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FSL  November 2013

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Subject:

Re: Questions about the FMRI Pre-Processing and Model-Based Statistics PPT

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 11 Nov 2013 10:59:14 +0000

Content-Type:

text/plain

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Hi,

> I am going over the slides and encountered some questions. Could you please clarify?
> 
> 1. Under "Image Reconstruction", it reads "Scanner artifacts can be found by:" The remaining part is missing. Could you please let me know?

By looking at the data.

> 2. Under "Effect of Motion Correction"
> a) In each panel, there are two brain images. What are they?

They are labelled as "With MC" or "Without MC" for the columns and "Uncorrelated motion" and "Stimulus correlated motion" for the rows.  In each of these four cases (which might be what you refer to as a "panel") you are just shown different slices from one 3D image.

> b) Is the take home message of this slide: With MC, the number of false alarms is reduced?

Only for the "Stimulus correlated motion" case.  In the "Uncorrelated motion" case there are no false positives and the main effect of MC is to be more sensitive and be able to find more true activations (reducing false negatives).

> 3. Under "Motion Problems", "Motion correction eliminates gross motion changes but assumes rigid-body motion - not true if slices acquired at different times." What is not true? Why?

Rigid-body motion is not true due to slices being acquired at different times (so a single rotation/translation does not apply equally to all slices).

> 4. Under "Spatial Filtering: How?", What is "ID convolution" in "(cf. ID convolution with HRF for model)"?

Convolution is a mathematical process.  The details are not that important to understand, but I'm sure there are plenty of textbooks and pages on the internet that explain convolution if you are interested.

> 5. Under "Spatial Filtering: Results at Different FWHM". Could you please let us know what the six panels represent?

They are different slices.  This actually comes from a movie that is shown during the course, so is not so informative on its own.

> 6. Under "Effect of Temporal Filtering", What are the 8 images with number on the top left represent? What is the take home message here?

The rows are labelled as showing "No Temporal Filtering" or "Highpass Temporal Filtering".  The columns are just different slices, and the numbers are the slice numbers.

All the best,
	Mark

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