Hi Doug, I sincerely apologize for being unclear! I'm still relatively new to freesurfer and learning the ropes. I've attached the three aforementioned .stats files. The lh.aparc.stats and DKTatlas40.stats were generated from running recon-all. When comparing them it appears the grey matter volume data between the same ROIs can vary significantly. I have also been running the commands individually from the recon-all v5.3 dev table (listed here https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable). When I ran the mri_segstats command to generate the wmparc.stats file: mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject TB0204U_FREESURFER_THIRDRUN --surf-wm-vol --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt
The cortical ROIs were listed alongside the white matter segmentations in wmparc.stats, and now have different grey matter volumes than either of the previous two .stats files, which has left me even more confused. Since these cortical volumes all differ from one another, it makes me wonder which .stats file has the most accurate cortical volumetric data. Best, Kody J. Zalewski Message: 4 Date: Wed, 27 May 2015 14:58:44 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Stats file question To: freesurfer@nmr.mgh.harvard.edu Message-ID: <556613e4.3060...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Can you list the 3 stats files you are talking about? I can't quite follow from below doug On 05/26/2015 02:21 PM, zal...@u.washington.edu wrote: Hello Freesurfer team, When generating the .stats files for grey matter volumetric data, this information appears in multiple places and I'm not sure which data I should be using for my final results. There appears to be cortical information generated in both the .stats file based off the DKT atlas and the l/rh.aparc.stats file. The information in these files is quite different from one another. Using the FreeSurferColorLUT.txt (as listed in the recon-all dev table) instead of WMParcStatsLUT.txt (which is used when running recon-all) in generating the mri_segstats wmparc.stats file also produces cortical volumetric data. This third set of data differs significantly from the DKT Atlas, and differs less-so from the cortical volumes produced in the aparc.stats file. Which of the .stats files containing grey matter volume data is most accurate? Best, Kody J. Zalewski _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
lh.aparc.DKTatlas40.stats
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lh.aparc.stats
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wmparc.stats
Description: Binary data
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