Hi,

If the output of robustfov does not look obvious wrong then I doubt -b will do anything useful.  Can you upload your original image to:

https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C

I'll then have a look and see if I can see why there is a problem and how to fix it.

As for your other question, the answer is yes.  You would use the reduced FOV output from robustfov in all subsequent analyses; as if the original one never existed, as we never need the neck, unless you are doing spinal cord imaging, where it is quite helpful!  ;)

All the best,

Mark

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Laura Banu <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Thursday, 6 August 2015 18:21

To: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [FSL] Problematic Brain Extraction

Unfortunatly, I am still not getting a good output. I will try the -b option next.

Another question: if I use robustfov for brain extraction, and then use BBR for registration later on, I'm assuming the non-brain extracted input for BBR should be the output from robustfov?

---

Laura Banu

Research Assistant

Cardiac Neuroscience Laboratory

Center of Alcohol Studies

Rutgers University

Work: (848) 445-3577

Cell: (646) 643-6917

On Thu, Aug 6, 2015 at 1:09 PM, Mark Jenkinson <[log in to unmask]> wrote:

Hi,

You don't need the -f and -c options.

The rest looks good.

All the best,

Mark

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Laura Banu <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Thursday, 6 August 2015 18:04
To: "[log in to unmask]" <[log in to unmask]>
Subject: Re: [FSL] Problematic Brain Extraction

Dear Mark,

Thank you for the speedy reply!

I will give this a try. Just to make sure I understand, the commands would look something like this?

robustfov -r 245016_RFOV -i 245016_Structural

bet 245016_RFOV 245016_Structural_brain -f .45 -c 78 130 110 -R

or, do I no longer need to specify the -f and -c options?

Laura

---

Laura Banu

Research Assistant

Cardiac Neuroscience Laboratory

Center of Alcohol Studies

Rutgers University

Work: (848) 445-3577

Cell: (646) 643-6917

On Thu, Aug 6, 2015 at 12:20 PM, Mark Jenkinson <[log in to unmask]> wrote:

Hi,

We have found that the following prescription works quite well:

 - run robustfov to save out an ROI (-r option) without any neck

 - run bet with the -R option

Depending on your subjects and alignment the first stage may be too tight in the z-direction, in which case you should alter the size of brain in z (the -b option) but in general it works well.

Give it a try and let us know how you get on.

All the best,

Mark

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Laura Banu <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Thursday, 6 August 2015 16:24
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] Problematic Brain Extraction

Dear experts,

I have been working on a particular brain extraction for quite some time and can't seem to get a good result. The most recent parameters I tried are as follows:

bet 245016_Structural 245016_Structural_brain -f 0.45 -c 78 130 110 -B

No matter what I try, there seems to be a fair amount of frontal lobe missing and a fair amount of non-brain at the top. Any advice is greatly appreciated.

Thanks,

Laura

ps. Sorry if this message posted twice. I tried to attach the files, but they were too large