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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 >>>>> >>>>> >>>> >>>>