Data from the Siemens Prisma comes off in DICOM format. DICOM is nice in that it can save anything in any format for us, be it single slice images, 3D volumes, EPI time-series, or spectra. DICOM is less nice in that at best your BOLD run will have one image per 3D volume and at worst it’s one image per slice. It’s also not natively used by most of our analysis packages, so we need to convert it to something like NIFTI.
One thing to know is that you are responsible for your own data backups. FIBRE maintains scans on a local NAS (RAID-6) for as long as we can and odds are that if you lose something, we’ll have the raw data. But, don’t use this as your main backup. Always, always check your data transfers soon and back up your own raw data.
Getting your MRI data
If you followed the normal procedure for transferring the data from the scanner to fibredata (Transfer, Export to offline on the console), you will have a folder on the NAS that has everything in DICOM format in something like mridata/upload/PIName). This is a share that lives on our local NAS.
You’ll then want to get these data files from the FIBRE NAS to your local machines. For any of the methods, you get DICOM files. DICOM is the native format for Siemens and you’ll need to convert it to something like NIFTI for your normal work. There are nice tools like “dcm2nii”, “dcm2niix“, and “dinifti” that do this. The Linux box at the facility has all these installed and at some point, we’ll have this running automatically for people as soon as you transfer.
One easy way to get the data from the NAS is to use the web interface to the file manager. Log in (you can use the same login as the stimulus delivery computer), click on File Station and navigate to “mridata”, “upload” and your folder. Right-click on that, and you’ll get an option to download the folder. At this point, the NAS will .zip it and send the data to your local machine via a secure transfer (you’re on an https connection here).
Don’t like GUIs and want to just directly copy the files? You can use sftp as well. You’ll want to ‘sftp email@example.com’ and inside of that, navigate and transfer to your heart’s content with commands like ‘get dirname’. Or, transfer from the command line with ‘sftp -r firstname.lastname@example.org:/mridata/upload/yourdirname .’ If you don’t remember the yourdirname bit, you can either browse the web interface or ssh onto fibre-data to figure it out. Or, you can use sshfs …
sshfs has rapidly become one of our favorite tools. It lets you mount a remote machine directory and treat it as if it were a local directory (folder) on your machine and it does so via ssh/scp/sftp. So, anything you could sftp from, you can mount via sshfs.
- First, you’ll want to install sshfs (options are available for Linux, Mac, and Windows). On Linux systems, it’s as simple as ‘sudo apt-get install sshfs‘ and it’s not much tougher on others.
- Next, make a local directory that will serve as the mountpoint. In your home directory, you might ‘mkdir fibreNAS’
- Finally do the mount with ‘sshfs email@example.com:/mridata fibreNAS’ (of course changing fibreNAS if you used a different name in the step above)
Now, have a look in that directory and you’ll see the data on the NAS. Copy from it however you like. When you’re done, on Linux systems you can ‘fusermount -u fibreNAS’ and on Macs you can ‘umount fibreNAS’
Finally, for those of you who like PACS, we have the Syngo Via/Frontier setup here. You can transfer to the syngo setup from the scanner console. Let us know if you’re looking to use this and we can make sure it’s setup properly for you.
Getting the data into NIFTI
Most of us use NIFTI files (.nii or .nii.gz files) for our analyses or at least know how to handle them. There are a number of tools out there that convert a folder (or folder of folders) of DICOM files into NIFTI format for you, taking care of all of the geometry info and even DTI gradient info. At the facility, we have several installed on the Linux workstation there. Two popular ones are dcm2niix (updated version of dcm2nii) and dinifti.
For example, let’s say all the DICOM files are in a directory below you called “dicom” and that you want NIFTI versions of them in the current directory. You might do something like:
dinifti --name="%I_%D_%S_%Y" dicom/*IMA .
or Craig’s preference:
dcm2niix -o . -f %p_%s dicom
Have a look at the docs of whatever program you use as there are lots of naming conventions you can end up with.
At some point, we’ll have the local Linux box doing the conversion on the fly for you.