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FSL  July 2007

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Subject:

Re: How to understand sigloss

From:

David Lythgoe <[log in to unmask]>

Reply-To:

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

Date:

Thu, 12 Jul 2007 13:48:56 +0100

Content-Type:

text/plain

Parts/Attachments:

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text/plain (117 lines)

On 12/7/07 12:39, "Mark Jenkinson" <[log in to unmask]> wrote:

> Hi,
> 
> Yes - sigloss is not the most accurate estimate of signal loss as it
> only accounts for
> the through-slice component of the signal loss, and does this assuming a
> perfect
> slice profile.  The main use it has in FSL is to provide some simple
> deweighting
> in the FUGUE steps within FEAT.  For this we threshold on the signal
> loss image
> in a conservative way so that we are relatively sure of ignoring areas
> for registration
> purposes where the signal loss is substantial.
> 
> I'd be interested to know what use you put sigloss to.

Cheating! I wrote a pulse sequence to do interleaved SE/ASE images, and post
processing of multi-channel data. When I was giving a talk about it, I used
sigloss & fugue to fool the audience into thinking the magnitude image from
the spin echo was an EPI.
As well of course, using it in the distortion correction processing chain.

DAe

> 
> All the best,
>     Mark
> 
> 
> David Lythgoe wrote:
> 
>> Hi,
>> 
>> I've used sigloss, and find it to be quite useful. One thing, try
>> experimenting with the TE value, and comparing it with your echo planar
>> images. I find I have to give sigloss a higher TE than the acquired value to
>> get an equivalent image to our EPIs.
>> 
>> 
>> Dave
>> 
>> 
>> On 12/7/07 12:15, "wolf zinke" <[log in to unmask]> wrote:
>> 
>>  
>> 
>>> Hi Mark,
>>> 
>>> Thanks for the detailed reply, it was very helpful.
>>> 
>>> cheers,
>>> wolf
>>> 
>>> 
>>> Mark Jenkinson wrote:
>>>    
>>> 
>>>> Hi,
>>>> 
>>>> This program calculates signal loss as a dimensionless fraction such
>>>> that if you multiply
>>>> the image without loss by this image then you would get the equivalent
>>>> image with
>>>> signal loss.  Hence the output is actually more like signal retained.
>>>> That is, a value of
>>>> 1 in the output means no signal loss, while a value of 0 means all the
>>>> signal was lost.
>>>> 
>>>> The default value of TE is set to a ridiculous value so that you can't
>>>> run it sensibly
>>>> with the default, as you really must specify a correct TE value and
>>>> there is no
>>>> typical value that would work for any sizable number of people.
>>>> 
>>>> This program is very simple in concept, and just works out the signal
>>>> loss factor
>>>> for the through slice dephasing, based on an ideal slice selection -
>>>> which is a sinc
>>>> function.  Any number of papers/books will probably contain this,
>>>> although the
>>>> formula here is derived from scratch given that I do several slightly
>>>> tricky things
>>>> with estimating field-gradients separately in different sub-components
>>>> of the voxel.
>>>> 
>>>> Hope this helps.
>>>> 
>>>> All the best,
>>>>   Mark
>>>> 
>>>> 
>>>> wolf zinke wrote:
>>>> 
>>>>      
>>>> 
>>>>> Hi all,
>>>>> 
>>>>> I came across the sigloss tool, which might do exactly what I want.
>>>>> So, instead of reinventing wheels I would like to understand this
>>>>> program a bit better.
>>>>> 
>>>>> The output is in the range of 0 to 1 if I got everything right. What
>>>>> is the dimension and how do I interpret the values.
>>>>> There is the --te option. Do I understand it right that this results
>>>>> in an estimate of signal loss for a given TE? Why is it than set per
>>>>> default to 1s, which is far beyond normally used values? Is there any
>>>>> reference this program is based on?
>>>>> 
>>>>> Thanks in advance for your help,
>>>>> wolf
>>>>>        
>>>>> 
>>>>      
>>>> 

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