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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
