Hello,

I have not used dicom2nii enough to help you with that. Another tool you could try is MRTrix, which can be downloaded from http://www.brain.org.au/software/mrtrix/ for either Linux, Windows or Mac.

With a command:

mrconvert folder_with_the_dicom_files/ output_filename.nii

you can convert all the dicom files from a folder into a single nii-file.

If you're working with diffusion, you can also extract the gradient orientations with a command:

mrinfo -grad grad.txt folder_with_the_dicom_files/

Hopefully this helps!

Cheers,

Timo

I don't know it MRITRix will help you (maybe it will). If MRIConvert gives the "Unsupported transfer syntax" when trying to convert DICOM, the usual problem is that the DICOM files are stored as jpeg.

A solution to this is to dejpeg them. I use DCMTK dcmdjpeg.

http://support.dcmtk.org/docs/dcmdjpeg.html

This of course will have to run it on all files in a directory

that means for Windows

for %%i in (.\*) do dcmdjpeg %%i %%i

or with find in linux.

Can you tell us the whole transfer syntax of your files?

Dear Olga,

Have you tried to use ImageJ with latest DICOM plugins? I know there are several issues with recent DICOM file formats, but by this time they should have been solved.

If not, please let me know, I will have a look at it.

Good luck!

Harrie

Thanks everyone for your input. The solution that Amir suggested worked. I only ran dcmdjpeg on one file, but that file converted to nifti (using MRIConvert) without problems. Amir would you have input on how to scale the command up to include all files in a folder? I use .tsch shell on linux. Thank you for your help.

In that case I think

find ./* -printf 'dcmdjpeg %p %p \n' | sh

in the directory you want to djpeg will do the trick

it will also include subdirectories. If dcmdjpeg is not in your path just add the path to the command like

find ./* -printf '/home/olga/dcmtk/dcmdjpeg %p %p \n' | sh

To dejpeg just .dcm files in the current directory,

find ./* -maxdepth 0 -name '*.dcm' -printf 'dcmdjpeg %p %p \n' | sh

Always backup your directories before running such commands on them, the files will be changed forever and there is no undo.

Amir

I tried it, it gives me permission denied error:

F: Permission denied: writing file: ./view0206.dcm

I changed permissions on the folder and tried to run the command as a sudoer, didn't work. Is there a way to change the filename to something else when running dcmdjpeg?

Make a new subdirectory, say subdir

Try %h/subdir/%f instead of the second %p

A

Hello,

There are many ways to convert DICOM images to NIFTI format. The easiest way would be downloading free software called MRIconvert, in which you can change the image formats and it will generate right headers for your multiple files, saving you time of manually chosing the headers. It is the direct and most easy way.

I know this is an old thread, but I was just having the same problem and have found a different solution, so I thought I'd record it for posterity! If you import the compressed DICOM files into Osirix (http://www.osirix-viewer.com/) you can then export them again with the option to decompress them. Works great!

Hi Olga,

Kindly, can you post the code for the script that you applied on your DICOMs. Actually I have the same problem and I highly appreciate your help.

Thanks

Mohamad:

I don't know what Olga uses but for me

find . -printf "~/dcmtk/bin/dcmdjpeg %p %p \n" |sh

run in the DICOM directory works anytime without the need for a script. Do substitute the path for dcmdjpeg with your own though. 

Dear all,

I have the same problem as Olga has. I have some compressed DICOm files (starting with 1.2.840.113619.2) and cannot use the data with MRIConverter. 

Can anyone explain me how to use 'DCMTK dcmdjpeg'?

Best regards,

Necip

Osirix solved the problem easily. If you are a Mac user, I strongly recommend to use Osirix (a demo version is available).

Best,

Necip

There is a floating license for Jim at the Kessler foundation, which should convert the DICOMs to NIFTI.  Please contact me directly ([email protected]) if you would like to know who holds the license. In the unlikely event of the conversion failing when using Jim, you can send me a sample of your DICOMs and we will make it work.

dcm2nii, dcm2niix, and mrtrix3 do a great job at  converting dicoms to niifti format.

