Hi Sim,

What values to use for -thr and -uthr entirely depends on the values that the image contains in the brain region that you want to be your ROI. Therefore, this is something you need to decide by looking at the image you are using to create your mask (in fslview), so there cannot be a rule of thumb.

Cheers,

Janine

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Dr Janine Bijsterbosch
Postdoctoral Researcher
FMRIB Centre, University of Oxford
John Radcliffe Hospital
Oxford, United Kingdom
[log in to unmask]ac.uk

On 28 Feb 2017, at 18:22, Sim Luck <[log in to unmask]> wrote:

Hi, Janine,

Thanks so much. Then how to decide the -thr and -uthr parameters? Is there any a thumb law?

Thanks - I did not know the applywarp command in the ROI analysis. But when I do the ROI analysis, I use the "convert_xfm", and then "flirt" (i.e., register ROIs to subject space, and apply the transformation matrix to the ROI), followed by "fslstats"

Thank you very much,

Sim Luck

On Tue, Feb 28, 2017 at 12:06 PM, Janine Bijsterbosch <[log in to unmask]ac.uk> wrote:

Hi Sim,

When deciding which commands you need to use to make an ROI it is import to understand what type of image you are working with and in what space it is. For example, if you look at the Harvard-Oxford atlas image you can see that it contains values everywhere in the brain, and therefore to isolate the brain region you are interested in you need to apply a threshold (to remove everything below a value using -thr and/or to remove everything above a value using -uthr). It is also important to make sure that the resulting ROI image only contains 0s outsize the ROI and 1s inside the ROI, which is achieved by binarising using -bin. Lastly, the ROI image and the EPI image need to be in the same space before extracting the BOLD timeseries, so you may need to use the applywarp command (followed by binarisation) to make sure your ROI image is in the right space.

You can find out more information about all of these by looking at the FSL wiki and usage information for commands.

Best wishes,

Janine

On 28 Feb 2017, at 17:51, Sim Luck <[log in to unmask]> wrote:

A further question: if I get a mask from others (it is not necessarily made using FSL), should I also use the command fslmaths, -thr, -bin to process it first before I use it?

Thank you very much,

Sim Luck

On Tue, Feb 28, 2017 at 11:25 AM, Sim Luck <[log in to unmask]> wrote:

Hi, List experts,

I am still not very clear with the  option "-thr 10 -bin" in the ROI making process. For instance, the right amygdala (top plot) was made directly using FSL atlas database. The bottom part was made based on the above one, but using the command, fslmaths Left_Amygdala -thr 10 -bin Left_Amygdala_thr10. Which one should I use?

When should we use both "-thr" and "-uthr", and how to choose the parameters? In some examples, people use -thr 2, -uthr 2; while someone use -thr 6, -uthr 6, and others use -thr 10, -uthr 10. I am not clear on how should I use them, or just use one, say "-thr". What is the thumb law?

Is that not good if we do not use "-bin"? If I do not use it, what is the influence?

Thank you very much,

Sim Luck

-----
Dr Janine Bijsterbosch
Postdoctoral Researcher
FMRIB Centre, University of Oxford
John Radcliffe Hospital
Oxford, United Kingdom
[log in to unmask].uk