dcm2niix | dcm2nii DICOM to NIfTI converter | Messaging library
kandi X-RAY | dcm2niix Summary
kandi X-RAY | dcm2niix Summary
dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. This web page hosts the developmental source code - a compiled version for Linux, MacOS, and Windows of the most recent stable release is included with MRIcroGL. A full manual for this software is available in the form of a NITRC wiki. The DICOM format is the standard image format generated by modern medical imaging devices. However, DICOM is very complicated and has been interpreted differently by different vendors. The NIfTI format is popular with scientists, it is very simple and explicit. However, this simplicity also imposes limitations (e.g. it demands equidistant slices). dcm2niix is also able to generate a BIDS JSON format sidecar which includes relevant information for brain scientists in a vendor agnostic and human readable form. The [Neuroimaging DICOM and NIfTI Primer]provides details.
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Community Discussions
Trending Discussions on dcm2niix
QUESTION
I want to add a new key into the pre-existing .json file.
- Is it possible to put the new key in the specific location? (ex) "SliceThickness" = 3 Add "SliceTiming" = 0.1 right after "SliceThickness" key
How can I check the added one? I cannot see the added one in the pre-existing .json file.
- I'm using python3 with the Jupyter notebook.
- pre-existing .json file (name: task-rest_bold.json) looks like this
In short, I want to put "SliceTiming" right after "SliceThickness". Additionally, I want to check in on the .json file, because with the code below, it says that SliceTiming has been successfully added, however, I could not find it on the "task_rest_bold.json" file.
...ANSWER
Answered 2019-Sep-17 at 07:17Looking at other sources it doesn't seem possible to add a value in the middle of a json object.
The answer on this question: https://stackoverflow.com/a/23111697/6928839
opens the file with a write flag:
QUESTION
I was writing a bash script for using Dcm2niix. Dcm2niix's command includes single quotation marks. I tried to add single quotation marks on the script in many ways but it doesn't work.
My working system (environment?) is: Ubuntu 18.04.1 LTS.
Dcm2niix is a DICOM to NifTI converter. It convert .dcm files to .nii files.
Its command is normally like:
dcm2niix [options]
is like:
'sourcedir'
(It doesn't work without single quotation marks)
On the terminal, I type
...ANSWER
Answered 2019-Jul-17 at 11:56You need '' around your file_path in terminal only in case you have special characters like spaces or globs inside it. Which is not the case for Desktop/test/. But in your script, you have a variable $file_path which you want to expand into Desktop/test/, so the '' prevent this. Try using double quotes " instead of '. Or try to escape the special meaning of the single quote marks using \' instead of '.
QUESTION
Background:
I wrote a python script to convert files from format to another. This code uses a text file (subject_list.txt) as input and iterates through source directory names listed in that text file (several hundred directories, each with thousands of files), converting their contents and storing them in a specified output directory.
Issue:
To save time, I would like to use this script on a high performance cluster (HPC) and create jobs to convert the files in parallel, rather than sequentially iterating through each directory in the list.
I am new both to python and to HPCs. Our lab had previously written primarily in BASH and had not had access to an HPC environment, but we recently gained access to the HPC and the decision has been made to switch to Python, so everything is pretty new.
Question:
Is there a module in python that will allow me to create jobs within the python script? I've found documentation on the multiprocessing and the subprocess python modules, but it isn't clear to me how I would use them. Or is there perhaps a different approach I should take? I've also read a number of posts here on stackoverflow about using slurm and python together, but I'm stymied with too much information and not enough knowledge to distinguish which thread to pick up. Any help is greatly appreciated.
Environment:
HPC: Red Hat Enterprise Linux Server release 7.4 (Maipo)
python3/3.6.1
slurm 17.11.2
Housekeeping part of the code:
...ANSWER
Answered 2018-Jan-27 at 10:37This is a possible solution for your code. It has not been tested.
QUESTION
I have a CSV file with 3 columns and many rows.
I want to run a command in a Windows cmd prompt, and supply input variables to the command from a CSV file, such that:
...ANSWER
Answered 2017-Jun-13 at 17:54Assuming the code and sample file that you posted are accurate, then you have two unrelated problems.
1)
Your IN() clause uses single quotes, which means the FOR /F will try to execute the csv file rather than simply read the contents.
You must drop the single quotes
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Install dcm2niix
Github Releases provides the latest compiled executables. This is an excellent option for MacOS and Windows users. However, the provided Linux executable requires a recent version of Linux (e.g. Ubuntu 14.04 or later), so the provided Unix executable is not suitable for very old distributions. Specifically, it requires Glibc 2.19 (from 2014) or later. Users of older systems can compile their own copy of dcm2niix or download the compiled version included with MRIcroGL Glibc 2.12 (from 2011, see below).
Run the following command to get the latest version for Linux, Macintosh or Windows: curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_mac.zip curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_mac_arm.pkg curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_win.zip
MRIcroGL (NITRC) or MRIcroGL (GitHub) includes dcm2niix that can be run from the command line or from the graphical user interface (select the Import menu item). The Linux version of dcm2niix is compiled on a holy build box, so it should run on any Linux distribution.
If you have a MacOS computer with Homebrew or MacPorts you can run brew install dcm2niix or sudo port install dcm2niix, respectively.
If you have Conda, conda install -c conda-forge dcm2niix on Linux, MacOS or Windows.
On Debian Linux computers you can run sudo apt-get install dcm2niix.
It is often easier to download and install a precompiled version. However, you can also build from source.
cmake and pkg-config (optional) can be installed as follows:. Ubuntu: sudo apt-get install cmake pkg-config. MacOS: brew install cmake pkg-config or sudo port install cmake pkgconfig. dcm2niix will be created in the bin subfolder. 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. In rare case if cmake fails with the message like "Generator: execution of make failed", it could be fixed by sudo ln -s `which make` /usr/bin/gmake.
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