Try removing the --rip-unknown
On 09/12/2017 11:09 AM, Gonzalo Rojas Costa wrote: > Hi: > > I created the following script (for freesurfer 5.3.0) to compute the > lobes volume (including GM and WM). > > mri_annotation2label --subject pac --hemi rh --lobesStrict lobulos > --seg lobulos --stat lobulos > mri_annotation2label --subject pac --hemi lh --lobesStrict lobulos > --seg lobulos --stat lobulos > mris_anatomical_stats -a lobulos -f pac.lobulos.rh pac rh > mris_anatomical_stats -a lobulos -f pac.lobulos.lh pac lh > mri_aparc2aseg --s pac --labelwm --hypo-as-wm --rip-unknown > --volmask --o $SUBJECTS_DIR/pac/mri/lobulitos.mgz --annot lobulos > --wmparc-dmax 20 > mri_segstats --seg $SUBJECTS_DIR/pac/mri/lobulitos.mgz --ctab > /usr/local/freesurfer/LobulesColorLUT.txt --excludeid 0 --sum > $i.lobulo.aseg.sum --id 1001 1004 1005 1006 2001 2004 2005 2006 3001 > 3004 3005 3006 4001 4004 4005 4006 251 252 253 254 255 > > But, I didn't got the complete WM volume for each lobe (frontal lobe > for example... see red arrow in attached image)... why ?... Any > solution ?... > > Sincerely, > > > Gonzalo Rojas Costa > Laboratory for Advanced Medical Image Processing > Department of Radiology > Clínica las Condes > Lo Fontecilla 441, Las Condes, Santiago, Chile. > Tel: 56-2-2105170 > Cel: 56-9-97771785 > www.clc.cl > http://www.aribrain.info > https://scholar.google.com/citations?user=LO7LZ3oAAAAJ > https://www.researchgate.net/profile/Gonzalo_Rojas2 > https://cl.linkedin.com/in/gonzalorojascosta > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
