Dear all,
I am new freesurfer user (version 5.0.0 installed to windows using virtual machine), during the installation i was trying to test the installation, following the recommended steps. The recon-all -s terminated with errors, andi can't find the bug.
I send you the command line and the report including the error message to help you.
------------------------------------------------------ FREESURFER_HOME /home/virtualuser/freesurfer SUBJECTS_DIR /home/virtualuser/freesurfer/subjects ------------------------------------------------------------------
FreeSurfer:~> recon-all -s ernie -i $SUBJECTS_DIR/sample-001.mgz -i $SUBJECTS_DIR/sample-002.mgz -autorecon1 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz... /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-002.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Mon Apr 23 04:55:18 EDT 2012 Found 2 runs /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /home/virtualuser/freesurfer/subjects/ernie mri_robust_template --mov /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz --average 1 --template /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001-iscale.txt /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002-iscale.txt --subsample 200 --lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz as movable/source volume. --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /home/virtualuser/freesurfer/subjects/ernie/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 '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz'... reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz ) to TP 1 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1.32812)mm and dim (256, 256, 128) Dst: (1, 1, 1.32812)mm and dim (256, 256, 128) Asserting both images: 1mm isotropic and (256, 256, 170) voxels Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels. Reslicing using trilinear interpolation Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels. Reslicing using trilinear interpolation
Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 42 ) -- gpT ( 64 , 64 , 42 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0356683 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 0 ( -1 ), max sat: 8 ( 0.132346 ), sat diff: 8 -- Iteration: 3 trying sat: 4 min sat: 4 ( 0.391276 ), max sat: 8 ( 0.132346 ), sat diff: 4 -- Iteration: 4 trying sat: 6 min sat: 6 ( 0.21266 ), max sat: 8 ( 0.132346 ), sat diff: 2 -- Iteration: 5 trying sat: 7 min sat: 6 ( 0.21266 ), max sat: 7 ( 0.16739 ), sat diff: 1 -- Iteration: 6 trying sat: 6.5 - final SAT: 7 ( it: 6 , weight check 0.16739 <= 0.175 )
Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.0652797588760 0 1.0000000000000 0 0.2680379336344 0 0 1.0000000000000 0.4401045835282 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 3 S( 32 32 21 ) T( 32 32 21 ) Iteration(f): 1 -- diff. to prev. transform: 0.706674 Iteration(f): 2 -- diff. to prev. transform: 0.0752789 Iteration(f): 3 -- diff. to prev. transform: 0.0228908 Iteration(f): 4 -- diff. to prev. transform: 0.0664109 Iteration(f): 5 -- diff. to prev. transform: 0.0548568 max it: 5 reached! Resolution: 2 S( 64 64 42 ) T( 64 64 42 ) Iteration(f): 1 -- diff. to prev. transform: 0.192344 Iteration(f): 2 -- diff. to prev. transform: 0.0308604 Iteration(f): 3 -- diff. to prev. transform: 0.0187651 Iteration(f): 4 -- diff. to prev. transform: 0.00839767 < 0.01 :-) Resolution: 1 S( 128 128 85 ) T( 128 128 85 ) Iteration(f): 1 -- diff. to prev. transform: 0.128598 Iteration(f): 2 -- diff. to prev. transform: 0.0134286 Iteration(f): 3 -- diff. to prev. transform: 0.00837132 < 0.01 :-) Resolution: 0 S( 256 256 170 ) T( 256 256 170 ) Iteration(f): 1 (subsample 200) terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s ernie exited with ERRORS at Mon Apr 23 04:56:44 EDT 2012 FreeSurfer:~> which freesurfer /home/virtualuser/freesurfer/bin/freesurfer --------------------------------------------------------------------------------------------------------------------------------
Thanks in advanced, Stratos
Hi Statos
how much RAM do you have in your machine? It looks like not enough.
cheers Bruce On Mon, 23 Apr 2012, Eustratios Karavasilis wrote:
Dear all,
I am new freesurfer user (version 5.0.0 installed to windows using virtual machine), during the installation i was trying to test the installation, following the recommended steps. The recon-all -s terminated with errors, andi can't find the bug.
