External Email - Use Caution The aparc stats with T2 changed using this script. Now the stats with/without T2 are different, thanks! It seems that in 5.3 the aparc stats are computed before refining the pial.
Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> 于2018年10月11日周四 上午2:24写道： > 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
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