Also the ch2 dataset that comes with MRICro suffers from the same problem. It's the averaging of several acquisition from one brain.

Is it possible to infer that too many acquisitions is worse than one acquisition?

-- PPJ


2009/11/30 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Hi Mishkin,

yes, I generates surfaces for the Colin27 dataset. It actually doesn't
have great gray/white contrast, probably due to differential B0
distortions in the different sessions. Maybe we should include it as part
of our release? In any case, I can send it to you.

cheers
Bruce


On Mon, 30 Nov 2009, Mishkin
Derakhshan wrote:

> Hi,
> I'm trying to get the surfaces for the colin27 brain that is included
> with the mni packages. Has anyone managed to do this before?
>
> I thought I would have an easy time given that this linear average of
> 27 brains has very good signal to noise and nice contrasts, and even
> though recon-all completes without errors, the surfaces are way off.
> The main problem appears to be the skull stripping.
>
> My input volume is here:
> http://opus.bic.mni.mcgill.ca/public/colin27_t1_tal_lin.mnc.gz
>
> These are the steps I took and where I think the problem might be:
> 1. gunzip colin27_t1_tal_lin.mnc.gz
> 2. recon-all -i colin27_t1_tal_lin.mnc -subjid colin27
> 3. tkmedit conlin27 orig/001.mgz
> At this point the image the brightness and contrast levels of the
> image look very washed out. I am hoping this is only a display issue
> and that the underlying intensities of the image are still intact and
> is not a result of something going on in mri_convert, but maybe this
> is what is causing the downstream skull strip to fail. Can someone
> take a look?
> http://opus.bic.mni.mcgill.ca/public/001.mgz
> 4. recon-all  -autorecon1 -subjid colin27
> 5. tkregister2 --mgz --s colin27 --fstal
> Results are not perfect but reasonable ie. about the same as many
> other runs I've had that have passed so I don't think it is the
> registration.
> 6. tkmedit colin27 brainmask.mgz -aux T1.mgz
> It is clear this is where the problem is.
> http://opus.bic.mni.mcgill.ca/public/brainmask.mgz
> http://opus.bic.mni.mcgill.ca/public/T1.mgz
> 7. I have subsequently tried:
> recon-all -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -subjid
> colin27 (basically extract the entire head)
> recon-all -skullstrip -wsthresh 5 -clean-bm -no-wsgcaatlas -subjid
> colin27 (basically extracted the entire head)
> recon-all -skullstrip -wsthresh 5 -clean-bm -subjid colin27 (extracted
> the brain, but left large chunks of skull)
> recon-all -skullstrip -wsthresh 2 -clean-bm -subjid colin27 (extracted
> the brain, but left quite a few chunks of skull)
>
> I'm concerned that the -wsthresh is so low in order to get a
> reasonable result, that's why I think the intensities might be off
> (see step 3).
>
> I'm re-running -autorecon2/3 now to see if the surfaces are better,
> but if someone could take a look at my input file and the converted
> 001.mgz to see if it isn't a problem there it would be much
> appreciated.
>
> thanks,
> mishkin
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