Convert T1/T2 DICOMs from Renown to NIFTI and/or BRIK

Standard Steps

1.    Move the DICOM folders to ~/MR_DATA/anatomy/{subject_id}/dicom/

2.    Open Osirix

3.    Select Import and choose the directory where the Renown DICOM files reside

4.    OsiriX will ask if you would like to copy the files to the OsiriX database.  This is unnecessary and         

       will just waste hard drive space.  Select "Copy Links"

5.    You should see something like this:

Common Problems, Possible Solutions, Alternate Options, Etc.

• Osirix Download

• Steps 4-6

If, after you import your current dataset to the OsiriX database, there are multiple datasets listed in the upper-middle panel, and you aren't sure which is yours (the names are not particularly helpful in this respect), you should feel free to select all of the datasets and delete them from the OsiriX database to start "fresh".  We are only using OsiriX temporarily for this conversion step, and people should be cleaning up after themselves.  Select all the files and then click on the Trash icon.  Be sure to select "Remove Links" and do not delete the files themselves.

• Download MRIcron - the folder in downloads will be called osx. Move the folder to applications and change the name to MRIcron. In the terminal window, type:

set path ( $path = /Applications/MRIcron/ )

cd ~/MR_DATA/anatomy/{subject_id}/dicom/...

(fill in directory to uncompressed T1 or T2 dicoms)

• Proceed to step 14

• To-Do: In the above, it would be better to install MRIcron and then add /Applications/MRIcron to the path using the .cshrc file, so that dcm2nii is always available from any directory.  In addition, note that '%' is not the appropriate comment indicator for the shell.  It should be '#'.  We can also format the above as "code".  I made these changes. -REBM

• To-Do: installation instructions for MRIcron should probably be its own tutorial, so that it can be linked from any number of other tutorials that require dcm2nii

• N.B. I'm not sure that OsiriX will always create the same folder names for the T1 and T2

The 6 image icons represent 3 views each of the T1 and T2 images (you should be able to tell them apart by their contrast).

6.    Right-click on the Saggittal image icon for either the T1 or the T2 (you'll do the other next) and select 

       "Export to DICOM Files(s)".

7.    Select a Folder tree = 'Hierarchical' and Compression = 'Decompress all DICOM files'.  For the 

       location, select the dicom directory that you created in Step 1 (which is where you just imported the     

       data from).  Press "Choose" to decompress the files.

8.    Repeat Steps 6-7 for the other type of scan.  Be sure to select "Merge" when prompted that the 

       output folder already exists.

9.    You will now have a set of directories under ~/MR_DATA/anatomy/{subject_id}/dicom/ that contain 

       the uncompressed DICOMs.  You should be able to tell which is the T1 and the T2 based on their 

       names.

10.    Before closing OsiriX, it is a good idea to delete these files from the OsiriX database so that it is 

        clean for the next time.  In the upper-middle panel, right-click on the data you just imported and     

        select "Delete Selected Lines" (or highlight this entry and press the Delete icon at the top).  Be sure 

        to select "Remove Links" and do not delete the files themselves.  Remember, we only copied links 

        to the database - we want the raw DICOMs to stick around.

11.    Quit OsiriX.

12.    Open a Terminal

13.    Move to the newly created uncompressed-DICOM directory for the T1 images.

14.    Run dcm2nii (more info and download, part of MRIcron)

dcm2nii *

15.    This will output 3 new .nii.gz files.  One will start with a date (e.g., 20131119_...), one with 'o' (for 'reoriented'; e.g., o20131119_...), and one with 'co' (for cropped, e.g., co20131119_...).  We want the one that start with 'o', which means it has been reoriented (i.e., it will look normal in fslview). *Note: The T2 might output only 2 files as opposed to 3 in the T1. *

Rename this file {subject_id}_T1.nii.gz (or T2, if you just converted the T2).

16.    Move this final file to ~/MR_DATA/anatomy/{subject_id}/orig/

17.    Repeat Steps 13-16 for the T2 volume.

Optional

    If you want AFNI formatted BRIKs instead of NIFTI files, use 3dcopy.

3dcopy GC_T1.nii.gz GC_T1+orig