Hi all, Mac OS 10.6.5 freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0
I want to run func2roi-sess with a functionally defined label (lh_MT.label). I have a label stored as : subjects/VM20/label/lh_MT.label and I can see this label with tksurfer-sess. When I ran: func2roi-sess -roidef lh_MT -analysis VMfwhm5lh -motioncor -rawstem fmcsm5 -df sessdirfile -reg register.dof6.dat -s VM20 -anatlabel lh_MT I got an error (roisummary-sess results filled with 0). Below shows some lines from log file that might be related to this problem. All logs are pasted at the end of this message. > Lxyz2Scrs: > -1.000 -0.020 0.021 69283.891; > 0.019 -1.000 -0.021 -1.705; > 0.022 -0.021 1.000 -19.485; > 0.000 0.000 0.000 1.000; > > INFO: label2mask_linear: there were 0 label hits > voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 > INFO: label2mask_linear: there were 0 hits in final mask > label2mask_linear: done > > Lxyz2Scrs: > -1.000 -0.020 0.021 69283.891; > 0.019 -1.000 -0.021 -1.705; > 0.022 -0.021 1.000 -19.485; > 0.000 0.000 0.000 1.000; > > INFO: label2mask_linear: there were 0 label hits > voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 > INFO: label2mask_linear: there were 0 hits in final mask > label2mask_linear: done > Averging over ROI Looks like somehow my label was rejected, or didn't meet some criteria? I don't want any functional thresholds for this analysis, though I see clear activation within this label during task. Please let me know what I need to add/change to make func2roi-sess work. Thank you! Yuko Yotsumoto ############################################### fucn2roi-sess log file $Id: func2roi-sess,v 1.16 2010/03/25 16:22:53 greve Exp $ /Users/yuko/Documents/FreeSurfer/sessions/VM/VMan /Applications/freesurfer/fsfast/bin/func2roi-sess -roidef lh_MT -analysis VMfwhm5lh -motioncor -rawstem fmcsm5 -df sessdirfile -reg register.dof6.dat -s VM20 -anatlabel lh_MT Darwin Yukos-iMac.local 10.5.0 Darwin Kernel Version 10.5.0: Fri Nov 5 23:20:39 PDT 2010; root:xnu-1504.9.17~1/RELEASE_I386 i386 Tue Nov 30 13:08:07 JST 2010 ----------------------------------------------------- Session: VM20 1/1 Tue Nov 30 13:08:07 JST 2010 Tue Nov 30 13:08:07 JST 2010 --------------------------------------------------- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h --roiavg bold/VMfwhm5lh/lh_MT/h --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h.txt --------------------------------------------------- -------------------------------------------------------- /Users/yuko/Documents/freesurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h --roiavg bold/VMfwhm5lh/lh_MT/h --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h.txt version $Id: mri_vol2roi.c,v 1.31 2010/03/25 16:00:50 greve Exp $ -------------------------------------------------------- roifile = bold/VMfwhm5lh/lh_MT/h roitxtfile = bold/VMfwhm5lh/lh_MT/h.txt oldtxtstyle = 0 srcvol = bold/VMfwhm5lh/h.nii srcfmt = bvolume srcreg = bold/register.dof6.dat srcregold = 0 srcwarp unspecified label file = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/VMfwhm5lh/h.nii ...done srcreg Dsrc ------------- 1.000 0.020 -0.021 -0.890; 0.022 -0.021 1.000 -19.985; -0.019 1.000 0.021 2.205; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -1.000 0.000 0.000 69283.000; -0.000 -0.000 -1.000 0.500; -0.000 1.000 -0.000 0.500; 0.000 0.000 0.000 1.000; ---------------------------------- INFO: Source volume detected as selxavg format INFO: Adjusting Frame Power Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 0 WARNING: there were no voxels in the input mask > 0.5 Done averging over ROI (nhits = 0) INFO: Readjusting Frame Power --------------------------------------------------- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h-offset --roiavg bold/VMfwhm5lh/lh_MT/h-offset --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h-offset.txt --------------------------------------------------- -------------------------------------------------------- /Users/yuko/Documents/freesurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/VMfwhm5lh/h-offset --roiavg bold/VMfwhm5lh/lh_MT/h-offset --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/h-offset.txt version $Id: mri_vol2roi.c,v 1.31 2010/03/25 16:00:50 greve Exp $ -------------------------------------------------------- roifile = bold/VMfwhm5lh/lh_MT/h-offset roitxtfile = bold/VMfwhm5lh/lh_MT/h-offset.txt oldtxtstyle = 0 srcvol = bold/VMfwhm5lh/h-offset.nii srcfmt = bvolume srcreg = bold/register.dof6.dat srcregold = 0 srcwarp unspecified label file = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/VMfwhm5lh/h-offset.nii ...done srcreg Dsrc ------------- 1.000 0.020 -0.021 -0.890; 0.022 -0.021 1.000 -19.985; -0.019 1.000 0.021 2.205; 0.000 0.000 0.000 1.000; ---------------------------------- ras2vox src (tkreg) Qsrc ------------- -1.000 0.000 0.000 69283.000; -0.000 -0.000 -1.000 0.500; -0.000 1.000 -0.000 0.500; 0.000 0.000 0.000 1.000; ---------------------------------- Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Lxyz2Scrs: -1.000 -0.020 0.021 69283.891; 0.019 -1.000 -0.021 -1.705; 0.022 -0.021 1.000 -19.485; 0.000 0.000 0.000 1.000; INFO: label2mask_linear: there were 0 label hits voxsize = 1, rszthresh = 1e-07, thresh = 1e-07 INFO: label2mask_linear: there were 0 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 0 WARNING: there were no voxels in the input mask > 0.5 Done averging over ROI (nhits = 0) ------------------------------------------- /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/001/ --roiavg bold/VMfwhm5lh/lh_MT/-001 --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/-001.txt ------------------------------------------- corRead(): can't open file bold/001/COR-.info -------------------------------------------------------- /Users/yuko/Documents/freesurfer/sessions/VM/VM20 mri_vol2roi --srcvol bold/001/ --roiavg bold/VMfwhm5lh/lh_MT/-001 --srcreg bold/register.dof6.dat --label /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label --finalmskvol bold/VMfwhm5lh/lh_MT/mask --roiavgtxt bold/VMfwhm5lh/lh_MT/-001.txt version $Id: mri_vol2roi.c,v 1.31 2010/03/25 16:00:50 greve Exp $ -------------------------------------------------------- roifile = bold/VMfwhm5lh/lh_MT/-001 roitxtfile = bold/VMfwhm5lh/lh_MT/-001.txt oldtxtstyle = 0 srcvol = bold/001/ srcfmt = bvolume srcreg = bold/register.dof6.dat srcregold = 0 srcwarp unspecified label file = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_MT.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/001/ ... _______________________________________________ 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. 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