Are you sure you're using the new version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/funcroi-sess ? I tested this yesterday, and it worked fine using the -surface self option. Double check and let me know.
doug
Yuko Yotsumoto wrote:
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/ ...
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