yes, we have found that with 3T and >=12 channels one is probably better
than 2. Although having 2 is good for other reasons
On Tue, 1 Dec 2009,
Pedro Paulo de Magalhães Oliveira Junior wrote:
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 <fis...@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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