DICOM and PAREC Conversion

MRI files are often exported from the scanner in DICOM format. DICOM is the most common format, but it is very broad and often new scans will not convert properly.

PARREC is old and there are few reliable conversion programs. Despite it being more efficient, it’s best to avoid.

CSPM DICOM rename/convert

The CSPM DICOM rename/convert GUI gives access to custom functions. This uses SPM’s dicom convert functions, with various tweaks over the years to deal with specific scans.

A more maintained conversion function, and the one that is compatible with the DICOM formats, is the conversion utility with mricrogl. This is the development of the dcm2nii that came with mricron, but the tool within mricrogl is being continually developed.

Note: As of Sep 2022, this function can use MRIcroGL to convert. Works with 7T and Philips data.

Converting with MRICroGL for CSPM (incorporates dcm2nii that used to come with mricron)

Install MRICroGL Software for CSPM
Place DICOM files for one series (to keep it simple) in a folder
Create a second folder to save the nifti files
Open the Import GUI in MRICroGL (right)
- Select DICOM to Nifti
Carefully set the parameters
- If you just want to test, you can skip step 3

For Output Directory, Select custom folder… and choose the nifti folder you created
Select Output Format Uncompressed Nifti
For Output Filename, type the following (no spaces):
1. Protocol ID
  1. Can prepend with “E”, makes it easier to read
2. Series number with “S%s” (the capital letter “S” followed by “%s”, the code to insert the series number read from DICOM)
3. Image number with “I%r” (the capital letter “I” (for image) followed by “%r”, the code to insert the instance number read from DICOM)
  1. This is not essential for single-volume scans
4. If T2 or any scan with multiple echos, add the echo number with “E%e”
5. Example: E99990320220115S%sI%r would be protocold ID 99990320220115 (subject code 9999, visit 3, date 15th Jan 2022), with the series and image number in the filename.
Adjust other settings; saving the BIDS Sidecar is a good idea (contains details read from the DICOME files; see below)
From Explorer, drag the folder with DICOM files into the GUI (see right); this will run the conversion right away
Move the files to series subfolders MRI Raw Data - Series folder structure

1.

2.

3 b. (click to view properly; or copy and paste into graphics program)

5.

BIDS file in json format

Drag into/Open with Notepad to view; here’s an example:

DICOM note

Instance Number (0020,0013) - A number that identifies this image. Acquisition Number (0020,0012) - A number identifying the single continuous gathering of data over a period of time that resulted in this image.