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

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