Hi Bruce, A copy of the surfaces would be much appreciated. Just let me know where I can download them from. Ideally if you can tar the whole colin27 directory so I have the aseg and aparc info as well that would be great. I think including this and/or the mni152 and average_305 surfaces would be great, though this might bloat the size of the download.
Not sure if you had a chance to look at my files, but do you think the problem I have is just a bad skullstrip, or is it an intensity issue from the conversion? thanks, mishkin On Mon, Nov 30, 2009 at 8:53 PM, Bruce Fischl <fis...@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: >> 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
