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/ ...