hi Karen
> I was going through the functional images visually using the display function and noticed that there is a great amount of signal dropout in the orbitofrontal area. It seems to have been present even before I run any preprocessing steps but I was just wondering, are there ways in which I can minimize this signal dropout before conversion from DICOM to NIFTI? Could you advise on this?
I am guessing that what you are seeing is normal, and due to
susceptibility effects (these typically show up along inferior
temporal and orbitofrontal cortex). Thus, it is something in the
initial acquisition, and nothing introduced during the conversion or
preprocessing. Unfortunately that also means there's not much you can
do about it once the data are collected. There are EPI sequences
designed to minimize these effects, for example:
Deichman et al (2003) Optimized EPI for fMRI studies of the
orbitofrontal cortex. NeuroImage 19, 430-441.
http://dx.doi.org/10.1016/S1053-8119(03)00073-9
Weiskopf et al (2007) Optimized EPI for fMRI studies of the
orbitofrontal cortex: compensation of susceptibility-induced gradients
in the readout direction. Magn. Reson. Mater. Phys. 20, 39–49.
http://dx.doi.org/10.1007/s10334-006-0067-6
If orbitofrontal regions are important for what you are interested in,
it might be worth considering an optimized sequence.
Hope this helps,
Jonathan
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