Are you working around this with funcroi-sess? func2roi-sess cannot be used with version 5.
doug Yuko Yotsumoto wrote: > 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 > > > -- 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.
