Those are warnings, not errors, and you can ignore them. Looks like it is still running Bruce
On Feb 4, 2013, at 5:48 PM, <std...@virgilio.it> wrote: > Hi list, > > I'm running : > recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject > $SUBJECTS_DIR/hptu_sub001 > In bold the error that I'm visualizing: > > Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff01 > Actual FREESURFER_HOME /Applications/freesurfer > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001 > \n mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz > \n > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from > /Applications/freesurfer/subjects/subject_prova/Diff01/MPRAGE.nii.gz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998454, 0.00426797, -0.0554224) > j_ras = (0.0151969, 0.980022, -0.198308) > k_ras = (-0.0534688, 0.198844, 0.978572) > writing to > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz... > #-------------------------------------------- > #@# MotionCor Mon Feb 4 20:34:08 CET 2013 > Found 1 runs > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz > Checking for (invalid) multi-frame inputs... > 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. > \n cp > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgz > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz > \n > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001 > \n mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz > --conform \n > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz > --conform > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/rawavg.mgz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998454, 0.00426797, -0.0554224) > j_ras = (0.0151969, 0.980022, -0.198308) > k_ras = (-0.0534688, 0.198844, 0.978572) > Original Data has (0.8, 2, 0.8) mm size and (320, 85, 320) voxels. > Data is conformed to 1 mm size and 256 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz... > \n mri_add_xform_to_header -c > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach.xfm > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz > > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig.mgz > \n > INFO: extension is mgz > #-------------------------------------------- > #@# Talairach Mon Feb 4 20:34:17 CET 2013 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > \n talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm \n > \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n > #-------------------------------------------- > #@# Talairach Failure Detection Mon Feb 4 20:34:49 CET 2013 > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri > \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n > talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4903, > pval=0.1531 >= threshold=0.0050) > \n awk -f /Applications/freesurfer/bin/extract_talairach_avi_QA.awk > /Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/transforms/talairach_avi.log > \n > TalAviQA: 0.96699 > z-score: -2 > #-------------------------------------------- > > 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: 008: -log(p) = > 1145838.5 tol 0.000000 > final transform: > 1.009 0.068 0.121 -29.003; > -0.086 0.984 0.166 -21.039; > -0.120 -0.163 1.074 15.915; > 0.000 0.000 0.000 1.000; > > writing output transformation to transforms/talairach_with_skull.lta... > registration took 14 minutes and 43 seconds. > \n mri_watershed -T1 -brain_atlas > /Applications/freesurfer/average/RB_all_withskull_2008-03-26.gca > transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n > > Mode: T1 normalized volume > Mode: Use the information of atlas (default parms, --help for > details) > gcaAllocMax: node dims 64 64 64 > gcaAllocMax: prior dims 128 128 128 > gcaAllocMax: max_labels 0 > > ********************************************************* > The input file is T1.mgz > The output file is brainmask.auto.mgz > Weighting the input with atlas information before watershed > > > ********FINAL ITERATIVE TEMPLATE DEFORMATION******** > Compute Local values csf/gray > Fine Segmentation...38 iterations > > mri_strip_skull: done peeling brain > > Brain Size = 1931109 voxels, voxel volume = 1.000 mm3 > = 1931109 mmm3 = 1931.109 cm3 > > > > dt = 5.00e-06, momentum=0.80, tol=1.00e-05 > l_intensity = 1.0000 > Aligning input volume to GCA... > Transform matrix > 0.97624 0.08548 0.05852 -18.68727; > -0.08544 1.05705 -0.07489 3.31129; > -0.06540 0.06526 0.99572 -9.04030; > 0.00000 0.00000 0.00000 1.00000; > nsamples 2772 > Quasinewton: input matrix > 0.97624 0.08548 0.05852 -18.68727; > -0.08544 1.05705 -0.07489 3.31129; > -0.06540 0.06526 0.99572 -9.04030; > 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: 007: -log(p) = 7093.2 > tol 0.000010 > Resulting transform: > 0.976 0.085 0.059 -18.687; > -0.085 1.057 -0.075 3.311; > -0.065 0.065 0.996 -9.040; > 0.000 0.000 0.000 1.000; > ************************************************** > EM alignment process ... > Computing final MAP estimate using 312841 samples. > ************************************************** > dt = 5.00e-06, momentum=0.80, tol=1.00e-07 > l_intensity = 1.0000 > Aligning input volume to GCA... > Transform matrix > 0.97624 0.08548 0.05852 -18.68727; > -0.08544 1.05705 -0.07489 3.31129; > -0.06540 0.06526 0.99572 -9.04030; > 0.00000 0.00000 0.00000 1.00000; > nsamples 312841 > Quasinewton: input matrix > 0.97624 0.08548 0.05852 -18.68727; > -0.08544 1.05705 -0.07489 3.31129; > -0.06540 0.06526 0.99572 -9.04030; > 0.00000 0.00000 0.00000 1.00000; > dfp_em_step_func: 008: -log(p) = 844596.4 > after pass:transform: ( 0.98, 0.09, 0.06, -18.69) > ( -0.08, 1.06, -0.07, 3.31) > ( -0.07, 0.06, 1.00, -9.04) > 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 TOLERANCESpass 2 through quasi-newton minimization... > 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: 010: -log(p) = > 844596.4 tol 0.000000 > final transform: > 0.984 0.092 0.065 -18.687; > -0.079 1.063 -0.069 3.311; > -0.066 0.064 0.996 -9.040; > 0.000 0.000 0.000 1.000; > > > > **************** pass 1 of 1 ************************ > setting smoothness coefficient to 0.039 > blurring input image with Gaussian with sigma=2.000... > 0000: dt=0.000, rms=0.876, neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 18445.328 ms > 0001: dt=129.472000, rms=0.781 (10.831%), neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 19654.701 ms > 0002: dt=369.920000, rms=0.748 (4.319%), neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 19650.012 ms > 0003: dt=129.472000, rms=0.730 (2.388%), neg=0, invalid=766 > gcamFindOptimalTimeStep: Complete in 19766.332 ms > 0004: dt=73.984000, rms=0.729 (0.156%), neg=0, invalid=766 > 0005: dt=73.984000, rms=0.726 (0.308%), neg=0, invalid=766 > 0006: dt=73.984000, rms=0.722 (0.547%), neg=0, invalid=766 > 0007: dt=73.984000, rms=0.718 (0.635%), neg=0, invalid=766 > 0008: dt=73.984000, rms=0.713 (0.737%), neg=0, invalid=766 > > Thanks, > > > Stefano > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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