Re: [Freesurfer] error in mri_segstats, important

Hi Knut, when did you download mri_segstats? Can you send me the result of mri_segstats --all-info doug

On 10/02/2012 01:42 AM, Knut J Bjuland wrote:

I have download the latest verion of mri_segstats from the release notes. But it does not generate asegstats.

4 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# ASeg Stats Tue Oct 2 07:36:17 CEST 2012 /home/knutjb/freesurfer/20_ucsd_automatic_version2/004

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 004

ERROR: Option --sum unknown

#------------------------------------------

recon-all -s 004 finished without error at Tue Oct 2 07:36:17 CEST 2012 done

knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats USAGE: mri_label2vol

   Possible inputs:
 --label labelid<--label labelid>
 --annot annotfile : surface annotation file
 --seg   segpath : segmentation
 --aparc+aseg  : use aparc+aseg.mgz in subjectdir as seg

 --temp tempvolid : output template volume

 --reg regmat : VolXYZ = R*LabelXYZ
 --regheader volid : label template volume (needed with --label or

--annot) for --seg, use the segmentation volume --identity : set R=I --invertmtx : Invert the registration matrix

 --fillthresh thresh : between 0 and 1 (def 0)
 --labvoxvol voxvol : volume of each label point (def 1mm3)
 --proj type start stop delta

 --subject subjectid : needed with --proj or --annot
 --hemi hemi : needed with --proj or --annot
 --surf surface  : use surface instead of white

 --o volid : output volume
 --hits hitvolid : each frame is nhits for a label
 --label-stat statvol : map the label stats field into the vol
 --stat-thresh thresh : only use label point where stat>  thresh
 --offset k : add k to segmentation numbers (good when 0 should not

be ignored)

 --native-vox2ras : use native vox2ras xform instead of tkregister-style
 --version : print version and exit
 --help

$Id: mri_label2vol.c,v 1.39 2012/06/08 17:29:54 greve Exp $

knutjb@dmed4960:~/freesurfer/20_ucsd_automatic_version2$ mri_segstats --sum ERROR: Option --sum unknown

Knut J _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer