoTime: 0.00255 PhaseEncodingDirection: j- TotalReadoutTime: 0 comments: TOURNIER DONALD (BRI) [MR] t1_mpr_1mm iso qk study: BRI_Temp_backup Donald DOB: 09/03/1977 DOS: 03/10/2007 15:37:34  We can see that the relevant series is obtained using the choices 2 (to get the second patient) and 1 (to get the second series for that patient). This can be scripted using the echo command to pipe these numbers directly to the relevant command, with no further user interaction required, for example: $ echo "2 1" | mrconvert DICOM_folder/ T1_anat.nii
mrconvert: [done] scanning DICOM folder "DICOM_folder/"
Select patient (q to abort):
1 - WILLATS LISA (000188) 06/04/1981
2 - TOURNIER DONALD (BRI) 09/03/1977
? patient: TOURNIER DONALD (BRI) 09/03/1977
Select series ('q' to abort):
0 -    9 MR images 15:31:22 localiser (*fl2d1) [1]
1 -  160 MR images 15:37:34 t1_mpr_1mm iso qk (*tfl3d1_ns) [2]
2 -   60 MR images 15:38:33 AX MPR T1 (*tfl3d1_ns) [3]
3 -   60 MR images 15:38:56 COR MPR T1 (*tfl3d1_ns) [4]
4 -   51 MR images 15:39:28 SAG MPR T1 (*tfl3d1_ns) [5]
5 -    8 MR images 15:46:57 svs_se_30 PWM NWS (*tfl3d1_ns) [6]
6 -    8 MR images 15:52:32 svs_se_30 PWM WS 32 ACQ (*tfl3d1_ns) [7]
7 -  167 MR images 15:58:40 diff60_b3000_2.3_iPat2+ADC (*ep_b3000#93) [8]
9 -  108 MR images 16:16:50 diff60_b3000_2.3_iPat2+ADC_TRACEW (*ep_b3000t) [10]
10 -   54 MR images 16:16:51 diff60_b3000_2.3_iPat2+ADC_FA (*ep_b0_3000) [11]
mrconvert: [100%] reading DICOM series "t1_mpr_1mm iso qk"
mrconvert: [100%] copying from "TOURNIER D...BRI) [MR] t1_mpr_1mm iso qk" to "T1_anat.nii"


#### 2. Using environment variables¶

It is also possible to select datasets by string matching on specific DICOM fields. There are currently four selectors available:

• DICOM_PATIENT to match PatientName
• DICOM_ID to match PatientID
• DICOM_STUDY to match StudyName
• DICOM_SERIES to match SeriesName

To use a selector, simply set the corresponding environment variable to the desired pattern. It is simplest in practice to set it directly before the command, on the same line – this ensures that the environment variable does not apply to other commands than that intended. The matching pattern can include the * and/or ? wildcard characters, and you can use several selectors at the same time. Note that matching is not case-sensitive. If you set any selector, you won’t be prompted for input, but the command will abort if there is no match or if there are too many matches.

Example usage:

$DICOM_SERIES='diff*iPat2' DICOM_PATIENT='*donald*' mrinfo dicom/  ## When the DICOM import goes wrong¶ Errors can occur in the DICOM import for several reasons. In some cases, we can identify the problem in the MRtrix3 code and provide a fix to handle these data. In other cases, the data are simply not complete, not standards-compliant, or stored using encodings that MRtrix3 doesn’t currently handle. ### The application crashes¶ If running a simple command such as: $ mrconvert DICOM/ out.nii
mrconvert: [SYSTEM FATAL CODE: SIGSEGV (11)] Segmentation fault: Invalid memory access


crashes without a relevant error message, then this is an overt bug that needs fixing within the MRtrix3 code. Even if the data are not DICOM-compliant, the code should nonetheless be able to detect this and exit gracefully with a clear indication of what the problem is. In these cases, please send the problematic data sets to members of the MRtrix3 team for inspection.

### ERROR: missing image frames for DICOM image¶

Note

This also applies to the “dimensions mismatch in DICOM series” error message.

