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Several artifacts were encountered when using the silent EPI sequence. The choice of TR may bear some relevance to the presence of these artifacts. Three different TR are available for the silent EPI sequence, TR=4s (TE=44; 32 slices; 24db quieter than the standard CBU_EPI); TR=2.7s (TE=44; 32 slices; 21db quieter); TR=2.2s (TE=38ms; 32 slices; 8db quieter).[is these right? the sequences differ wrt noise level as compared to normal]. Several artifacts were encountered when using the silent EPI sequence. The choice of TR may bear some relevance to the presence of these artifacts. Three different TR are available for the silent EPI sequence, TR=4s (TE=44; 32 slices; 24db quieter than the standard CBU_EPI); TR=2.7s (TE=44; 32 slices; 21db quieter); TR=2.2s (TE=38ms; 32 slices; 8db quieter). 

Several artifacts were encountered when using the silent EPI sequence. The choice of TR may bear some relevance to the presence of these artifacts. Three different TR are available for the silent EPI sequence, TR=4s (TE=44; 32 slices; 24db quieter than the standard CBU_EPI); TR=2.7s (TE=44; 32 slices; 21db quieter); TR=2.2s (TE=38ms; 32 slices; 8db quieter).

Artifacts

* Dropout

Dropout and distortion scale up with TR, so would be best to use TR=2.2s to avoid these artifacts. However, this does not seem to be a good sequence for regions that are susceptible to the dropout artifact, e.g. inferior temporal and frontal lobes. In addition, Matt pointed out that there are artifacts (e.g. ghosting) in other ventral structures, such as cerebellum.

* Distortion, including squashing of the brain. Similar to old Brooker data. Field-maps could be used for undistortion.

Action point: Rhodri would liaison with Gayaneh, Matt, and Jonathan.

* Wrap around. In some cases the nose ended up at the back of the brain.

After these images were acquired Marta received a new sequence from the developers, which seems to avoid the wrap around effect. Which sequence is this? It this the one that we’ll use from now on?

* Ghosting, in the form of streaks of image at the back of the head. Also, there is what looks like tiger stripes on the brain surface, around the edges.)

It could be helped by adopting a small field of view. Or, one could use a normal field of view and then remove the data after acquisition. Careful orientation of the slices might avoid the problem of ghosting. However, whether this is feasible depends on which region is of interest for the data acquisition.

* High inter-subject variability in the data quality. In two different datasets, the subject acquired earlier in time had worse data than the later subject.

The inter-subject variability may be caused by the shimming of the scanner.

To address these questions about the data quality there will be some piloting of the silent sequence. A number of acquisitions are going to be acquired from subjects that are being run at CBU from week 04/10/2010. There will be two sessions of 20s each. Field-maps would be acquired for each participant.

Action point: Marta would organize these acquisitions and feed back to the group. Some parameters remain to be decided?

The data would be pre-processed with AA to explore the data quality with regards to the artifacts. Undistortion could be applied to see whether this improves the data quality. The mean EPI image and tsdiffana can be used to explore data quality. Lower slices are expected to have higher inter-slice variability. The piloting could also help to see whether the inter-subject variability is affected by the shimming of the scanner, by looking at whether noise/artifacts change over the acquisition time across subjects.

How about BOLD sensitivity? It is not clear whether these problems affect the sequence’s BOLD sensitivity. But, see paper by Peele et al 2010 http://dx.doi.org/10.1016/j.neuroimage.2010.05.015

Action point: Lorina and Annika may be able to pilot the silent EPI with a functional task and compare it to the ISSS.

Please improve these notes and add any other issues that you have encountered.

CbuImaging: UsingTheSilentSequence (last edited 2013-03-07 21:22:57 by localhost)