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FSL  June 2013

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Subject:

Re: Poor registration troubleshooting

From:

Benjamin Philip <[log in to unmask]>

Reply-To:

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

Date:

Fri, 21 Jun 2013 15:25:45 +0100

Content-Type:

text/plain

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text/plain (61 lines)

Mark,

Sorry, in my parlance, "second-level" is across multiple runs within an individual participant. So, yes, it's combining across scans within an individual.

This is an excellent idea here, and certainly a pitfall I didn't know about... But, alas, after some testing it doesn't eliminate the problem.  I've successfully avoided the double-unwarping problem (confirmed because there's no longer an "unwarping" link on report_reg in the second step of 1st-level analysis), but the same registration problems arise: they may not look terrible at the first level, but they have huge non-brain activation at the second level.

This new 2nd-level result looks virtually the same as the one I uploaded last time. There are differences, but only small and subtle ones.

What files can I send for the next stage of troubleshooting?

Thanks again,

-Benjamin

On Wed, 19 Jun 2013 17:50:54 +0000, Mark Jenkinson <[log in to unmask]> wrote:

>Dear Benjamin,
>
>I'm not quite sure what image you've sent me as you say it is a second-level result, yet it looks like it is rendered on an individual structural and not the standard template image.  Is your second level combining over subjects or over sessions?
>
>Unfortunately, the combination of fieldmap correction and registration means that if you run either prestats _or_ registration at the moment then it will apply BBR with the fieldmap correction.  So even though you've only selected Stats + Post-stats, it will still be applying the fieldmap correction during the Registration part. Therefore the best thing is to turn off the fieldmap correction prior to selecting Stats+Poststats when you run the GUI for the second time.  We are going to try and make this behaviour more streamlined in the future, as currently splitting up analyses like this is complicated and has these pitfalls.  So that is definitely why you are seeing the fieldmap being applied twice.  Therefore I suggest you try that and see if it fixes the problems.
>
>All the best,
>	Mark
>
>
>
>On 18 Jun 2013, at 11:59, Benjamin Philip <[log in to unmask]> wrote:
>
>> Mark-
>> In my pipeline, I did my first-level analysis in two steps: a pre-stats analysis including unwarping and denoising, followed by a second step that included stats and standard-brain registration.  The included .fsf file (motor1.fsf) is the second step only - you may note it's set for "Stats + Post-stats only", thus it shouldn't apply the fieldmap again - which would indeed, as you note, cause problems. It's a good idea, but I believe I'm already avoiding this pitfall.
>> 
>> But in the context of fieldmap-only-applied-once: Even if example_func2standard looks okay, a second-level analysis based on these data still produce terrible registration results.  Since there's no second-level reg directory, I'm not sure what information I can provide to help you identify the problem.  So, for the moment, here's something that demonstrates the problem: I've uploaded a second-level rendered_thresh_zstat file to demonstrate the immense non-brain activity. Since it was just a single file, I put it on the upload link you provided previously (https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C)
>> 
>> Apologies on the deleting of threads - I hadn't figured out how to include a quote on the Jiscmail web interface. Got it now, obviously.
>> 
>> Thank you for your continuing help - I really appreciate it!
>> 
>> -Benjamin Philip
>> 
>> On Tue, 18 Jun 2013 15:16:18 +0000, Mark Jenkinson <[log in to unmask]> wrote:
>> 
>>> Dear Benjamin,
>>> 
>>> I've tried several different options with your data (fieldmaps applied in +x/-x/+y/-y and no fieldmaps).  In the end the result with no fieldmaps is clearly the best. I notice that your input data is called "denoised_data" - so have you run this through FEAT/MELODIC or some other denoising process that might already have corrected for the fieldmap distortions?  That would explain why it works worse with fieldmaps now, as that would be applying the correction twice.  Alternatively, maybe there is something wrong in the scaling of your fieldmaps, or the echo time difference, such as not taking into account parallel accelerations.
>>> 
>>> Try it with no fieldmap correction and see the results yourself.  There is still some intensity outside of the outlines of the standard brain in the example_func2standard, but this is to be expected with the peripheral CSF that you see in your functional images.
>>> 
>>> All the best,
>>> 	Mark
>>> 
>>> P.S. Can I please ask you not to erase the previous thread from your emails in future, as it makes it harder for us to trace back what has been said and tried before.
>>> 
>>> 
>>> On 17 Jun 2013, at 07:03, Benjamin Philip <[log in to unmask]> wrote:
>>> 
>>>> I believe I am still waiting for a reply to this question?  As noted in my post on June 6th, I've applied both of the fixes that Mr. Jenkinson suggested, but I'm still getting registrations with the same substantial non-brain activation (especially at the second level).  I'm looking forwards for suggestions to how I might troubleshoot this problem.  If any files or information are needed beyond those offered in the June 6 post, please let me know.
>>>> 
>>>> Thanks,
>>>> 
>>>> Benjamin Philip

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