DICOM data are often stored with individual slices in separate files. Unfortunately, there is no requirement in the DICOM standard that the files for a given dataset should all reside within the same folder. This means that it’s not uncommon for files belonging to the same series to be spread over multiple different sub-folders. This makes it all too easy for some of the images in a DICOM series to go missing, due to users forgetting to copy over all of the folders. Another way this can happen is when users copy the data from their DICOM client (e.g. PACS system) before the DICOM sender has finished sending the data (these transfers can take a long time…). Attempts to read the data will fail with a message like this:

$mrinfo DICOM/ mrinfo: [done] scanning DICOM folder "DICOM/" mrinfo: [100%] reading DICOM series "DWI_60" mrinfo: [ERROR] missing image frames for DICOM image "Joe Bloggs [MR] DWI_60" mrinfo: [ERROR] error opening image "DICOM/"  In these cases, it is simply not possible to load the data, since there are missing frames within it. The only solution here is to go back to the data source, find the missing data, and try again. ### ERROR: no diffusion encoding information found in image¶ This indicates that MRtrix3 was unable to find any information regarding the DW gradient directions (bvevcs/bvals) in the DICOM headers, leading to errors like: $ dwi2tensor DICOM/ dt.mif
dwi2tensor: [done] scanning DICOM folder "DICOM/"
dwi2tensor: [100%] reading DICOM series "DWI_60"
dwi2tensor: [ERROR] no diffusion encoding information found in image "Joe Bloggs [MR] DWI_60"


This can happen for a number of reasons:

• the information is simply not present. This can happen with custom sequences not explicitly designed to provide this information, or lack of support for providing this information from some manufacturers. The only possible solution in this case is to obtain the DW information from a different source, and provide it to MRtrix3 manually using the -grad or -fslgrad options in those commands that support it.
• the information is present, but in a format that MRtrix3 doesn’t yet support. This is a very rare occurence these days, but still possible. If you’re convinced your data should contain this information, please get in touch with members of the MRtrix3 team, so we can take a look and see if support can be added to the code.
• the information was present, but has been stripped out by third-party software, in particular anonymisation packages. These typically work by stripping out all potentially patient-identifiable information. This often includes removing any private (vendor-specific) DICOM entries, since it’s not possible for a computer program to guarantee that these entries contain no sensitive information. Unfortunately, these entries often do contain important information, notably the DW gradient information. In these cases, the only sensible solution is to request the raw non-anonymised data, convert these correctly, and anonymise the converted images.
• the image series is simply not a DWI series. Double-check that you in fact trying to read the correct dataset.

### ERROR: unsupported transfer syntax¶

The DICOM standard specifies a default transfer syntax to encode the information and the imaging data themselves. However, it also allows specifies a number of other storage formats to store the imaging data, notably compressed formats such as different variants of JPEG and MPEG (see the official DICOM standard for details). Importantly, these compressed formats are not mandatory: a compliant DICOM implementation does not need to support these features. This makes it entirely possible (and indeed, quite common) for a fully DICOM-compliant implementation to produce data that cannot be understood by another fully DICOM-compliant implementation – a less than ideal situation…

MRtrix3 does not currently support non-default transfer syntaxes – only those that the standard defines as mandatory, and variants thereof. For reference, these are:

• Implicit VR Little Endian (1.2.840.10008.1.2)
• Explicit VR Little Endian (1.2.840.10008.1.2.1)
• Explicit VR Big Endian (1.2.840.10008.1.2.2)

Any other transfer syntax will be flagged as unsupported, and MRtrix3 will be unable to read the data, providing an error message similar to this:

$mrinfo DICOM mrinfo: [done] scanning DICOM folder "DICOM" mrinfo: [ERROR] unable to read DICOM images in "DICOM": mrinfo: [ERROR] unsupported transfer syntax found in DICOM data mrinfo: [ERROR] consider using third-party tools to convert your data to standard uncompressed encoding mrinfo: [ERROR] See the MRtrix3 documentation on DICOM handling for details: mrinfo: [ERROR] http://mrtrix.readthedocs.io/en/latest/tips_and_tricks/dicom_handling.html#error-unsupported-transfer-syntax mrinfo: [ERROR] error opening image "DICOM"  Thankfully, other tools exist that should be able to convert the data to a format that MRtrix3 (and other DICOM tools) will read. The dcmtk DICOM toolkit in particular provides the dcmdjpeg command to decompress data stored using JPEG transfer syntax. On Linux, a directory of such files can be decompressed as follows (amend the various PATH as required for your system): $ export PATH=/opt/dcmtk/bin:$PATH$ export DCMDICTPATH=/opt/dcmtk/share/dcmtk/dicom.dic

$for img in dcmdir/* > do > dcmdjpeg$img ${img}.tmp > mv${img}.tmp $img > done  MRtrix3 commands should now be able to read the directory successfully: $ mrinfo dcmdir
mrinfo: [done] scanning DICOM folder "data/driss/t1"
mrinfo: [100%] reading DICOM series "AX FSPGR 3D ASSET  C+"
...