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
