INFO: /home/neuro/proc/OutPBS_GPU/ACR_103 exists with -i, but -force specified. Deleting any previous source volumes Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /home/neuro/proc/OutPBS_GPU Actual FREESURFER_HOME /home/neuro/freesurfer -rw-rw-r-- 1 neuro neuro 34477 Oct 20 15:18 /home/neuro/proc/OutPBS_GPU/ACR_103/scripts/recon-all.log Linux ww-neuro04.pic.es 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux /home/neuro/proc/OutPBS_GPU/ACR_103 mri_convert /home/neuro/orig/ACR_103/ACR_103_0002 /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig/001.mgz mri_convert /home/neuro/orig/ACR_103/ACR_103_0002 /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /home/neuro/orig/ACR_103/ACR_103_0002... Starting DICOMRead2() dcmfile = /home/neuro/orig/ACR_103/ACR_103_0002 dcmdir = /home/neuro/orig/ACR_103 Ref Series No = 301 Found 172 files, checking for dicoms Found 170 dicom files in series. First Sorting Computing Slice Direction Vs: -1.2 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 170 ndcmfiles = 170 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=6.70, TE=3.13, TI=0.00, flip angle=8.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed Oct 20 15:52:25 CEST 2010 Found 1 runs /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig/001.mgz /home/neuro/proc/OutPBS_GPU/ACR_103/mri/rawavg.mgz /home/neuro/proc/OutPBS_GPU/ACR_103 mri_convert /home/neuro/proc/OutPBS_GPU/ACR_103/mri/rawavg.mgz /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig.mgz --conform mri_convert /home/neuro/proc/OutPBS_GPU/ACR_103/mri/rawavg.mgz /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /home/neuro/proc/OutPBS_GPU/ACR_103/mri/rawavg.mgz... TR=6.70, TE=3.13, TI=0.00, flip angle=8.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) Original Data has (0.888889, 0.888889, 1.2) mm size and (288, 288, 170) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig.mgz... mri_add_xform_to_header -c /home/neuro/proc/OutPBS_GPU/ACR_103/mri/transforms/talairach.xfm /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig.mgz /home/neuro/proc/OutPBS_GPU/ACR_103/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Wed Oct 20 15:52:36 CEST 2010 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /home/neuro/proc/OutPBS_GPU/ACR_103/mri /home/neuro/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux ww-neuro04.pic.es 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux Wed Oct 20 15:52:36 CEST 2010 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.23925 /home/neuro/proc/OutPBS_GPU/ACR_103/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23925/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23925/nu0.mnc -odt float $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=6.70, TE=3.13, TI=0.00, flip angle=8.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.23925/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Oct 20 15:52:39 CEST 2010 nu_correct -clobber ./tmp.mri_nu_correct.mni.23925/nu0.mnc ./tmp.mri_nu_correct.mni.23925/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23925/0/ [neuro@ww-neuro04.pic.es:/home/neuro/proc/OutPBS_GPU/ACR_103/mri/] [2010-10-20 15:52:39] running: /home/neuro/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23925/0/ ./tmp.mri_nu_correct.mni.23925/nu0.mnc ./tmp.mri_nu_correct.mni.23925/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 19 CV of field change: 0.000972978 [neuro@ww-neuro04.pic.es:/home/neuro/proc/OutPBS_GPU/ACR_103/mri/] [2010-10-20 15:52:51] running: /home/neuro/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23925/nu0.mnc ./tmp.mri_nu_correct.mni.23925/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Oct 20 15:52:55 CEST 2010 nu_correct -clobber ./tmp.mri_nu_correct.mni.23925/nu1.mnc ./tmp.mri_nu_correct.mni.23925/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.23925/1/ [neuro@ww-neuro04.pic.es:/home/neuro/proc/OutPBS_GPU/ACR_103/mri/] [2010-10-20 15:52:55] running: /home/neuro/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23925/1/ ./tmp.mri_nu_correct.mni.23925/nu1.mnc ./tmp.mri_nu_correct.mni.23925/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 17 CV of field change: 0.000985572 [neuro@ww-neuro04.pic.es:/home/neuro/proc/OutPBS_GPU/ACR_103/mri/] [2010-10-20 15:53:07] running: /home/neuro/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23925/nu1.mnc ./tmp.mri_nu_correct.mni.23925/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.23925/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23925/ones.mgz $Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $ cwd /home/neuro/proc/OutPBS_GPU/ACR_103/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.23925/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23925/ones.mgz sysname Linux hostname ww-neuro04.pic.es machine x86_64 user neuro input ./tmp.mri_nu_correct.mni.23925/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.23925/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23925/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23925/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23925/input.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23925/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23925/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23925/input.mean.dat sysname Linux hostname ww-neuro04.pic.es machine x86_64 user neuro Loading ./tmp.mri_nu_correct.mni.23925/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.23925/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23925/ones.mgz --i ./tmp.mri_nu_correct.mni.23925/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23925/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23925/output.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23925/ones.mgz --i ./tmp.mri_nu_correct.mni.23925/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23925/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23925/output.mean.dat sysname Linux hostname ww-neuro04.pic.es machine x86_64 user neuro Loading ./tmp.mri_nu_correct.mni.23925/ones.mgz Loading ./tmp.mri_nu_correct.mni.23925/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.23925/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.23925/nu2.mnc ./tmp.mri_nu_correct.mni.23925/nu2.mnc mul 1.06327268147114676587 Saving result to './tmp.mri_nu_correct.mni.23925/nu2.mnc' (type=3) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.23925/nu2.mnc nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.23925/nu2.mnc nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from ./tmp.mri_nu_correct.mni.23925/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to nu.mgz... Wed Oct 20 15:53:48 CEST 2010 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Wed Oct 20 15:53:48 CEST 2010 /home/neuro/proc/OutPBS_GPU/ACR_103/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Oct 20 15:54:29 CEST 2010 /home/neuro/proc/OutPBS_GPU/ACR_103/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8180, pval=0.8469 >= threshold=0.0050) awk -f /home/neuro/freesurfer/bin/extract_talairach_avi_QA.awk /home/neuro/proc/OutPBS_GPU/ACR_103/mri/transforms/talairach_avi.log TalAviQA: 0.96762 z-score: -2 #-------------------------------------------- #@# Intensity Normalization Wed Oct 20 15:54:29 CEST 2010 /home/neuro/proc/OutPBS_GPU/ACR_103/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.145 0.014 0.004 -2.159; -0.039 1.060 0.150 -22.394; -0.033 -0.069 1.211 -50.254; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 1 minutes and 52 seconds. MRIsplineNormalize(): npeaks = 10 Starting OpenSpline(): npoints = 10 white matter peak found at 111 white matter peak found at 109 gm peak at 46 (46), valley at 35 (35) csf peak at 10, setting threshold to 34 white matter peak found at 111 white matter peak found at 110 gm peak at 77 (77), valley at 16 (16) csf peak at 16, setting threshold to 56 #-------------------------------------------- #@# Skull Stripping Wed Oct 20 15:56:21 CEST 2010 /home/neuro/proc/OutPBS_GPU/ACR_103/mri mri_em_register -skull nu.mgz /home/neuro/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/home/neuro/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (50, 26, 23) --> (206, 255, 226) using (102, 102, 125) as brain centroid... mean wm in atlas = 126, using box (83,74,100) --> (121, 130,150) to find MRI wm before smoothing, mri peak at 163 after smoothing, mri peak at 163, scaling input intensities by 0.773 scaling channel 0 by 0.773006 initial log_p = -10408.2 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-3.4, 3.4, -14.8): log p = -10340.8 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10332.0, old_max_log_p =-10340.8 (thresh=-10330.5) 1.055 -0.111 -0.048 8.447; 0.150 0.911 0.398 -61.100; 0.000 -0.453 1.148 13.188; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10329.7, old_max_log_p =-10332.0 (thresh=-10321.7) 1.020 -0.023 -0.100 8.834; 0.081 0.942 0.330 -43.302; 0.079 -0.399 1.165 -4.105; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 2 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10323.1, old_max_log_p =-10329.7 (thresh=-10319.4) 1.023 0.006 -0.081 3.476; 0.045 0.951 0.303 -35.437; 0.072 -0.374 1.170 -6.828; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02341 0.00571 -0.08058 3.47614; 0.04509 0.95097 0.30317 -35.43700; 0.07246 -0.37362 1.16995 -6.82782; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.02341 0.00571 -0.08058 3.47614; 0.04509 0.95097 0.30317 -35.43700; 0.07246 -0.37362 1.16995 -6.82782; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 005: -log(p) = 10323.1 tol 0.000010 Resulting transform: 1.023 0.006 -0.081 3.476; 0.045 0.951 0.303 -35.437; 0.072 -0.374 1.170 -6.828; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10323.1 (old=-10408.2) Abort Linux ww-neuro04.pic.es 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:50:31 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ACR_103 exited with ERRORS at Wed Oct 20 16:10:04 CEST 2010