Show Menu
Cheatography

MRI Terms for Neuroimaging Cheat Sheet by

This is a brief description of the terminology you are likely to encounter when setting up or analyzing neuroimaging research scans. In particular, it covers the sequences used in the in the sub-219 dataset available at https://osf.io/5q8fb/. For more in-depth coverage of MRI terms, see https://www.mr-tip.com/.

MRI Termin­ology for Neuroi­maging

localizers (scouts)
This is the first sequence acquired at the scanner. It takes ~17 seconds to acquire and help the scanner tech to to place a box around the head for optimal acquis­ition of the rest of the sequences. So, although you won't convert it to BIDS or use it, it is a necessary sequence.
T1w
You will usually acquire a T1-wei­ghted structural (a.k.a anatom­ical) image. It'll take about 5 minutes and have voxels ~one-m­ill­imeter in each dimension (1 mm isot­rop­ic). This is considered high resolu­tion because it is much better than typical fMRI or DWI.
AX_DE_TSE
This T2-wei­ghted Turbo Spin Echo is not a common anatomical image to acquire. However, the T2 tissue contrast may provide insight into tissue damage that is not readily visible on the T1w image. For this reason, it may be worth acquiring, especially if it does not take long and if you are working with a population that is likely to have tissue damage.
DTI_30­_DI­RS_A-P
This diffusion image is used to examine the integrity of white matter. It may be referred to as a DTI (Diffusion Tensor Image) or a DWI (Diffusion Weighted Image). This one has 30 direct­ions, which is probably the minimum you would want for research. However, it only takes about 5 minutes to acquire. If you double the number of direct­ions, you'll also double the acquis­ition time. Such images usually have voxels that are about 2 mm isotropic.
B0_ver­ify-P-A
This B0 (b-zero) image is a revers­e-p­has­e-e­ncode image intended for use in correcting the DTI image. It only takes about a minute to acquire because it only contains 2 or 3 volumes and no direct­ions. Otherwise it is matched to the DTI sequence in voxel size etc.
restin­gstate
This is a resting state fMRI (funct­ional magnetic resonance image). It includes 177 volumes, repeated every 2 seconds (i.e., repetition time, TR, is 2 seconds) (~ 6 minutes). Voxels are 2.5x2.5­x3.5 mm so they are anis­otr­opic (not the same in every dimens­ion..
field_­map­pings
Field maps take about 1.5 minutes to acquire and are extremely useful for correcting distor­tions in DTI or even fMRI sequences. This typical fieldmap sequence includes two magn­itude images and one phase image. The voxels are 3x3x4.
ASL_3D­_tr­a_iso, Perfus­ion­-we­ighted
These arterial spin labeling images are uncommon and used to measure perfusion in the brain.. I believe these two sequences are native Siemens sequences.
JJWANGS*
These are experi­mental ASL sequences that are not developed by Siemens. Because we have a research scanner, we will sometimes have these experi­mental sequences available. Again, these are uncommon.
It is worth thinking about the order of sequences. Localizers must come first. Without the T1w image, you can't do any recons­tru­ction, so it is often next. Besides, the tech can look at the T1w image to see if there is anything subtle but proble­matic in the partic­ipant's brain. For fMRI scans, even restin­g-state ones, you want the partic­ipant to be awake, so you may want to acquire this relatively early in the run.

Help Us Go Positive!

We offset our carbon usage with Ecologi. Click the link below to help us!

We offset our carbon footprint via Ecologi
 

Comments

No comments yet. Add yours below!

Add a Comment

Your Comment

Please enter your name.

    Please enter your email address

      Please enter your Comment.