Doug, I see. I tried to use funcroi-config and funcroi-sess, and got another error.
I did: mkanalysis-sess -analysis VMfwhm5lh -surface self lh -paradigm para.para -fwhm 5 -event-related -TR 2 -nconditions 5 -fir 4 20 -TER 1 -mcextreg -fsd bold -runlistfile runlist selxavg3-sess -sf sesslistfile -df sessdirfile -analysis VMfwhm5lh -overwrite funcroi-config -analysis VMfwhm5lh -label lh_DLPFC -roi lh.DLPFC.roicfg funcroi-sess -roi lh.DLPFC.roicfg -df sessdirfile -s VM20 Then, I got an error with funcroi-sess. >> Reading target surface >> /Users/yuko/Documents/freesurfer/subjects/self/surf/lh.white >> ERROR: could not read >> /Users/yuko/Documents/freesurfer/subjects/self/surf/lh.white I thought when I use "-surface self lh", it read's each subject's session and reconstructed data. Am I right? I can't figure out why it searches /subjects/self/surf/, which I don't have in my subject folder... Yuko Yotsumoto ##### log > [Yukos-iMac:sessions/VM/VMan] yuko% funcroi-sess -roi lh.DLPFC.roicfg -df > sessdirfile -s VM20 > ------------------------------------------- > /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20 > Wed Dec 1 10:00:40 JST 2010 > mri_label2label --hemi lh --srclabel > /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_DLPFC.label > --srcsubject VM20 --trglabel > /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold/VMfwhm5lh/tmp.funcroi-sess.lh.DLPFC/target.label > --trgsubject self --regmethod surface > > srclabel = /Users/yuko/Documents/freesurfer/subjects/VM20/label/lh_DLPFC.label > srcsubject = VM20 > trgsubject = self > trglabel = > /Users/yuko/Documents/FreeSurfer/sessions/VM/VM20/bold/VMfwhm5lh/tmp.funcroi-sess.lh.DLPFC/target.label > regmethod = surface > > srchemi = lh > trghemi = lh > trgsurface = white > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR /Users/yuko/Documents/freesurfer/subjects > FREESURFER_HOME /Applications/freesurfer > Loading source label. > Found 2235 points in source label. > MRISread(/Users/yuko/Documents/freesurfer/subjects/self/surf/lh.white): could > not open file > No such file or directory > Starting surface-based mapping > Reading source registration > /Users/yuko/Documents/freesurfer/subjects/VM20/surf/lh.sphere.reg > Rescaling ... original radius = 100 > Reading target surface > /Users/yuko/Documents/freesurfer/subjects/self/surf/lh.white > ERROR: could not read > /Users/yuko/Documents/freesurfer/subjects/self/surf/lh.white > [Yukos-iMac:sessions/VM/VMan] yuko% On Dec 1, 2010, at 2:43 AM, Douglas N Greve wrote: > 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. >
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