Nifti to dicom

Nifti to dicom

The file type can be specified in two ways. A note on specifying orientation: Do not use this to try to change the orientation for FSL. If it is correct, this will make it wrong! If you are having problems with fslview displaying your data, consult the FSL website for methods to reorient.

Ideally, the orientation information is derived from a DICOM file so that you have some confidence that it is correct. However, if you have some way of knowing which direction is which, you can use these options to incorporate this information into the header of the output format.

For analyze files, it will be stored in the output. First of all, determining and setting the orientation is hard. Don't fool yourself into thinking otherwise. Second, don't think you are going to learn all you need to know from this documentation. Finally, you risk incorporating a left-right flip in your data if you do it incorrectly. OK, there are two ways to specify this information on the command-line. If you don't know what a direction cosine is, don't use this method.

The ostring is three letters that roughly describe how the volume is oriented. This is usually described by the direction cosine information as originally derived from the dicom but might not be available in all data sets.

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You'll have to determine the correct ostring for your data. The first character of ostring determines the direction of increasing column. The second character of ostring determines the direction of increasing row. The third character of ostring determines the direction of increasing slice.

nifti to dicom

Eg, if the volume is axial starting inferior and going superior the slice is oriented such that nose is pointing up and the right side of the subject is on the left side of the image, then this would correspond to LPS, ie, as the column increases, you move to the patients left; as the row increases, you move posteriorly, and as the slice increases, you move superiorly.

Invalid combinations are detected immediately, an error printed, and the program exits. Note: you can use tkregister2 to help determine the correct orientation string.

An example of a transform file is talairach. This properly accounts for the case where the input volume does not have it's coordinate center at 0. The main and aux volumes should overlap very closely. If they do not, use tkregister2 to fix it. For a single frame, simply specify the output file name with a.

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This will save each frame as baseXXX. Frame numbers being at one. By default, the width of the zero padding is 3. This will be a data file with a single column of data. Example: 2 1 3 will swap row and colms. If using -r4, the output geometry will likely be wrong. Only makes sense for 8 bit images.

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Only operates on first frame. This function is applicable when the input geometry information is correct but the subject was in the scanner in the 'sphinx' position ie AP in line with the bore instead of head-first-supine HFS.

This is often the case with monkeys. Note that the assumption is that the geometry information in the input file is otherwise accurate. Input data is a stats table as produced by asegstats2table or aparcstats2table.It supports batch processing. Following a speedy setup operation that doesn't need complicated configurations and doesn't have software prerequisites, you're welcomed by the clean and intuitive window of DICOM to NIfTI, where you can begin by populating the conversion list with as many DICOM images as you wish, whether they have the.

A sample. In the following step, you can specify a custom location for saving the new NIfTI files, unless you want to keep them stored in the same location as the source, then click "Convert" to start the job. It's not possible to change the output filenames, though same as source.

Without modifying conversion options, the new files are created with the. You can also opt for. For the flipping operation, it would've been useful if the utility has a built-in previewer for the source and destination files, especially useful if you don't currently have a DICOM or NIfTI viewer on your PC. It's not possible to convert files to different types in one go, so the conversion options apply to all DICOMs in the list. We haven't experienced any compatibility issues with Windows 10 in our tests.

Thanks to its practical and intuitive settings, the tool should meet the requirements of many users looking for a straightforward solution for creating NIfTI files from DICOM images.


Load comments. All rights reserved.Updated 08 Aug Xiangrui Li Retrieved April 18, You can following there and provide more information, like the scanner manufacturer etc.


How can I use dcm2nii so that all output json, tsv is saved? Only the nii. Hi Roger Mullins, There is no option for that. When I convert Phillips. Is or will there be an option to turn this off similar to dcm2niix's -p n option? If you are sure the files are from 9 runs, it sounds like the dicom SeriesInstanceUID is messed up by some third party dicom tool. If this does not fix the problem, you may share with me xiangrui.

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I am not sure if I am doing something utterly wrong - any help would be highly appreciated. Many thanks! ProtocolDataBlock. Hi Jianzhang Li, I believe the dataset you are talking about is structural data with sagittal acquisition.

The converter re-orients the nii into xyz order in this case, and stores the original slice dim information in the nii header. This won't cause any problem, but bring some benefit to early version of FSLview.

So in my opinion, you don't need to worry for this at all. Hi Xiangrui, Thanks for this powerfull tool! A problem relating to dimentions showed up when I finished the converting. Do you know how to deal with this? Hi Jacob Levman, Could you provide the full error message? It also helps if you can send me xiangrui. Hi John, Thank you for reporting the problem.

nifti to dicom

The bug was introduced when I tried to take care of compatibility to matlab a or earlier.GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.

If nothing happens, download GitHub Desktop and try again. If nothing happens, download Xcode and try again. If nothing happens, download the GitHub extension for Visual Studio and try again. This software is open source.

The bulk of the code is covered by the BSD license. See the license. This software should run on macOS, Linux and Windows typically without requiring any other software. However, if you use dcm2niix to create gz-compressed images it will be faster if you have pigz installed.

You can get a version of both dcm2niix and pigz compiled for your operating system by downloading MRIcroGL. For more help see help: dcm2niix -h. It is often easier to download and install a precompiled version. However, you can also build from source. To install on the system run make install instead of make - this will copy the executable to your path so you do not have to provide the full path to the executable. As noted in the Image Conversion and Compression Support section, the software provides many optional modules with enhanced features.

To build with these options simply request them when configuring cmake:. The batch processing binary dcm2niibatch is optional. Skip to content. Dismiss Join GitHub today GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.

Sign up. Branch: master. Find file. Sign in Sign up.

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Go back.If your job involves frequently handling medical imaging files, you probably understand and agree with the fact that software assistance has a huge role in simplifying your tasks. If you want to convert files from various formats to a specific one, most of the times you can't do so without the appropriate set of tools. This application can be deployed to the target computer without significant efforts, as you don't need to perform any complicated configuration steps. After you run the installation kit, you simply need to decide whether or not desktop shortcuts should be created and follow the on-screen instructions, since the destination path is set automatically and the rest of the process unfolds without any further assistance.

Visually, this program's interface doesn't stand out, as it is pretty plain and simple, with no hidden menus, buttons or sections whatsoever. Most of its functions can be accessed by clicking the dedicated toolbar buttons. You can add individual files or entire folders' worth of documents and remove single items from the list or clear it altogether by using the toolbar functions.

Aside from its core file conversion functions, this application also enables you to tamper with its more advanced settings, if you want to. Here you can customize settings regarding tagging and compression, but also apply filters. You can configure the parameters by simply clicking the desired radio button or ticking the appropriate checkbox. It can be easily installed, comes with a plain user interface and lets you customize some of its settings easily.

Easily convert NII files from your computer to DICOM format by turning to this lightweight application that lets you configure tagging and compression settings. Load comments. All rights reserved.How do I best report problems to the FSL email list? What image format does FSL need? How can I modify the orientation of my data?

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How do I know right from left in the images? How do I run the GUIs or command lines? How do I get my command line to run? Installation What sort of system requirements does FSL have? How can I test if my installation works?

Why does an FSL program crash when it is trying to process a very large dataset? Further help can also be obtained via the public FSL email list.

Note that you must join the list in order to post questions. In order to understand and analyse problems please provide the following pieces of information: What part of FSL did not work as expected?

What type of input data were you running the sofware on? Please make sure that the data is not corrupted: check your input data by loading it into fslview or slices. If your input data is not what you expect, try and fix this first. If you need to report a problem, please provide this information in an email. If you cannot resolve the problem then please run the command: fslerrorreport in the directory that the problem occurred.

