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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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

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