Hi Mark,
Thank you very much for your explanations.
1. Under "Intro to FSLView" last line "They don't have to have the same number of timepoints." Supposing that one image file has 2 timepoints and the other has 100 timepoints. I load both to fslview to view them at the same time. Since they have different number
of timepoints, how do they synchronize with each other?
When possible, the same volume number is used in each.
2. Under Viewing Timeseries (4D Images) the paragraph above the Histogram Toolbox figure. " Could you please explain what is demeaning and how it works?
Demeaning = removing the mean (i.e. subtracting the mean)
3. Similarly, "choose to turn on the "%" button [4], which shows the y-axis as a % of the mean level". Could you please explain what you mean by "mean level" and how to calculate the % of the mean level? By pressing the %, the limits of the y-axis
in this example changes from [-600 600] to [-3 3].
Percentage signal change = 100*(signal - mean signal)/(mean signal)
4. In Section fslstats, "This is because there are lots of empty voxels in the image (because the data has been brain-extracted)." In the Ortho view, the brain is in the center of each of the 3 views. Does empty voxel means voxel in black color?
Does that include region surrounding the brain (i.e. every voxel/pixel in each view window that is outside the brain) or just voxels in black inside the brain?
Empty voxels contain zeros. They include all potential voxels, so mainly those outside of the brain.
5.The sentence above "Run fslstats highres -m -M" in Section fslstats. "..but there is a large tail of very low background voxels. Tell the histogram to use log scale..." What do you mean by "low background voxels"? The tail is to represent voxels
of HIGH intensity values.
Tails exist on both sides (right and left, or high and low).
6. Under Section fslmaths, 3rd paragraph: "the robust range is quiet small, with most change showing up as motion effects round the edge of the brain." The robust range is quiet small because "fslstats imdiffpercent -r -R" gives [-47.78 37.69]
as the robust range. Am I right? How can you tell "most change showing up as motion effects rund the edge of the brain"?
By looking at the image and seeing the changes at the edge.
7. Performing "fslmaths image0 -sub image1 imdiff" and "fslmaths imdiff -div image0 -mul 100 imdiffpercent" and then viewing the histogram of imdiff and imdiffpercent show that there are voxels of negative intensities. What does negative intensity
mean?
That the subtraction above formed a negative number.
8. Under "Using the gradient threshold option (-g)" in Section "Troubleshooting Brain Extraction (Optional)", a) What is mean by "cerebellum is underestimated"?
That there should be more cerebellum in the mask than is found.
b) "This option causes the overall fractional threshold (controlled globally by -f) to vary linearly with slice number - to get smaller to the bottom and bigger at the top, or vice versa." How do I change the direction?
You cannot - it is fixed as the z-direction, but you can change the sign.
c) In command line, we can set -f -g. How about in the bet GUI? It seems that under the GUI, we can only set the gradient threshold option (-g) under "Threshold gradient; positive values give larger brain outline at bottom, smaller at top."
No, the fractional intensity threshold is available in the GUI (in the main part, not in the advanced options).
9. There is a typo in "fslsplit and fslmerge". It should be "rm vol0002* vol0006*" rather than "rm vol0002* vol0005*"
No, the instructions are correct. Image numbering starts at zero, so vol0002 is the 3rd volume, and vol0005 is the 6th.
10. The line above Section fslroi. "Also try concatenating (merging) in z instead of t and view in fslview; why does nothing happen when you try to turn on the movie loop?"
Because you have not merged in time. This is what you should see.
a) I got 8 brain images lining up vertically on top of each other. Am I doing something wrong?
No, this is correct. It is simply a demonstration, not something you would normally do in practice.
b) Why does nothing happen when I try to turn on the movie loop?
See above.