PS: the dropout you see in orbitofrontal cortex seems the normal dropout for EPI in that region, caused by the air filled cavities around the sinusses leading to field inhomogeneities around there. Not much you can do, except make it smaller by narrower slices and shorter TE, and perhaps playing around with angulation. It will never go away completely. With Echo-Shifted 3D EPI sequences you can reduce TE even further and the dropout will be pretty small, but still there. You should see this for most EPIs you guys are running? There are many papers on this problem and possible remedies. Or perhaps I am wrong and this dropout at the lower brain is somewhere else, I couldn't tell with certainty from your attachments.

The dropout in the top of the cortex is something unusual and something to check. I'd second Donald that there could be some metal left in or on the skin of the subject around that area. Perhaps metal shrapnel from someone who has worked with metal, or something left there from an injury? We usually X-ray subjects when we suspect something like that, and it should be an exclusion criterion in your screening procedure as it poses a certain risk to the subjects when they have possibly ferromagnetic metal in or around their body. I don't want to lecture anyone but this can be a serious risk.

Or perhaps there is an issue with your SENSE coil (yes I scanned on your 3T Achieva once, about 3yrs ago ;-) ).

Good luck, and say hi to Sharika,

Bas

________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of MCLAREN, Donald [[log in to unmask]]
Sent: Wednesday, February 01, 2012 4:28 PM
To: [log in to unmask]
Subject: Re: [SPM] Normalization errors and Artifacts. Are they related?


On Wed, Feb 1, 2012 at 1:11 AM, Vaibhav Tyagi <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Dear SPMers,

I am acquiring EPI data to standardize fMRI paradigm for one of my
studies. Unfortunately, the acquired EPI images are having artifacts in
the form of a chunk of missing data (images 1 & 2 attached for reference
are raw EPI images). Can someone confirm whether I can use any specific
analysis to correctly analyze this data. In order to see how SPM handles
such data, I have already performed pre-processing and GLM analysis. The
activation map is shifted down with respect to standard MNI glass brain
window (image 3 attached for reference, at p < 1 uncorrected).

I have several questions regarding this problem -

1. What may be the possible cause of this kind of artifact in the images?

Metal on the head or in the scanner.


What can be the remedy?

Make sure there is nothing that could cause signal dropout.

You should see similar missing areas on your other scans from this same subject.


2. Are such image artifacts causing the normalization errors? If yes, then
I would expect 'SPM normalize' function to stretch EPI images up (to fill
the missing space). Why are the normalized images shifted down?

SPM normalizes the whole brain. As such if I take a chunk out, then it might align everything else, but not be able to normalize that portion. You have to remember, normalization can't create data that didn't exist. If can't pull data from one part of the brain into the part that is missing.

I'd look at the T1 and see if the artifact is there. Also, if you have the localizer or scout image still, it should be apparent in that image. If you have dropout that is potentially due to metal, I'd remove the subject and find the metal or figure out what is causing the artifact before continuing the scan.



Thanks in anticipation.

-Vaibhav Tyagi
Speech and language laboratory
National brain research centre
Gurgaon, India


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