Please attach the entire output of this command to your email. Also, please be as specific as possible about command line error messages. These files can be read and written in compressed gzip format or uncompressed form. These are described more fully in the nifti1 page. An image can be 2D or 3D or 4D multiple time points. You will need some other program to convert between formats e. In general, due to the multiple file formats, we recommend using the utility imglob for getting filenames.

Look at the labels in FSLView. However, the changes are relatively straightforward and are described in a separate scripting page.

DICOM Tool - Exporting Images from Analyze

It is also necessary to source a setup file. This can be done by: bash users :. In general these are best done in your shell startup file e. It is recommended that the following memory and disk requirements are met: RAM - 1GB or more at least 2GB if running a virtual machine on Windows Swap space - at least equal to RAM 2GB min recommended; check with top Disk space - at least 10 times the size of your data sets Be warned that too little swap space causes "unexplained" crashes!

Certain programs in FSL can require a large amount of memory RAM to run, depending on the size of the data that you are trying to analyse.

Swap is hard disk space that is used to act as additional memory on top of your actual memory, allowing programs larger than your physical memory to run, but much more slowly.

Your local sysadmin can easily increase swap space if you have spare hard disk space available. However, there is one further caveat.

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This limit is normally 2GB. The best solution to this is to move to a bit computer for example, all Apple computers are now bit, and it is easy to find cheap bit PCs to install bit Linux on.Since version This topic describes the steps performed when loading NIfTI files.

Since the performed steps are different for normalized MNI, Talairach and non-normalized Scanner space data, some information about how coordinate systems are stored in the NIfTI header is provided in the next section. For more information, consult the official description of the NIfTI-1 header.

The NIfTI format specifies two out of three methods to ensure that the orientation of the data in a NIfTI file is properly interpreted by imaging software. One method method 2, qform is based on a rotation matrix stored as a quaternionscaling values and a translation vector; this method is mainly used to map voxel coordinates to x,y,z coordinates in scanner world space or to another aligned data set.

If a data set is already transformed in MNI or Talairach space, the transformation matrix is simply the identity matrix eventually with some scaling and axes reorientation.

nifti to dicom

A third method is available that only supports scaling the data using the NIfTI pixdim values without defining a coordinate system; this method is not recommended and only included in the NIfTI specification for compatibility with the older Analyze 7.

Both affine transformation matrices can be present in the same NIfTI file. If both codes are 0, only the non-recommended third method using only scaling transformations is available. The two forms were introduced so that two transformations could be defined simultaneously e.

The same strategy is performed now as default when reading NIfTI files with a "Scanner" transformation matrix, i. An important advantage of the ortho transformation is that the data needs not to be resampled e. If, however, the sform or qform code value is 3 TAL or 4 MNIBrainVoyager applies the full transformation matrix eventually requiring resampling the data if not already in normalized 1 mm space ; this allows to link VTC data to the loaded VMR in case it has been normalized to the same space Talairach or MNI This default behavior can be changed in the Preferences dialog see below.

While the original NIfTI qform or sform is stored in the VMR or FMR header in any case, it is also recorded in the header whether an ortho, full or no transformation has been performed.

These data sets are useful to test proper interpretation of coordinate systems since they contain explicit labels for left and right see below.

The values of 2. For the actual transformation, this matrix is finally inverted since BrainVoyager iterates over voxel coordinates in the target x x volume and accesses the corresponding values in the original NIftI volume "backwards". The NIfTI tab can also be used to specify for what coordinate target spaces a full transformation application of the sform qform NIfTIvoxel-to-RAS matrix should be applied default for Talairach and MNI space or whether only a "reduced" otho-reorientation matrix should be used default for Scanner and Aligned space.

As default, a created native BrainVoyager document e. In case this is not desired, the Save automatically to disk option in the Created BV documents field can be unchecked. If not auo-saved, the created document can, of course, still be saved to disk using the standard Save Document icon in the main toolbar or the Save item in the File menu.

Furthermore, the dialog shows that the VMR header keeps the original affine sform or qform transformation matrix in the Past spatial transformations field.

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