Some versions of the multi-atlas segmentation pipeline labeled Multi_Atlas and Multi_Atlas_v2 were affected by a bug in a toolbox. The regional volumes reported in the VOL_TXT/target_processed_label_volumes.txt file were slightly underestimated in many cases.
The code here loads the multi-atlas segmentation result images (SEG/orig_target_seg.nii.gz, and TICV/orig_target_ticv.nii.gz if available) and computes correct regional volumes. It also reports the size of the error in the original output.
The bug is in the 20140122 (latest) version of this Matlab Nifti toolbox: https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
The load_nii function returns incorrect values for the pixdim fields of the Nifti header. The related functions load_nii_hdr and load_untouch_nii return the correct values for the pixdim fields.
As an alternative for the Matlab Nifti toolbox, newer versions of matlab have niftiread, niftiinfo, and niftiwrite functions. Another possibility is SPM12, which provides tools for reading and writing Nifti files.