I think this was a bug in 5.3. Try running recon-all like recon-all -s subject -parcstats -parcstats2 -parcstats3 to regenerate the stats files
On 10/09/2018 11:19 PM, Jianzhong Chen wrote: > > External Email - Use Caution > > They are different. I attached two screenshots of lh.thickness > overlaying on lh.inflated here. > > Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu>> 于2018年10月9日周二 下午10:22写道： > > But are the lh.thickness files the same or different? > > On 10/9/18 1:46 AM, Jianzhong Chen wrote: >> >> External Email - Use Caution >> >> Hi Dr. Greve, >> >> I checked the lh.aparc.stats and rh.aparc.stats, the thicknesses >> (and the other measures like volume and area) are all the same. >> >> Thanks, >> Jianzhong >> >> Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu >> <mailto:dgr...@mgh.harvard.edu>> 于2018年10月9日周二 上午10:16写道： >> >> The aseg.stats should be the same since that does not make >> reference to the surfaces. The aparc stats should have been >> different because the thickness should have been different. >> Can you check whether the thickness files are different? >> >> On 10/8/18 9:39 AM, Jianzhong Chen wrote: >>> >>> External Email - Use Caution >>> >>> Dear All, >>> >>> I tried recon-all with/without T2 image using FS 5.3.0. Then >>> I found that the aseg stats and aparc stats with/without T2 >>> are exactly the same. When I check the pial surfaces, I can >>> see that they are very similar but not the same. So is it >>> reasonable to see exactly the same stats? >>> An example of the pial surfaces with/without T2 is attached >>> here. The red line is lh.pial with T2 and the yellow line is >>> the lh.pial without T2 >>> My command for recon-all with T2 is: recon-all -s ${subject} >>> -i T1.nii -all -T2 T2.nii -T2pial -sd ${T2_dir} >>> My command for recon-all without T2 is: recon-all -s >>> ${subject} -i T1.nii -all -sd ${T1_dir} >>> >>> Thanks, >>> Jianzhong >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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
