selxavg3-sess log file /usr/local/freesurfer/dev/fsfast/bin/selxavg3-sess -s sess01 -analysis workmem.sm05.lh $Id: selxavg3-sess,v 1.62 2014/10/15 22:02:08 greve Exp $ uid=8481(zkaufman) gid=8481(zkaufman) groups=8481(zkaufman),160(fsdev),317(vboxusers),1046(recon),1538(lcnweb),1590(fsbuild),1601(b40atlas) /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional Linux sand 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Tue Dec 23 11:44:49 EST 2014 preproc-sess -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -a workmem.sm05.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.55 2014/11/26 01:16:57 greve Exp $ zkaufman setenv FREESURFER_HOME /usr/local/freesurfer/dev setenv SUBJECTS_DIR /space/sand/1/users/zkaufman/tutorial_data/fsfast-tutorial.subjects Linux sand 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/preproc-sess -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -a workmem.sm05.lh -nolog Tue Dec 23 11:44:50 EST 2014 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain sess01 Template ----------------------------- mktemplate-sess -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -fsd bold -nolog -update Session: /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01 ---------------- Tue Dec 23 11:44:50 EST 2014 Detected input format at nii.gz sess01 Update not needed Run: 001 ---------------- Tue Dec 23 11:44:50 EST 2014 sess01 001 Update not needed Run: 002 ---------------- Tue Dec 23 11:44:50 EST 2014 sess01 002 Update not needed Run: 003 ---------------- Tue Dec 23 11:44:50 EST 2014 sess01 003 Update not needed Run: 004 ---------------- Tue Dec 23 11:44:50 EST 2014 sess01 004 Update not needed Tue Dec 23 11:44:50 EST 2014 mktemplate-sess completed sess01 Registration ----------------------------- register-sess -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-fsl -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Tue Dec 23 11:44:50 EST 2014 setenv SUBJECTS_DIR /space/sand/1/users/zkaufman/tutorial_data/fsfast-tutorial.subjects cd /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/register-sess -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -fsd bold -delete-dat -dof 6 -bold -per-run -nolog -update -init-fsl freesurfer-Linux-centos6_x86_64-dev-20141222 Linux sand 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Session: /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01 ---------------- Tue Dec 23 11:44:50 EST 2014 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01 Run: 001 ---------------- Tue Dec 23 11:44:50 EST 2014 Update not needed Run: 002 ---------------- Tue Dec 23 11:44:50 EST 2014 Update not needed Run: 003 ---------------- Tue Dec 23 11:44:50 EST 2014 Update not needed Run: 004 ---------------- Tue Dec 23 11:44:50 EST 2014 Update not needed Tue Dec 23 11:44:50 EST 2014 register-sess completed sess01 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -nolog -update ------------------------------------------------ /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01 Tue Dec 23 11:44:50 EST 2014 sess01 Update not needed for session-level mask sess01 Update not needed for run 001 mask sess01 Update not needed for run 001 meanval sess01 Update not needed for run 002 mask sess01 Update not needed for run 002 meanval sess01 Update not needed for run 003 mask sess01 Update not needed for run 003 meanval sess01 Update not needed for run 004 mask sess01 Update not needed for run 004 meanval Tue Dec 23 11:44:51 EST 2014 mkbrainmask-sess done sess01 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -fsd bold -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01 RunList: 001 002 003 004 sess01 001 Update not needed sess01 002 Update not needed sess01 003 Update not needed sess01 004 Update not needed Tue Dec 23 11:44:51 EST 2014 mc-sess completed SUCCESSFULLY sess01 STC ----------------------------- stc-sess -i fmcpr -o fmcpr.up -so up -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -fsd bold -nolog -update Tue Dec 23 11:44:51 EST 2014 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional /usr/local/freesurfer/dev/fsfast/bin/stc-sess -i fmcpr -o fmcpr.up -so up -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -fsd bold -nolog -update $Id: stc-sess,v 1.10 2011/02/24 20:19:03 greve Exp $ sand sess01 ----------------- Tue Dec 23 11:44:51 EST 2014 -rw-rw-r-- 1 zkaufman fsdev 62636193 Mar 28 2011 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.up.nii.gz -rw-rw-r-- 1 zkaufman fsdev 61968910 Mar 28 2011 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/001/fmcpr.nii.gz Update not needed -rw-rw-r-- 1 zkaufman fsdev 62606871 Mar 28 2011 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.up.nii.gz -rw-rw-r-- 1 zkaufman fsdev 61851632 Mar 28 2011 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/002/fmcpr.nii.gz Update not needed -rw-rw-r-- 1 zkaufman fsdev 62592546 Mar 28 2011 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.up.nii.gz -rw-rw-r-- 1 zkaufman fsdev 61850233 Mar 28 2011 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/003/fmcpr.nii.gz Update not needed -rw-rw-r-- 1 zkaufman fsdev 62605062 Mar 28 2011 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.up.nii.gz -rw-rw-r-- 1 zkaufman fsdev 61838744 Mar 28 2011 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/004/fmcpr.nii.gz Update not needed Started at Tue Dec 23 11:44:51 EST 2014 Ended at Tue Dec 23 11:44:51 EST 2014 stc-sess Done sess01 To Surface ----------------------------- rawfunc2surf-sess -fwhm 5 -s sess01 -d /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional -fsd bold -hemi lh -trgsubject fsaverage -stc up -nolog -update -per-run instem fmcpr.up outstem fmcpr.up.sm5.fsaverage.hemi ------------------------------ 1/1 sess01 1/1 sess01 001 lh --------- Tue Dec 23 11:44:51 EST 2014 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/001/masks/brain.fsaverage.lh.nii.gz does not need updating sess01 001 Update not needed 1/1 sess01 002 lh --------- Tue Dec 23 11:44:51 EST 2014 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/002/masks/brain.fsaverage.lh.nii.gz does not need updating sess01 002 Update not needed 1/1 sess01 003 lh --------- Tue Dec 23 11:44:51 EST 2014 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/003/masks/brain.fsaverage.lh.nii.gz does not need updating sess01 003 Update not needed 1/1 sess01 004 lh --------- Tue Dec 23 11:44:51 EST 2014 /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/004/masks/brain.fsaverage.lh.nii.gz does not need updating sess01 004 Update not needed Tue Dec 23 11:44:51 EST 2014 rawfunc2surf-sess completed ---------------------------------------- Started at Tue Dec 23 11:44:50 EST 2014 Ended at Tue Dec 23 11:44:51 EST 2014 preproc-sess done ------------------------------------------- /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01 Tue Dec 23 11:44:51 EST 2014 anadir = /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh ------------------------------------------ % Tue Dec 23 11:44:51 EST 2014 % /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional % workmem.sm05.lh %-------------------------------- sxa3pwd = '/autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional' sxa3cmd = '/usr/local/freesurfer/dev/fsfast/bin/selxavg3-sess -s sess01 -analysis workmem.sm05.lh' which fast_selxavg3 okfile = '/tmp/selxavg3-sess-42512.ok'; if(fast_fileexists(okfile)) delete(okfile); end monly = 0; perrun = 0; jkrun = 0; DoGLMFit = 1; DoContrasts = 1; ConList = splitstring('distractor.avg-v-base encode-v-base emot.dist-v-neut.dist emot.dist-v-base probe.avg-v-base'); DoSynth = 0; SynthNoiseAmp = 1; SynthNoiseAR1 = .3; SynthSignalAmp = 0; SynthSeed = -1; sess = '/autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01'; ReduceToMask = 1; analysis = 'workmem.sm05.lh'; flacname = ''; outtop = ''; DoFWHM = 0; MatlabSaveRes = 0; SaveResUnwhitened = 0; fast_selxavg3; if(~fast_fileexists(okfile) && ~monly); quit; end quit; ------------------------------------------ ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored. < M A T L A B (R) > Copyright 1984-2012 The MathWorks, Inc. R2012b (8.0.0.783) 64-bit (glnxa64) August 22, 2012 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional >> sxa3cmd = /usr/local/freesurfer/dev/fsfast/bin/selxavg3-sess -s sess01 -analysis workmem.sm05.lh >> /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# sess01 ############################### /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01 ------------------------- $Id: fast_selxavg3.m,v 1.110 2014/11/11 18:42:45 greve Exp $ /usr/local/freesurfer/dev/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/dev/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/dev/matlab/MRIread.m ------------------------- outtop = /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional Extension format = nii.gz 1 distractor.avg-v-base.mat 2 emot.dist-v-base.mat 3 emot.dist-v-neut.dist.mat 4 encode-v-base.mat 5 probe.avg-v-base.mat Excluding 4 points nruns = 4 autostimdur = outanadir = /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh Excluding 4 points Excluding 4 points Excluding 4 points Excluding 4 points Found 149955/163842 (91.5) voxels in mask 1 Creating Design Matrix ... creation time = 0.027 sec DoMCFit = 1 ntptot = 568, nX = 33, DOF = 535 Saving X matrix to /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/Xtmp.mat XCond = 11.8857 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.492866 (t=0.064829) 2 -0.25 -0.259072 (t=0.222602) 3 0 -0.0290439 (t=0.282461) 4 0.25 0.193784 (t=0.440175) 5 0.5 0.400223 (t=0.500189) AR1 Correction M: 0.0417295 1.11591 Computing contrast matrices OLS Beta Pass run 1 t= 0.0 reading data ... 