You don't need to do 2b if all you want are the lobar wm segmentations. 2b should just copy the cortical labels into the new seg.
mri_segstats --seg mri/newseg.mgz --sum stats/newseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab newcolortable --subject<subject>
You can load the newseg.mgz into tkmedit as both a segmentation (-seg) and as the aux volume. When you click on a point, you can see the seg value associated with the given label.
doug
On 04/04/2012 11:15 PM, Irwin, William wrote:
Hi Doug-
I wanted to follow up on this procedure and ask for a bit of clarification. As an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz' lobar volume with both WM and GM for both RH and LH.
1: mri_annotation2label --s<subject> --hemi rh --lobesStrict lobe mri_annotation2label --s<subject> --hemi lh --lobesStrict lobe
2(a): mri_aparc2aseg --s<subject> --labelwm --annot lobe
2(b) mri_aparc2aseg --s<subject> --rip-unknown --ctxseg aparc+aseg.mgz --annot lobe I'm not sure if this the correct syntax to be analogous to that for WM in 2(a).
What would be the correct syntax to combine 2(a) and 2(b) into one command?
3: Per your suggestion for syntax, this can be found in recon-all.log following that for wmparc (and I have identified that). There is similar syntax for GM/ctx. I'm not sure if the following would need to be slightly modified for my objective:
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject<subject>
But, before proceeding with the step 3, how can one determine the lobar label numbers assigned such that a custom LUT can be created. The output of the 2(b) (if the syntax is correct) indicates that 8 entries are read (Frontal, Temporal, Parietal, Occipital for LH and RH?).
Thanks for your help.
-Wil
|-----Original Message----- |From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] |Sent: Monday, April 02, 2012 10:39 AM |To: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] lobar WM volumes | |use mri_segstats. You can look in subjid/scripts/recon-all.log for example |command lines (look for the one with wmparc). The command will require a |color table. The ones in the log file will use the default table, but this will not |have the numbers/names of your lobar regions, so you'll need to create a |new color table (or add to the one that is there). |doug | |On 04/02/2012 12:58 PM, Inês Violante wrote: |> Dear all, |> |> I need to obtain the white matter volume per lobe for a given numer of |subjects. |> I started by using the following: |> |> mri_annotation2label --subject<subjid> --hemi rh --lobesStrict lobe |> |> mri_aparc2aseg --s<subjid> --labelwm --annot lobe |> |> and now I have a lobe+aseg.mgz file. How can I create a stats file |> containing the wm volume for each lobe? |> |> Thank you, |> |> ines |> |> _______________________________________________ |> 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 |greve@nmr.mgh.harvard.edu |Phone Number: 617-724-2358 |Fax: 617-726-7422 | |Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting |FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html |