Thanks for this Chris. Have you any side by side fMRI analysis with and without the -B option? Ti would be interesting to see whether or the results of statistical treatments change and in what way.
Tony
Hi all,
I was having some problems bet extracting some of my structural scans, I was getting a lot of left over neck that was screwing up the alignment. I noticed the current version of bet has a new option flag (to me at least), which focuses on cleaning up the neck.
The option is -B . When using this flag the processing takes considerably longer, something along the lines of 10-15 mins per scan. However, not only did it resolve the issue, but the resulting image looks cleaner and more precise than I would expect from a normal bet. I've attached a comparison image so you can see the effect.
I did similar comparisons running this flag with functional data and it also shows improvements. At the moment I'm re-processing my data files in this way before running my analysis.
I thought I'd mention this in case it might be a useful option for other people to use, but also in case anyone knows any reason why it might be problematic. I'd be keen to know if anyone knows of any reason why I shouldn't use it? I notice the overall intensity seems slightly lower when this flag has been used, is this likely to be a problem?
Cheers,
Chris Racey
-- ynic-users mailing list ynic-users@ynic.york.ac.uk https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users
Thanks Tony,
That's a good point, I will be in a position to do this comparison in the next day or so, after the analysis I'm running finishes.
Actually, after my last message, Padraig came to see me and mentioned another option -R which iteratively repeats the BET procedure from different starting points. He suggested that this may achieve the same improved result. I tried this option instead and indeed it does still seem to be an improvement. However it runs considerably quicker and doesn't seem to result in intensity changes in the image.
I will investigate the results of these procedures on statistical outcomes and post a comparison in the next couple of days.
Chris
-----Original Message----- From: ynic-users-bounces@ynic.york.ac.uk [mailto:ynic-users-bounces@ynic.york.ac.uk] On Behalf Of am501@psych.york.ac.uk Sent: 13 September 2010 17:43 To: Chris Racey Cc: ynic-users@ynic.york.ac.uk Subject: Re: BET settings
Thanks for this Chris. Have you any side by side fMRI analysis with and without the -B option? Ti would be interesting to see whether or the results of statistical treatments change and in what way.
Tony
Hi all,
I was having some problems bet extracting some of my structural scans, I was getting a lot of left over neck that was screwing up the alignment. I noticed the current version of bet has a new option flag (to me at least), which focuses on cleaning up the neck.
The option is -B . When using this flag the processing takes considerably longer, something along the lines of 10-15 mins per scan. However, not only did it resolve the issue, but the resulting image looks cleaner and more precise than I would expect from a normal bet. I've attached a comparison image so you can see the effect.
I did similar comparisons running this flag with functional data and it also shows improvements. At the moment I'm re-processing my data files in this way before running my analysis.
I thought I'd mention this in case it might be a useful option for other people to use, but also in case anyone knows any reason why it might be problematic. I'd be keen to know if anyone knows of any reason why I shouldn't use it? I notice the overall intensity seems slightly lower when this flag has been used, is this likely to be a problem?
Cheers,
Chris Racey
-- ynic-users mailing list ynic-users@ynic.york.ac.uk https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users
-- ynic-users mailing list ynic-users@ynic.york.ac.uk https://www.ynic.york.ac.uk/mailman/listinfo/ynic-users
-
am501＠psych.york.ac.uk -
Chris Racey