Voxel size calculation questions

With DICOM MR images you need to disambiguate the thickness of the slice excited versus the distance between slice centers. We normally think of a 3D volume as a loaf of bread that has been sliced into contiguous slices. With this analogy, consider that we use a saw with a very thick blade to cut our loaf: if we stack the slices they are not as tall as the original loaf, as the spaces between the slices have been lost. In EPI scans (e.g. fMRI and DTI sequences) we often place a gap between slices so they are not spatially contiguous. In your example we excite a 3.5mm slice but leave a 0.7mm gap between each slice. This slice gap reduces the interference between slices. See this post for more details.

For an example, see this BIDS sidecar where dcm2niix reports a slice thickness of 3mm:

 "SliceThickness": 3,

But if you use fslhd to report the spatial dimensions it reports the dim[3] is 3.6mm. In this case, you have 3mm thick slices, with a 0.6mm gap.

I am more puzzled by your claim that the field of view of your image is 100mm, as it looks like dcm2niix has identified the FoV as 224mm. I am going to make a guess that the Percent Phase Field of View (0018,0094) is 100, and you are mistaking the unit % for mm. 100mm would be to small for an adult human brain, while 224mm sounds apprpriate.

1 Like