FMRI lab policies

Preparing for your experiment:

We require that all experiments be rehearsed once without the subject at least one day prior to the experiment. The purpose of this policy is to ensure that all equipment (especially the paradigms you write for the IFIS (from Psychology Software Tools) presentation system) is working properly and in concert with the MR scanner. There is no cost associated with this rehearsal.

Note that there is also a "Mock Scanner" for training purposes in the basement of East Hall. It can be very useful!

All investigators must be screened before entering the scanner room to insure everyone's safety. Keep in mind that most accidents are caused by investigators rather than subjects. New investigators will need to sign a safety screening questionaire.

Please don't forget to bring your IRB's consent forms, and copy of your IRB updated approval letter if this is the first time running your protocol.
Please try to have the subjects consented and trained by the time the scan is scheduled to start. This usually means having enough people so that you are training a subject while you are scanning another.

Pre-processing

The fMRI laboratory will provide its users with pre-processed data (see details ) (reconstruction, slice timing correction, realignment). As of Jan 20, 2007 the preprocessing stream has changed. The most significant change is that the output is in NIFTI format (see details). (Here is a matlab program to convert from NIFTI to 4D Analyze format).

Note that in the NIFTI format, it is specified that images be in radiological orientation. We stotre the first pixel in the file corresponds to the lower, right, back corner of the imaging volume.

The data will be burned into CDs for archival purposes. The users can request a copy of the CDs or download their data through the network. Network transfer is encouraged.

*The data will be PURGED from our server after SIX MONTHS. After that, the only back-up will be on CD's !!! *

File Transfers and Remote Logins

For security reasons, we have disabled telnet and ftp, so you'll need to use ssh and sftp instead. If you are on a windows platform, there is a nice free version of them HERE.

Note about sftp in Unix/Linux : there is no "mget *.img". Instead you'd use "get *.img"

Data Analysis

Processing the data is the responsibility of the users. The fMRI laboratory does have processing equipment and expertise, and arrangements can be made for such assistance on an individual basis.

Please see our Resources page for tips and software that we are happy to share with our users. If you have something you'd like to share too, please e-mail me.

Some tips on spatial normalization

Costs and Payment

The cost is $525 per hour of scanning plus the indirect costs associated with doing anything at a university. (note: a scan usually takes in the neighborhood of an hour. If it's more than that, we round to the nearest fifteen minutes)

How to pay for scans: Before you do anything, you should ask your account manager/administrator contact Eve Gochis, our lab's administrator. Your grant administrator will have to set up a sub account of your grant for scanning costs. There will also be a short form to be filled out. Our administrator will then transfer the money from your sub-account to ours. The info needed on this form is just then name and signature of the PI, info about the subject, and the account number stuff, which your administrator should have (specifically, the fields are: Account Number , Fund, Department, Program, Class, Budget Prd., Project/Grant).

You can download this file (but not yet)
http://www.umich.edu/~fmri/payform.pdf

In cases where no sub account can be established, the PI should contact Eve Gochis to discuss other methods of payment.

Scheduling

The scheduling procedures can be seen on the "Scheduling" page