Angel, I noticed you have problems with some remaining dura in your images. you might want to try a new utility that is being tested for inclusion in a future release. Its from a group in Singapore, and does a good job removing dura. Its called:
mri_gcut and can be downloaded for the linux and mac platforms from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/ copy it to your $FREESURFER_HOME/bin usage (with reference to paper) is found in: mri_gcut --help and intended usage is: cd subjid/mri mri_gcut -110 -mult brainmask.mgz T1.mgz brainmask.mgz then run: recon-all -s subjid -autorecon2 -autorecon3 but of course inspect the brainmask.mgz to see if actually helped. (bruce, can you point me at her image? i can run it locally) Nick On Sat, 2009-10-10 at 21:46 +0800, Angel Wong wrote: > My version is 4.3.0. I will download the latest version and try again. > > Thank you. > > 2009/10/10 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > I didn't do anything but run recon-all with the latest > version. Remind me what version you were running? > > > On Sat, 10 Oct 2009, Angel Wong wrote: > > Hi Bruce > > Thank you very much. The result looks much better than > mine. How did you do > that? Please let me know so that I can modify the > other datasets if I face > the same situation again. > > Cheers > Angel > > 2009/10/10 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > > Hi Angel, > > I'm just about done running the dataset and > the results actually look ok > (see attached tif). I didn't intervene at all, > although you would want to to > get rid of some non-brain tissue that the pial > surface is grabbing, but > that's pretty easy. Did you minimize your TE? > I don't know what your > gradient set is, but usually you can get your > TE down a bit more than that. > You also might be better off sacrificing a bit > of resolution and lengthening > your TR > cheers, > Bruce > > > On Thu, 8 Oct 2009, Angel Wong wrote: > > Thanks a lot with your help. This is because > we want to perform quite a > number of functional runs on the same > subject at the same session. So we > tried to shorten the T1 scan time to > minimize the motion artifacts come > from > the subject. > > Attached please find the orig.mgz for > your information. > > 2009/10/8 Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > > I see. Your TR is quite short and > your TE relatively long, so this is > probably pretty poor CNR > between gray and white. If you > send me the > orig.mgz > I'll take a look and see if > it's fixable > > On Thu, 8 Oct 2009, Angel Wong > wrote: > > Hi Bruce > > > Attached please find > the parameters for > acquiring the T1 > image. > > Thank you for your > help. > > Angel > > 2009/10/8 Bruce Fischl > <fis...@nmr.mgh.harvard.edu> > > eek, that looks > pretty bad. Can you > tell us what the > acquisition > > parameters > are? > > On Thu, 8 Oct > 2009, Angel > Wong wrote: > > Dear all > > > > > Actually I > would like to perform automated reconstruction for my T1 > image > and > then > obtain > anatomical > labels after cortical parcellation. I have > done > fully > automated > reconstruction using recon-all. But for my case, the > white > and > grey > matter > segmentation > appears to be weird. The green line seems > laying > on the > pial > surface > rather than on the white surface, and the > red > line > seems > including > some non-brain structures (including small > portion > of > CSF > and > skull). Thus, > the resultant cortical thickness appears to be > very > thin > after > the > segmentation. > I just doubt if anything was going wrong > during > the > procedure. Or > need any preprocessing to enhance the segmentation > quality > before > performing > the reconstruction? If you have had similar > situation > as > mine, > please > let me > know > how to > tackle > the > problem. > > Attached > please find the images for better illustration. > > > fs_image_brain.tiff - use brain.mgz as aux volume > > fs_image_norm.tiff - use norm.mgz as aux volume > > fs_image_brainmask.tiff - use brainmask.mgz as aux volume and load > segmentation > file aseg.mgz > > Thanks > Angel > > > > > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
