Brain Mapping Center

How2 Document -Reconstruct EPI data offline

Indications:

This procedure is only necessary when scanning 128x128 functionals (or 256x128, FOV 40x20)

Treatment:

Before hitting scan setup:turn save raw data onturn save images off

**It will give you a warning that images are not being saved, but as long as raw data is being saved, you are OK. While acquiring the data, hit the stop reconstruction button.
(DO NOT HIT THE STOP ACQUISITION BUTTON, AS THIS WILL STOP DATA ACQUISITION).

After your scanning is all done, please be very sure to turn save raw data off and save images on. (Everyone else assumes it is always set to this default position, so it is important to be left configured properly, and it is very easy to forget to do this).

After the subject is done:switch to research mode (instead of clinical, top left menu)make sure save raw data is off and save images is back onThen hit display series, and click once on a series that has not been reconstructedHit the reconstruct button. A menu will pop up, and hit proceed and it will reconstruct away

Once the reconstruction is done, verify that it performed successfully by scrolling through the images. Having both raw and reconstructed data takes up a lot of image space. Therefore, you should delete the raw data after reconstruction is done. We only backup reconstructed data. If you like, you can ftp raw data for your own backup purposes. After you have verified the reconstruction was successful (and have transferred the raw data if you wish), go to the raw directory (for example, /apd/3/anmr_scans/raw), do an ls, and delete the .raw files associated with your scan.
**Realize that for a 7or8 minute scan, the reconstruction will take approx. 30mins.
No one else can do EPI scanning during this time, so be nice about when you do it..