Or, you can use SPIN (http://www.mrimaging.com/category.103.html ) to convert the dicoms to 'standard' dicom format, and then use dcm2nii.

In SPIN, choose File, then 'Sort DICOM and convert'. Select you dicom folder, and click OK. After conversion (should only take a few seconds, depending on the number of dicoms you have), close SPIN, and check your dicom folder. There will now be a new folder with the enhanced dicoms relabelled as filenames that will convert into nii format using dcm2nii.

Dear all

Faced with a similar problem (converting CT images jpg to nifti) I've been following your posts.

I converted jpg to DICOM using MIPAV (manually completing some header information) and then to nifti using Reconvert - however when attempting to normalize the nifti files to MNI space using SPM clinical toolbox it failed to do so adaquatly. Has anyone faced a similar issue?

Thank you for the helpful posts and discussions

Greg

To state the problem: it appears as if file compression is the issue for the DICOM images (i.e.- they are use jpg). We've encountered this problem with jpg compression of the files from the DICOM server. If you remove the compression (we use OSIRIX, which has that option on export) and rewrite the DICOM, this usually repairs the issue.  Alternately, you can decompress the dicom files using MIPAV or SPIN or dcm4chee.

I've reached adequate results and wanted to share the procedure:

1. Cleaned header text embedded in the jpg using matlab (using imread and placing zero values at the margins to erase the text)

2. Converted jpgs to dicom and autocompleted header information using MIPAV 

3. Convert dicom to nifti using MIPAV

4. Read nifti using matlab spm_vol and spm_read_vol, and reset the transformation matrix (mat and mat0) to a matrix read from a nifti CT file converted from dicom (and not jpg) 

5. Manually correct position in SPM (mainly rotation parameters )

6. Apply the same correction to lesion map (if you have one)

7. At this point I used SPM's clinical toolbox and preformed CT normalization

When the lesion wasn't too big I've got very nice results

Thank you for the helpful discussions

Dear all,

I think using the selected option in Osirix Lite during the export process as shown in the attached image would fix the problem.

Best wishes,

Jamaan

I just faced a similar problem recently (in my case the original images had the 1.2.840.10008.1.2.4.90 transfer syntax).

For me the most practical option was to use the gdcmconv tool in linux with option 'raw' (used to decompress the dicom file):

gdcmconv --raw -i compresed_dicom_image.dcm -o dicom_image.dcm"

This command is included in the libgdcm-tools library, which I installed using the synaptic package manager in neurodebian.

Since this command only decompresses one file at a time, I used a python script to change all dicom files in a dicom folder, which I will be happy to provide if anyone is interested.

Cheers,

Christian

I met the same problem when I was using dcm2nii tool in MRIcroN: Unsupported Transfer Syntax 1.2.840.10008.1.2.4.90 Solution: use MRIcro. And the problem was still there if I used MRIConvert.

However, I found that SPM12 can do that, just click DICOM Import button. But for DTI data, SPM is not very good at it. For T1/T2... this is to date I think the most convenient to me.

I had to import and re-export in dicom format with 3dslicer: https://youtu.be/BcnpzYE8VO8

You can try our free ProSurgical3D software. It can export to Nifti as well as anonymize the DICOM. It can also load a wide variety of DICOM formats and transfer syntaxes:

https://www.stratovan.com/products/pro-surgical-3d?utm_source=rgps3d&utm_medium=ans&utm_campaign=nii2

If you find that it does not, please send us a sample file in the built-in Support tab within the software and we can take a look at it for you.

You can try the open source dicom2nifti package: https://github.com/icometrix/dicom2nifti

I am writing code in python and I used dicom2nifti package

https://github.com/icometrix/dicom2nifti

I have found 3D slicer to be most reliable for dcm to nii. You could also try MedSeg which lets you convert DICOM to nifti directly in the web-browser without installing anything. Here is a demo: https://youtu.be/pTa7ZTIHyx8

MRIcron is so good. I recommend it.

Hope the links below can help.

http://web2.bilkent.edu.tr/vision/intranet/lab-wiki/wiki/fmri/dicom2nifti/

https://www.nitrc.org/projects/mricrogl

Olga Boukrina