I did create my own ctab and works perfectly!
Regards,
Gabriel
El 18/10/12, Douglas N Greve <gr...@nmr.mgh.harvard.edu> escribió:
Hi Gabriel, don't use the ASegStatsLUT.txt ctab file. It will only
report the volumes of structure in the ctab, and that ctab does not have
the WM parcellations. You can use FreeSurferColotLUT.txt instead. When
you use --empty, this will report on *everything* in the ctab, which
will probably be overwhelming. If you run it without --empty, then some
subjects may have a different number of structures. The only alternative
is to create your own ctab with only the structures you are interested in.
doug
On 10/17/2012 02:36 PM, Gabriel Gonzalez Escamilla wrote:
> Dear Freesurfer Experts
>
> Sorry for many mail, but I'm working on may things at the time.
>
> Apart from my corticalGM problems I'm trying to obtain the WM volumes
> from some regions in the apparc.annot such as precuneus, for this I'm
> using
>
> mri_aparc2aseg --s MySubj --labelwm --annot aparc --o
> /root/trabajo/freesurfer/subjects/MySubj/mri/NEWaparc+aseg.mgz
>
> to convert the apparc into a volume file, and then obtaining such
> voxels correponding to the asigned WM using:
>
> mri_segstats --seg
> /root/trabajo/freesurfer/subjects/MySubj/mri/NEWaparc+aseg.mgz --sum
> /root/trabajo/freesurfer/subjects/MySUbj/stats/Newaparc+aseg.stats
> --pv /root/trabajo/freesurfer/subjects/MySubj/mri/norm.mgz --empty
> --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in
> /root/trabajo/freesurfer/subjectsMySubj/mri/norm.mgz
> --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
> --surf-ctx-vol --totalgray --ctab
> /root/trabajo/freesurfer/ASegStatsLUT.txt --subject MySubj
>
>
> the problem is that even when it seems to work, some of the structures
> have no WM volume in the stat table, but they do have assigned voxels
> on the Newaparc+aseg (see attached image),
> Is there something I've been doing wrong? the command gives me the
> same results when I use the aparc+aseg.mgz created during recon-all
> process.
>
> Can anyone guide me?
>
> Best Regards,
> Gabriel
>
>
>
> _______________________________________________
> 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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
--
--------------------------
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -
Email: ggon...@upo.es
http://www.upo.es/neuroaging/es/
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
