are your data really .46 mm in plane? It looks you are running out of memory, but even if you weren't it's very hard to reconstruct data that is that anisotropic (0.4688, 0.4688, 1.19996). You are better off getting 1mm isotropic and using it, which these days with 3T and 32 channels is only 4-6 min of imaging time.
cheers Bruce
On Wed, 11 Apr 2012, ?? wrote:
Dear FS expert?
Today i put two contrast in the file {subjects},and run the command line "recon-all -s mgz -all", several minutes later,the terminal tells error,it says:
[brain@localhost ~]$ recon-all -s mgz -all
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux localhost.localdomain 2.6.25-14.fc9.i686 #1 SMP Thu May 1 06:28:41 EDT 2008 i686 i686 i386 GNU/Linux
#--------------------------------------------
#@# MotionCor Wed Apr 11 17:49:05 HKT 2012
Found 3 runs
/usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz
/usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz
/usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz
Checking for (invalid) multi-frame inputs...
Checking for (invalid) multi-frame inputs...
Checking for (invalid) multi-frame inputs...
#-----------------------------------------------
/usr/local/freesurfer/subjects/mgz
mri_robust_template --mov /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz /usr/local/fr eesurfer/subjects/mgz/mri/orig/004.mgz --average 1 --template /usr/local/freesurfer/subjects/mgz/mri/rawavg.mgz --satit --inittp 1 --fixtp --noi t --iscale --iscaleout /usr/local/freesurfer/subjects/mgz/mri/orig/002-iscale.txt /usr/local/freesurfer/subjects/mgz/mri/orig/003-iscale.txt /us r/local/freesurfer/subjects/mgz/mri/orig/004-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/mgz/mri/orig/002.lta /usr/local/fre esurfer/subjects/mgz/mri/orig/003.lta /usr/local/freesurfer/subjects/mgz/mri/orig/004.lta
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
--mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz as movable/source volume.
--mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz as movable/source volume.
--mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz as movable/source volume.
Total: 3 input volumes
--average: Using method 1 for template computation.
--template: Using /usr/local/freesurfer/subjects/mgz/mri/rawavg.mgz as template output volume.
--satit: Will estimate SAT iteratively!
--inittp: Using TP 1 as target for initialization
--fixtp: Will map everything to init TP!
--noit: Will output only first template (no iterations)!
--iscale: Enableing intensity scaling!
--iscaleout: Will perform intensity scaling and output results
--subsample: Will subsample if size is larger than 200 on all axes!
--lta: Will output LTA transforms
reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz'...
reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz'...
reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz'...
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ==============================
Register TP 2 ( /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz )
to TP 1 ( /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz )
Registration::setSourceAndTarget ...
Mov: (0.4688, 0.4688, 1.19996)mm and dim (512, 512, 156)
Dst: (0.4688, 0.4688, 1.20005)mm and dim (512, 512, 156)
Asserting both images: 0.4688mm isotropic and (512, 512, 400) voxels
Original : (0.4688, 0.4688, 1.19996) mm size and (512, 512, 156) voxels.
Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 400) voxels.
Reslicing using trilinear interpolation
Original : (0.4688, 0.4688, 1.20005) mm size and (512, 512, 156) voxels.
Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 400) voxels.
Reslicing using trilinear interpolation
Registration::findSaturation
- Gaussian Pyramid
MRIalloc(512, 512, 400): could not allocate 1048576 bytes for 367th slice
Cannot allocate memory
Linux localhost.localdomain 2.6.25-14.fc9.i686 #1 SMP Thu May 1 06:28:41 EDT 2008 i686 i686 i386 GNU/Linux
recon-all -s mgz exited with ERRORS at Wed Apr 11 17:51:20 HKT 2012
For more details, see the log file /usr/local/freesurfer/subjects/mgz/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
could you tell me what is wrong in the process? Thank you very much.