Data Processing

Data Pre-Processing

The fMRI laboratory will provide its users with pre-processed data (k-space despiking, reconstruction, slice timing correction, realignment). Data output is in NIFTI format. Download the matlab program to convert data from NIFTI to 4D Analyze format. Note that in the NIFTI format, it is specified that images be in radiological orientation. We store images with the first pixel in the file corresponding to the lower, right, back corner of the imaging volume.

File Transfers and Remote Logins

Users are expected to transfer their data from our server in a timely manner. Data will be retained on our server for up to six months, so investigators are encourage to download their data as soon as it is available.

For security purposes, we have disabled 'telnet' and 'ftp' network protocols. Investigators should use 'ssh' and 'sftp' network protocols to access our server. These software programs are available for Windows platforms, at the website: (Note: when using sftp in Unix/Linux there is no 'mget *.img'. Instead you'd use get '*.img').

Data Back-ups

Raw data will be burned onto disk for archival purposes within two weeks of a scan. Users may request a copy of the disk, but this is discouraged due to the associated administrative cost.

Data Processing

Processing data is the responsibility of the user. Please see our Resources page for software we are happy to share with our users, as well as tips for processing data.

Help with Data Transfers

For assistance with transfer of your data please contact our Research Computer Specialist.

Help with Data Processing

For assistance with data processing, please contact our Technical Director.