1.59565 Global Mean 866.32 run 2 t= 3.0 reading data ... 1.51706 Global Mean 864.74 run 3 t= 2.9 reading data ... 1.63471 Global Mean 862.92 run 4 t= 2.8 reading data ... 1.56786 Global Mean 864.08 Global In-Mask Mean = 864.512 (873.344) Rescale Target = 100 RescaleFactor = 0.115672 OLS Residual Pass run 1 t= 0.0 reading data ... 1.52198 Saving rho1 run 2 t= 4.7 reading data ... 1.70546 Saving rho1 run 3 t= 4.6 reading data ... 1.55221 Saving rho1 run 4 t= 4.5 reading data ... 1.62473 Saving rho1 Smoothing ACF /usr/local/freesurfer/dev/bin/mris_fwhm --mask /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/mask.nii.gz --i /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/rho1mn.nii.gz --o /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/rho1mn.sm.nii.gz --fwhm 20.000000 --smooth-only --s fsaverage --hemi lh --sd /space/sand/1/users/zkaufman/tutorial_data/fsfast-tutorial.subjects fsaverage lh white Number of vertices 163842 Number of faces 327680 Total area 65416.984375 GroupSurface 82219.960938 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195470 Loading mask /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/mask.nii.gz Found 149955 voxels in mask Not Polynomial detrending Smoothing input by fwhm=20.000000, gstd=8.493218, niters=294 Only smoothing, so saving and exiting now Found 0 voxels with corrected AR1 > 0.90 Whitening Computing whitening matrices Alloc Sinv: 568 568 30 ... done t = 0.455351 sec seg 1 4999 nrho1 = 0.131 seg 2 4999 nrho1 = 0.246 seg 3 4999 nrho1 = 0.303 seg 4 4999 nrho1 = 0.347 seg 5 4999 nrho1 = 0.378 seg 6 4999 nrho1 = 0.400 seg 7 4999 nrho1 = 0.420 seg 8 4999 nrho1 = 0.438 seg 9 4999 nrho1 = 0.454 seg 10 4999 nrho1 = 0.469 seg 11 4999 nrho1 = 0.482 seg 12 4999 nrho1 = 0.495 seg 13 4999 nrho1 = 0.507 seg 14 4999 nrho1 = 0.517 seg 15 4999 nrho1 = 0.527 seg 16 4999 nrho1 = 0.537 seg 17 4999 nrho1 = 0.545 seg 18 4999 nrho1 = 0.552 seg 19 4999 nrho1 = 0.559 seg 20 4999 nrho1 = 0.567 seg 21 4999 nrho1 = 0.575 seg 22 4999 nrho1 = 0.583 seg 23 4999 nrho1 = 0.592 seg 24 4999 nrho1 = 0.600 seg 25 4999 nrho1 = 0.609 seg 26 4999 nrho1 = 0.620 seg 27 4999 nrho1 = 0.634 seg 28 4999 nrho1 = 0.649 seg 29 4999 nrho1 = 0.664 seg 30 4984 nrho1 = 0.693 GLS Beta Pass run 1 t= 0.0 run 2 t= 2.8 run 3 t= 5.4 run 4 t= 8.0 GLS Residual Pass run 1 t= 0.0 run 2 t= 3.6 run 3 t= 7.2 run 4 t=10.8 Found 13887 zero-valued voxels Computing contrasts Starting contrasts distractor.avg-v-base J=1 ------------- /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/distractor.avg-v-base exists, deleting Saving efficiency 33.4862 Testing Motion Correction Parameters -5.40 0.39 -0.26 -0.32 -1.44 -1.97 0.64 0.43 2.10 3.04 2.40 -0.44 -0.49 -0.46 0.65 0.45 -0.61 -0.40 emot.dist-v-base J=1 ------------- /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/emot.dist-v-base exists, deleting Saving efficiency 33.4862 Testing Motion Correction Parameters -5.40 0.39 -0.26 -0.32 -1.44 -1.97 0.64 0.43 2.10 3.04 2.40 -0.44 -0.49 -0.46 0.65 0.45 -0.61 -0.40 emot.dist-v-neut.dist J=1 ------------- /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/emot.dist-v-neut.dist exists, deleting Saving efficiency 21.8536 Testing Motion Correction Parameters -3.12 2.42 -2.34 0.05 -1.30 -1.26 -0.79 -0.75 0.39 4.67 0.12 -0.80 0.31 -0.67 -0.77 -0.72 0.81 0.77 encode-v-base J=1 ------------- /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/encode-v-base exists, deleting Saving efficiency 55.0851 Testing Motion Correction Parameters -0.73 -1.01 2.05 0.10 -0.96 -3.23 2.02 1.46 2.97 -0.26 2.40 0.52 -2.47 -1.60 2.05 1.52 -1.98 -1.41 probe.avg-v-base J=1 ------------- /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/probe.avg-v-base exists, deleting Saving efficiency 55.1902 Testing Motion Correction Parameters 0.33 -0.32 0.02 -0.96 1.67 -0.90 1.97 1.90 0.61 -0.49 -0.20 -0.33 0.89 0.15 1.94 1.93 -1.97 -1.90 Saving h.dat to /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01/bold/workmem.sm05.lh/h.dat cputime-min 1.580500 fast_selxavg3 done for /autofs/space/sand_001/users/zkaufman/tutorial_data/fsfast-functional/sess01 >> >> >> >> ------------------------------------------ Started at Tue Dec 23 11:44:49 EST 2014 Ended at Tue Dec 23 11:47:03 EST 2014 selxavg3-sess completed