Thanks, Doug. I actually want lobar both GM and WM.
So would this be the correct syntax to generate lobar GM and WM labels? mri_aparc2aseg --s<subject> --labelwm --rip-unknown --ctxseg aparc+aseg.mgz --annot lobe Yes, I started to do as you suggest with tkmedit using FreeView, but I thought there might be a less manual way of doing this. Thanks, Wil |-----Original Message----- |From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] |Sent: Thursday, April 05, 2012 8:30 AM |To: Irwin, William |Cc: freesurfer@nmr.mgh.harvard.edu |Subject: Re: [Freesurfer] lobar WM volumes | |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:gr...@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 |> |gr...@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 |> | |> |> |> |> | |-- |Douglas N. Greve, Ph.D. |MGH-NMR Center |gr...@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 | | | |The information in this e-mail is intended only for the person to whom it is |addressed. If you believe this e-mail was sent to you in error and the e-mail |contains patient information, please contact the Partners Compliance |HelpLine at http://www.partners.org/complianceline . If the e-mail was sent |to you in error but does not contain patient information, please contact the |sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
