View source for Conversion from DICOM

MRI Scanners generate and save data to a native file type. These files may be proprietary, but can be converted to standard .nii files using a conversion utility.
=to3d=
This is an AFNI utility that converts a series of 2D DICOM or similar files, assuming sequential filenames, to a 3D file type.
==Preparation==
===Organization===
The first step will be to ensure that all the DICOM files are grouped by series. That is, it may be that your working directory contains DICOM files from multiple sequences (e.g., the folder may contain files from a scout image, and a T1 and T2 weighted scan). It makes sense to reorganize the data so that each directory contains only DICOM files from a single series.
===Naming=== 
Each DICOM file represents a 2D slice of a volume. The to3d program assembles a series of 2D slices to create a single 3D volume. Because the script infers the sequence order from the order in which the files are provided, the file names should reflect their position in the sequence. The files are likely to be sequentially numbered (e.g., file1.dcm, file2.dcm, ..., fileN.dcm), however you should check that the list of file names reflects their sequence. In particular, if there are more than 9 files, it matters whether the file numbers are zero-padded. For example:
 $ ls -1 *.dcm
 file10.dcm
 file1.dcm
 file2.dcm
 file3.dcm
 file4.dcm
 file5.dcm
 file6.dcm
 file7.dcm
 file8.dcm
 file9.dcm
Here we see that there are 10 slices, numbered 1-10, but as listed, the 10th slice comes before the 1st slice, which will likely cause the slices to be reconstructed out of order. Basically, the person's chin will be moved to the top of their head, or something similar. We need to change how the sequence of numbers is formatted by zero-padding it.
I have written a script called <code>renumber.sh</code> that can be found in the ubfs Scripts/Shell folder. The syntax of the file usage:
 renumber.sh fileprefix fileextension
In the above example:
 renumber.sh file .dcm
This will create a new subdirectory called '''renumbered''' that contains a renumbered copy of each of the files:
 cd renumbered/
 ls -1
 file001.dcm
 file002.dcm
 file003.dcm
 file004.dcm
 file005.dcm
 file006.dcm
 file007.dcm
 file008.dcm
 file009.dcm
 file010.dcm
Now the files are listed in the correct sequence.
==Running to3d==
The to3d command will try to launch a GUI window unless you provide an output file name as a file prefix. We generally want to convert our data to .nii (or .nii.gz) files:
 to3d <span style="color:red;">-prefix T1.nii</span> file*.dcm
After this executes, you will have a new .nii file in your working directory.