I am having an issue when running the preprocess script in fs-fast. It
failed once and I tried something and ran the script again and it failed
the same way. The command I ran is:
preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh
-mni305 -fwhm 5 -per-run
Below is the part where the error appears to occur, but the full log is
attached. Any help would be appreciated.
-Ronny
1/1 subj007
1/1 subj007 008 lh ---------
Fri Jun 7 10:50:50 EDT 2013
mri_vol2surf --mov
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz
--reg
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat
--trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz
--noreshape --cortex --surfreg sphere.reg
srcvol =
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz
srcreg =
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Loading label
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label
Reading surface
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white
Done reading source surface
Reading thickness
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 19272
Reading source surface registration
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg
Done loading source registration surface
surf2surf_nnfr(): Vals and Reg dimension mismatch
nVals = 157755, nReg 157894
Reading target registration
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
Done loading target registration surface
Mapping Surfaces (subj007 -> fsaverage)
ERROR: mapping surfaces
preproc-sess
subj007
$Id: preproc-sess,v 1.50 2013/01/22 22:08:44 greve Exp $
Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Fri Jun 7 10:50:39 EDT 2013
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
-s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
ProjectDir /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
subj007 Template -----------------------------
mktemplate-sess -s subj007 -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -update
Session: /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007 ----------------
Fri Jun 7 10:50:40 EDT 2013
Detected input format at nii
subj007 Update not needed
Run: 008 ----------------
Fri Jun 7 10:50:40 EDT 2013
subj007 008 Update not needed
Run: 010 ----------------
Fri Jun 7 10:50:40 EDT 2013
subj007 010 Update not needed
Run: 012 ----------------
Fri Jun 7 10:50:41 EDT 2013
subj007 012 Update not needed
Fri Jun 7 10:50:41 EDT 2013
mktemplate-sess completed
subj007 Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s subj007 -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -update
------------------------------------------------
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007
Fri Jun 7 10:50:42 EDT 2013
subj007 Update not needed for session-level mask
subj007 Update not needed for run 008 mask
subj007 Update not needed for run 008 meanval
subj007 Update not needed for run 010 mask
subj007 Update not needed for run 010 meanval
subj007 Update not needed for run 012 mask
subj007 Update not needed for run 012 meanval
Fri Jun 7 10:50:46 EDT 2013
mkbrainmask-sess done
subj007 Registration -----------------------------
register-sess -s subj007 -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -dof 6 -per-run -update
--------------------------------------------------------------
register-sess logfile is /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/log/register-sess.subj007.log
--------------------------------------------------------------
Fri Jun 7 10:50:47 EDT 2013
setenv SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
cd /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
/usr/local/freesurfer/dev/fsfast/bin/register-sess -s subj007 -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -dof 6 -per-run -update
freesurfer-Linux-centos6_x86_64-dev-20130606
Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Session: /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007 ----------------
Fri Jun 7 10:50:47 EDT 2013
Run: 008 ----------------
Fri Jun 7 10:50:47 EDT 2013
Update not needed
Run: 010 ----------------
Fri Jun 7 10:50:47 EDT 2013
Update not needed
Run: 012 ----------------
Fri Jun 7 10:50:47 EDT 2013
Update not needed
Fri Jun 7 10:50:47 EDT 2013
register-sess completed
subj007 MC -----------------------------
mc-sess -fstem f -fmcstem fmcpr -s subj007 -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -per-run -update
Logfile is /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/log/mc-subj007-bold.log
-------------------------------------------
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007
RunList: 008 010 012
subj007 008 Update not needed
subj007 010 Update not needed
subj007 012 Update not needed
Fri Jun 7 10:50:49 EDT 2013
mc-sess completed SUCCESSFULLY
subj007 STC -----------------------------
stc-sess -i fmcpr -o fmcpr.siemens -so siemens -s subj007 -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -update
Fri Jun 7 10:50:49 EDT 2013
/autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast
/usr/local/freesurfer/dev/fsfast/bin/stc-sess
-i fmcpr -o fmcpr.siemens -so siemens -s subj007 -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -update
$Id: stc-sess,v 1.10 2011/02/24 20:19:03 greve Exp $
quito
subj007 -----------------
Fri Jun 7 10:50:49 EDT 2013
-rw-rw-r-- 1 preciado birn 379957459 Jun 7 10:00 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/fmcpr.siemens.nii.gz
-rw-rw-r-- 1 preciado birn 376796212 Jun 7 09:48 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/fmcpr.nii.gz
Update not needed
-rw-rw-r-- 1 preciado birn 380014202 Jun 7 10:04 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/010/fmcpr.siemens.nii.gz
-rw-rw-r-- 1 preciado birn 376754156 Jun 7 09:53 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/010/fmcpr.nii.gz
Update not needed
-rw-rw-r-- 1 preciado birn 380319026 Jun 7 10:07 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/012/fmcpr.siemens.nii.gz
-rw-rw-r-- 1 preciado birn 377251894 Jun 7 09:57 /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/012/fmcpr.nii.gz
Update not needed
Started at Fri Jun 7 10:50:49 EDT 2013
Ended at Fri Jun 7 10:50:49 EDT 2013
stc-sess Done
subj007 To Surface -----------------------------
rawfunc2surf-sess -fwhm 5 -s subj007 -d /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast -fsd bold -trgsubject fsaverage -stc siemens -update -per-run
instem fmcpr.siemens
outstem fmcpr.siemens.sm5.fsaverage.hemi
------------------------------
1/1 subj007
1/1 subj007 008 lh ---------
Fri Jun 7 10:50:50 EDT 2013
mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg
srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz
srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label
Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white
Done reading source surface
Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 19272
Reading source surface registration
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg
Done loading source registration surface
surf2surf_nnfr(): Vals and Reg dimension mismatch
nVals = 157755, nReg 157894
Reading target registration
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
Done loading target registration surface
Mapping Surfaces (subj007 -> fsaverage)
ERROR: mapping surfaces_______________________________________________
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