Identifying the fornix in DTIStudio using a multiple ROI approach

Written 7/25/08 by Aimee Zisner. Updated 02/17/2009 by Owen Phillips. Email Dr. Katherine Narr if you have any questions. This protocol explains how to identify the fornix in DTIStudio. For more information on identifying white matter tracts using DTIStudio, see


Note: Tractography shown in this protocol was performed in DTIStudio using 30 direction diffusion data.


To identify the fornix (FX):

First ROI First ROI: Identify the axial slice in which the crus of the fornix is visible. In the color map, this is the most inferior slice in which a bright light blue spot is connected to surrounding green fibers. Select this portion as the first ROI.
Second ROI: Identify the coronal slice in which the cerebral peduncles are most visible. In the color map, this slice is distinguished by the most intense bilateral color change of the corticospinal fibers from blue to violet (marked by arrows). Select fibers inferior to the corpus callosum as the second ROI.

* Be sure to remove all fibers that are clearly not a part of the tract.
Second ROI
Sagittal view of the fornix Sagittal view of the fornix


  1. Concha L, Beaulieu C, Gross DW. Bilateral limbic diffusion abnormalities in unilateral temporal lobe epilepsy. Ann Neurol. 2005 Feb; 57(2): 188-96. Click here to view.


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