Hi Dough, I took another subject, which was analyzed recently with the latest FS and the result of the masking is gook!
I found another issue in my experimenting! Here is exactly what I did: 1. mri_convert -i brainmask.mgz -o brainmask.nii.gz 2. fslswapdim brainmask.nii.gz x z -y brainmask.axial.nii.gz (reslice to axial) Now when I load brainmask.mgz (or brainmask.nii.gz) and brainmask.axial.nii.gz to tkmedit there is a 1 voxel shift in inferior to superior direction. Can you reproduce that and do you know where it comes from? Thanks, Martin On Monday 06 April 2009 23:13:48 Doug Greve wrote: > but you are using aparc+aseg to generate the mask, so if aparc+aseg is > perfect, the mask should be as well. Do the mask and aparc+aseg match? > > On Mon, 6 Apr 2009, Martin Kavec wrote: > > Doug, > > > > ribbon (aparc+aseg) looks perfect, and corresponds to the surfaces > > ?h.white. > > > > Thanks, > > > > Martin > > > > On Monday 06 April 2009 22:17:18 Doug Greve wrote: > >> I thought it was 4.0.3, so maybe that's not it. Can you look at the > >> ribbon.mgz file? You can load it as a segmentation, ie, > >> > >> tkmedit subject orig.mgz -seg ribbon.mgz > >> > >> aparc+aseg is suppossed to inherit the cortex from ribbon.mgz > >> > >> doug > >> > >> On Mon, 6 Apr 2009, Martin Kavec wrote: > >>> Hi Dough, > >>> > >>> this data were analyzed using 4.0.4. So indeed it not the latest, which > >>> I am running normally. From which version has this been fixed, so I can > >>> check, before re-runing. From which point should I rerun the analysis. > >>> > >>> Thanks, > >>> > >>> Martin > >>> > >>> On Monday 06 April 2009 18:42:36 Douglas N Greve wrote: > >>>> This looks like a problem we had with an older version. What version > >>>> of freesurfer are you running? > >>>> > >>>> Martin Kavec wrote: > >>>>> Hi, > >>>>> > >>>>> I am trying to mask a non-brain tissue left by watershed based on the > >>>>> cortical surfaces. I found that all what I need to be left is in > >>>>> aparc+aseg.mgz, so I converted it to nifiti, along with brainmask.mgz > >>>>> and used FSL to binarize aparc+aseg and mask the brainmask. I found > >>>>> that at many places the results is too conservative and too much of > >>>>> the GM is missing, see the attached images, and particularly the > >>>>> temporal lobes. > >>>>> > >>>>> Is there a better approach to what I am trying to do and what could > >>>>> be the explanation to the results I get. > >>>>> > >>>>> Thanks, > >>>>> > >>>>> Martin _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
