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.
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
>>>>
>>>>
>>>
>>>