I send you the command line and the report including the error message to help you.
FREESURFER_HOME /home/virtualuser/freesurfer SUBJECTS_DIR /home/virtualuser/freesurfer/subjects
FreeSurfer:~> recon-all -s ernie -i $SUBJECTS_DIR/sample-001.mgz -i $SUBJECTS_DIR/sample-002.mgz -autorecon1 Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz... /home/virtualuser/freesurfer/subjects/ernie mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz mri_convert /home/virtualuser/freesurfer/subjects/sample-002.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from /home/virtualuser/freesurfer/subjects/sample-002.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Mon Apr 23 04:55:18 EDT 2012 Found 2 runs /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /home/virtualuser/freesurfer/subjects/ernie mri_robust_template --mov /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz --average 1 --template /home/virtualuser/freesurfer/subjects/ernie/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001-iscale.txt /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002-iscale.txt --subsample 200 --lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.lta /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz as movable/source volume. --mov: Using /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /home/virtualuser/freesurfer/subjects/ernie/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 '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz'... reading source '/home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/002.mgz ) to TP 1 ( /home/virtualuser/freesurfer/subjects/ernie/mri/orig/001.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1.32812)mm and dim (256, 256, 128) Dst: (1, 1, 1.32812)mm and dim (256, 256, 128) Asserting both images: 1mm isotropic and (256, 256, 170) voxels Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels. Reslicing using trilinear interpolation Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels. Reslicing using trilinear interpolation
Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 42 ) -- gpT ( 64 , 64 , 42 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0356683 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 0 ( -1 ), max sat: 8 ( 0.132346 ), sat diff: 8 -- Iteration: 3 trying sat: 4 min sat: 4 ( 0.391276 ), max sat: 8 ( 0.132346 ), sat diff: 4 -- Iteration: 4 trying sat: 6 min sat: 6 ( 0.21266 ), max sat: 8 ( 0.132346 ), sat diff: 2 -- Iteration: 5 trying sat: 7 min sat: 6 ( 0.21266 ), max sat: 7 ( 0.16739 ), sat diff: 1 -- Iteration: 6 trying sat: 6.5 - final SAT: 7 ( it: 6 , weight check 0.16739 <= 0.175 )
Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.0652797588760 0 1.0000000000000 0 0.2680379336344 0 0 1.0000000000000 0.4401045835282 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 3 S( 32 32 21 ) T( 32 32 21 ) Iteration(f): 1 -- diff. to prev. transform: 0.706674 Iteration(f): 2 -- diff. to prev. transform: 0.0752789 Iteration(f): 3 -- diff. to prev. transform: 0.0228908 Iteration(f): 4 -- diff. to prev. transform: 0.0664109 Iteration(f): 5 -- diff. to prev. transform: 0.0548568 max it: 5 reached! Resolution: 2 S( 64 64 42 ) T( 64 64 42 ) Iteration(f): 1 -- diff. to prev. transform: 0.192344 Iteration(f): 2 -- diff. to prev. transform: 0.0308604 Iteration(f): 3 -- diff. to prev. transform: 0.0187651 Iteration(f): 4 -- diff. to prev. transform: 0.00839767 < 0.01 :-) Resolution: 1 S( 128 128 85 ) T( 128 128 85 ) Iteration(f): 1 -- diff. to prev. transform: 0.128598 Iteration(f): 2 -- diff. to prev. transform: 0.0134286 Iteration(f): 3 -- diff. to prev. transform: 0.00837132 < 0.01 :-) Resolution: 0 S( 256 256 170 ) T( 256 256 170 ) Iteration(f): 1 (subsample 200) terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s ernie exited with ERRORS at Mon Apr 23 04:56:44 EDT 2012 FreeSurfer:~> which freesurfer /home/virtualuser/freesurfer/bin/freesurfer
Thanks in advanced, Stratos
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Eustratios Karavasilis