ROI analysis

To aid ROI-based analysis, ACID-SC provides a tool under ACID-SC->Miscellaneous->ROI analysis which extracts mean values of diffusion measures (FA, MD, etc.) from specified ROIs. An important feature of this tool is that multiple types of ROIs can be specified including (i) global ROIs that are applied on all subjects, (ii) subject-specific ROIs that are applied only on the corresponding subject, and (iii) reliability masks. This gives flexibility for a variety of situations. For example, a set of subject-specific ROIs are needed for non-normalized data, while a single global mask is sufficient for normalized data (with optional reliability masks in both cases). If multiple types of masks are specified, the DTI measures are extracted from the intersection of the masks.

The Check registration tool can be found under SPM -> Tools -> ACID Toolbox -> Miscellaneous -> Check registration

Fig. 3: Image cropping tool within the ACID-SC toolbox

Inputs:

• DTI maps:
• Global masks: select global binary masks in which metrics will be extracted
• Subject-specific masks: select subject-specific binary masks in which metrics will be extracted
• Reliability masks: select reliability masks. More information on reliability masks can be found here:
• Slice-wise extraction: