Hello, I am also very interested in having a copy of colin27's FS data! roberto
On Tue, Dec 1, 2009 at 2:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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:
- gunzip colin27_t1_tal_lin.mnc.gz
- recon-all -i colin27_t1_tal_lin.mnc -subjid colin27
- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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