Hi list, I'm running :recon-all -all -i $SUBJECTS_DIR/MPRAGE.nii.gz -subject $SUBJECTS_DIR/hptu_sub001In bold the error that I'm visualizing: Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova/Diff01Actual FREESURFER_HOME /Applications/freesurferDarwin 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 \nmri_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=0.00i_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 2013Found 1 runs/Applications/freesurfer/subjects/subject_prova/Diff01/hptu_sub001/mri/orig/001.mgzChecking for (invalid) multi-frame inputs...WARNING: only one run found. This is OK, but motioncorrection cannot be performed on one run, so I'llcopy 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 \nmri_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=0.00i_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 directionschanging 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 \nINFO: 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 \ntalairach_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 \nTalAviQA: 0.96699z-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 0.000000final 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 volumeMode: Use the information of atlas (default parms, --help for details)gcaAllocMax: node dims 64 64 64gcaAllocMax: prior dims 128 128 128gcaAllocMax: max_labels 0 *********************************************************The input file is T1.mgzThe output file is brainmask.auto.mgzWeighting the input with atlas information before watershed
********FINAL ITERATIVE TEMPLATE DEFORMATION********Compute Local values csf/grayFine 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-05l_intensity = 1.0000Aligning 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 2772Quasinewton: 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 0.000010Resulting 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-07l_intensity = 1.0000Aligning 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 312841Quasinewton: 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) = 844596.4after 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 0.000000final 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 0.039blurring input image with Gaussian with sigma=2.000...0000: dt=0.000, rms=0.876, neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 18445.328 ms0001: dt=129.472000, rms=0.781 (10.831%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19654.701 ms0002: dt=369.920000, rms=0.748 (4.319%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19650.012 ms0003: dt=129.472000, rms=0.730 (2.388%), neg=0, invalid=766gcamFindOptimalTimeStep: Complete in 19766.332 ms0004: dt=73.984000, rms=0.729 (0.156%), neg=0, invalid=7660005: dt=73.984000, rms=0.726 (0.308%), neg=0, invalid=7660006: dt=73.984000, rms=0.722 (0.547%), neg=0, invalid=7660007: dt=73.984000, rms=0.718 (0.635%), neg=0, invalid=7660008: dt=73.984000, rms=0.713 (0.737%), neg=0, invalid=766 Thanks,
Stefano
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, stdp82@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 brainBrain 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
stdp82＠virgilio.it