Hi haochuanxi
please post to the list so that others can help! It looks to me like your voxel size is (0.4688, 0.4688, 1.19996). Is that the case? If so, it's going to be har to reconstruct good surfaces even if you find a machine with enough memory. "in plane" means the resolution of your data in one of the acquisition planes
cheers Bruce
On Wed, 11 Apr 2012, ?? wrote:
Dear Bruce? Something you said I could not understand fully: what is ".46 mm in plane", and what is anisotropic (0.4688, 0.4688, 1.19996). the data I processed is 3D volume data.
haochuanxi
At 2012-04-11 21:44:38,"Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
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. >> >> >> >> >> >> >>>>
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... but does not contain patient information, please contact the sender and properly >dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl