Logfile for infant_recon_all Mon Sep 21 11:18:40 SAST 2020 --s 002B --age 0 $Id: infant_recon_all,v 1.00 2017/01/10 12:27:40 lzollei Exp $ buddha Linux buddha 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux INPUT FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz mri_nu_correct.mni --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz --n 2 /usr/bin/bc /home/fleur /usr/local/infantFS/bin/mri_nu_correct.mni --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux buddha 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Mon Sep 21 11:18:40 SAST 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.59646 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /home/fleur mri_convert /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc -odt float mri_convert /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc -odt float $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz... TR=2540.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (0.0139622, -0, -0.999903) k_ras = (-0.999903, -0, -0.0139622) changing data type from short to float (noscale = 0)... writing to /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Sep 21 11:18:40 SAST 2020 nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu1.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.59646/0/ [fleur@buddha:/home/fleur/] [2020-09-21 11:18:40] running: /usr/local/infantFS/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /dev/shm/tmp.mri_nu_correct.mni.59646/0/ /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu1.imp Processing:.................................................Done 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Processing:.................................................Done Processing:.................................................Done Number of iterations: 33 CV of field change: 0.000953628 -------------------------------------------------------- Iteration 2 Mon Sep 21 11:18:50 SAST 2020 nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.59646/nu1.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.59646/1/ [fleur@buddha:/home/fleur/] [2020-09-21 11:18:50] running: /usr/local/infantFS/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /dev/shm/tmp.mri_nu_correct.mni.59646/1/ /dev/shm/tmp.mri_nu_correct.mni.59646/nu1.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.imp Processing:.................................................Done Processing:.................................................Done 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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: 28 CV of field change: 0.000989219 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/fleur cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz sysname Linux hostname buddha machine x86_64 user fleur input /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 5308416 values in range Counting number of voxels in first frame Found 5308415 voxels in final mask Count: 5308415 5308415.000000 5308416 99.999981 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --sum /dev/shm/tmp.mri_nu_correct.mni.59646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.59646/input.mean.dat $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --sum /dev/shm/tmp.mri_nu_correct.mni.59646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.59646/input.mean.dat sysname Linux hostname buddha machine x86_64 user fleur whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz Loading /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to /dev/shm/tmp.mri_nu_correct.mni.59646/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc --sum /dev/shm/tmp.mri_nu_correct.mni.59646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.59646/output.mean.dat $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc --sum /dev/shm/tmp.mri_nu_correct.mni.59646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.59646/output.mean.dat sysname Linux hostname buddha machine x86_64 user fleur whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to /dev/shm/tmp.mri_nu_correct.mni.59646/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc mul 1.01379943233959615991 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc' (type = MINC ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz --like /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz --like /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (0.0139622, -0, -0.999903) k_ras = (-0.999903, -0, -0.0139622) INFO: transform src into the like-volume: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 79.2454 1000, flo=0, fhi=0.999, dest_type=0 writing to /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz... Mon Sep 21 11:19:05 SAST 2020 mri_nu_correct.mni done NU FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz mri_convert --conform-dc /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz mri_convert --conform-dc /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz... TR=2540.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (0.0139622, -0, -0.999903) k_ras = (-0.999903, -0, -0.0139622) keeping DC 2 1 0 ostr PIL, width 256, size 1 K --------------- 0.00000 0.00000 1.00000 56.00000; 0.00000 1.00000 0.00000 32.00000; -1.00000 0.00000 0.00000 224.00000; 0.00000 0.00000 0.00000 1.00000; Kinv --------------- 0.00000 0.00000 -1.00000 224.00000; 0.00000 1.00000 0.00000 -32.00000; 1.00000 0.00000 0.00000 -56.00000; 0.00000 0.00000 0.00000 1.00000; Smri --------------- -0.00000 0.01396 -0.99990 73.44720; -1.00000 -0.00000 -0.00000 64.08650; 0.00000 -0.99990 -0.01396 109.13969; 0.00000 0.00000 0.00000 1.00000; Stemp --------------- -0.99990 0.01396 0.00000 128.99495; 0.00000 0.00000 1.00000 -159.91350; -0.01396 -0.99990 0.00000 141.91846; 0.00000 0.00000 0.00000 1.00000; ---------------------- Reslicing using trilinear interpolation writing to /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz... CONFORMED FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz sscnn_skullstrip -i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz -o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/sscnn -c t1w --gpu -1 2020-09-21 11:19:14.016922: I tensorflow/core/platform/cpu_feature_guard.cc:137] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA Using TensorFlow backend. /usr/local/infantFS/python/scripts/sscnn_skullstrip:93: UserWarning: The argument 'neighbors' is deprecated and will be removed in scikit-image 0.18, use 'connectivity' instead. For neighbors=8, use connectivity=3 label_img_data = skimage.measure.label(np.int8(hard_img_data), neighbors=8) mri_convert --conform /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg/002B/work/mprage.nu.conf.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/sscnn/conformed.nii.gz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg/002B/work/mprage.nu.conf.nii.gz... TR=2540.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999903, 0, -0.0139622) j_ras = (0.0139622, 0, -0.999903) k_ras = (0, 1, 0) Reslicing using trilinear interpolation writing to /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/sscnn/conformed.nii.gz... [, , , , , , , , , , , ] 12 Loaded model file: /usr/local/infantFS/average/sscnn_skullstripping/cor_sscnn.h5 1.3144329896907216 Image max is :1.3144329896907216 [, , , , , , , , , , , ] 12 Loaded model file: /usr/local/infantFS/average/sscnn_skullstripping/ax_sscnn.h5 1.3144329896907216 Image max is :1.3144329896907216 [, , , , , , , , , , , ] 12 Loaded model file: /usr/local/infantFS/average/sscnn_skullstripping/sag_sscnn.h5 1.3144329896907216 Image max is :1.3144329896907216 mv /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/sscnn/sscnn_skullstrip.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.mask.nii.gz MASK FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.mask.nii.gz mri_mask /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.mask.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz DoAbs = 0 MRImask(): AllowDiffGeom = 1 INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz...done. MASKED FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz MASKED FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz find_neighbors_byAge_extended.csh --age 0 --trages 9 7 6 5 18 12 0 0 3 8 10 10 18 4 2 14 3 16 0 12 0 15 5 17 16 0 --trpool Template1 Template2 Template3 Template4 Template5 Template6 Template7 Template8 Template9 Template10 Template11 Template12 Template13 Template14 Template15 Template16 Template17 Template18 Template19 Template20 Template21 Template22 Template23 Template24 Template25 Template26 --k 4 --outfile /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/selectedtrainingsubjects.txt --gmwm --gmwmtrpool Template5 Template6 Template8 Template10 Template13 Template18 Template20 Template22 Template26 --gmwmtrages 18 12 0 8 18 16 12 15 0 Template7 Template8 Template19 Template21 reg_aladin -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.affine.txt -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.affine.nii.gz -voff Padding value here nan reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] Command line: [reg_f3d] reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] OpenMP is used with 32 thread(s) [NiftyReg F3D] *********************************************************** [NiftyReg F3D] INPUT PARAMETERS [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Reference image: [NiftyReg F3D] * name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38] [NiftyReg F3D] * binnining size for timepoint 0/0: 64 [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] [NiftyReg F3D] Floating image: [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] * name: /usr/local/infantFS/average/CNYBCH/Template7/norm.nii.gz [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38] [NiftyReg F3D] * binnining size for timepoint 0/0: 64 [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] [NiftyReg F3D] Warped image padding value: nan [NiftyReg F3D] [NiftyReg F3D] Level number: 3 [NiftyReg F3D] [NiftyReg F3D] Maximum iteration number during the last level: 150 [NiftyReg F3D] [NiftyReg F3D] Final spacing in mm: -5 -5 -5 [NiftyReg F3D] [NiftyReg F3D] The NMI is used as a similarity measure. [NiftyReg F3D] Similarity measure term weight: 0.989 [NiftyReg F3D] [NiftyReg F3D] Bending energy penalty term weight: 0.001 [NiftyReg F3D] [NiftyReg F3D] Linear energy penalty term weight: 0.01 [NiftyReg F3D] [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 1 / 3 [NiftyReg F3D] Maximum iteration number: 600 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1 [NiftyReg F3D] * image spacing: 4 x 4 x 4 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1 [NiftyReg F3D] * image spacing: 4 x 4 x 4 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 16 x 16 x 16 [NiftyReg F3D] * image spacing: 20 x 20 x 20 mm [NiftyReg F3D] Initial objective function: 1.07208 = (wSIM)1.07208 - (wBE)5.57221e-14 - (wLE)1.60795e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [10] Current objective function: 1.07621 = (wSIM)1.07621 - (wBE)5.02e-07 - (wLE)1.67e-06 [+ 6 mm] [NiftyReg F3D] [19] Current objective function: 1.07649 = (wSIM)1.07649 - (wBE)1.17e-06 - (wLE)1.73e-06 [+ 2 mm] [NiftyReg F3D] [28] Current objective function: 1.07727 = (wSIM)1.07727 - (wBE)1.57e-06 - (wLE)1.75e-06 [+ 2.06875 mm] [NiftyReg F3D] [36] Current objective function: 1.07772 = (wSIM)1.07773 - (wBE)1.78e-06 - (wLE)1.75e-06 [+ 2.06875 mm] [NiftyReg F3D] [44] Current objective function: 1.07784 = (wSIM)1.07784 - (wBE)2.13e-06 - (wLE)1.76e-06 [+ 1.03437 mm] [NiftyReg F3D] [54] Current objective function: 1.07836 = (wSIM)1.07836 - (wBE)2.74e-06 - (wLE)1.80e-06 [+ 1.75973 mm] [NiftyReg F3D] [64] Current objective function: 1.07854 = (wSIM)1.07854 - (wBE)3.52e-06 - (wLE)1.83e-06 [+ 1.18837 mm] [NiftyReg F3D] [73] Current objective function: 1.079 = (wSIM)1.07901 - (wBE)4.56e-06 - (wLE)1.87e-06 [+ 1.27007 mm] [NiftyReg F3D] [82] Current objective function: 1.07941 = (wSIM)1.07942 - (wBE)5.29e-06 - (wLE)1.89e-06 [+ 1.35739 mm] [NiftyReg F3D] [90] Current objective function: 1.07954 = (wSIM)1.07954 - (wBE)5.70e-06 - (wLE)1.91e-06 [+ 0.678693 mm] [NiftyReg F3D] [97] Current objective function: 1.07962 = (wSIM)1.07962 - (wBE)6.24e-06 - (wLE)1.93e-06 [+ 0.678693 mm] [NiftyReg F3D] [106] Current objective function: 1.07974 = (wSIM)1.07975 - (wBE)6.80e-06 - (wLE)1.96e-06 [+ 1.1033 mm] [NiftyReg F3D] [113] Current objective function: 1.07981 = (wSIM)1.07982 - (wBE)7.17e-06 - (wLE)1.97e-06 [+ 0.55165 mm] [NiftyReg F3D] [119] Current objective function: 1.07989 = (wSIM)1.0799 - (wBE)7.52e-06 - (wLE)1.99e-06 [+ 0.55165 mm] [NiftyReg F3D] [128] Current objective function: 1.08004 = (wSIM)1.08005 - (wBE)8.03e-06 - (wLE)2.01e-06 [+ 0.938495 mm] [NiftyReg F3D] [135] Current objective function: 1.08009 = (wSIM)1.0801 - (wBE)8.63e-06 - (wLE)2.03e-06 [+ 0.938495 mm] [NiftyReg F3D] [142] Current objective function: 1.08012 = (wSIM)1.08013 - (wBE)9.24e-06 - (wLE)2.05e-06 [+ 0.469247 mm] [NiftyReg F3D] [149] Current objective function: 1.08026 = (wSIM)1.08027 - (wBE)9.60e-06 - (wLE)2.06e-06 [+ 0.985419 mm] [NiftyReg F3D] [156] Current objective function: 1.08026 = (wSIM)1.08027 - (wBE)9.96e-06 - (wLE)2.07e-06 [+ 0.49271 mm] [NiftyReg F3D] [162] Current objective function: 1.08044 = (wSIM)1.08045 - (wBE)1.02e-05 - (wLE)2.08e-06 [+ 0.49271 mm] [NiftyReg F3D] [168] Current objective function: 1.08045 = (wSIM)1.08046 - (wBE)1.04e-05 - (wLE)2.09e-06 [+ 0.49271 mm] [NiftyReg F3D] [174] Current objective function: 1.08047 = (wSIM)1.08048 - (wBE)1.05e-05 - (wLE)2.09e-06 [+ 0.246355 mm] [NiftyReg F3D] [180] Current objective function: 1.08052 = (wSIM)1.08053 - (wBE)1.06e-05 - (wLE)2.10e-06 [+ 0.38185 mm] [NiftyReg F3D] [185] Current objective function: 1.08052 = (wSIM)1.08053 - (wBE)1.06e-05 - (wLE)2.10e-06 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 2 / 3 [NiftyReg F3D] Maximum iteration number: 300 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1 [NiftyReg F3D] * image spacing: 2 x 2 x 2 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1 [NiftyReg F3D] * image spacing: 2 x 2 x 2 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 29 x 29 x 29 [NiftyReg F3D] * image spacing: 10 x 10 x 10 mm [NiftyReg F3D] Initial objective function: 1.06405 = (wSIM)1.06406 - (wBE)1.02817e-05 - (wLE)8.06882e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [10] Current objective function: 1.06482 = (wSIM)1.06484 - (wBE)1.24e-05 - (wLE)8.13e-06 [+ 3 mm] [NiftyReg F3D] [19] Current objective function: 1.06525 = (wSIM)1.06528 - (wBE)1.84e-05 - (wLE)8.36e-06 [+ 2 mm] [NiftyReg F3D] [29] Current objective function: 1.06571 = (wSIM)1.06574 - (wBE)2.41e-05 - (wLE)8.59e-06 [+ 2.25 mm] [NiftyReg F3D] [38] Current objective function: 1.06579 = (wSIM)1.06584 - (wBE)3.29e-05 - (wLE)8.92e-06 [+ 2 mm] [NiftyReg F3D] [49] Current objective function: 1.06618 = (wSIM)1.06623 - (wBE)3.98e-05 - (wLE)9.13e-06 [+ 2.15937 mm] [NiftyReg F3D] [58] Current objective function: 1.06643 = (wSIM)1.06648 - (wBE)4.94e-05 - (wLE)9.42e-06 [+ 2 mm] [NiftyReg F3D] [67] Current objective function: 1.06646 = (wSIM)1.06654 - (wBE)6.44e-05 - (wLE)9.91e-06 [+ 2 mm] [NiftyReg F3D] [77] Current objective function: 1.06674 = (wSIM)1.06682 - (wBE)7.47e-05 - (wLE)1.02e-05 [+ 2.25 mm] [NiftyReg F3D] [86] Current objective function: 1.06684 = (wSIM)1.06693 - (wBE)8.23e-05 - (wLE)1.04e-05 [+ 1 mm] [NiftyReg F3D] [94] Current objective function: 1.06693 = (wSIM)1.06703 - (wBE)8.70e-05 - (wLE)1.05e-05 [+ 1 mm] [NiftyReg F3D] [102] Current objective function: 1.06694 = (wSIM)1.06705 - (wBE)9.46e-05 - (wLE)1.08e-05 [+ 1 mm] [NiftyReg F3D] [113] Current objective function: 1.06709 = (wSIM)1.0672 - (wBE)9.68e-05 - (wLE)1.08e-05 [+ 1.62562 mm] [NiftyReg F3D] [123] Current objective function: 1.06711 = (wSIM)1.06722 - (wBE)9.94e-05 - (wLE)1.09e-05 [+ 0.462287 mm] [NiftyReg F3D] [131] Current objective function: 1.06717 = (wSIM)1.06729 - (wBE)1.03e-04 - (wLE)1.10e-05 [+ 0.970803 mm] [NiftyReg F3D] [142] Current objective function: 1.06718 = (wSIM)1.0673 - (wBE)1.09e-04 - (wLE)1.11e-05 [+ 0.588853 mm] [NiftyReg F3D] [152] Current objective function: 1.06724 = (wSIM)1.06737 - (wBE)1.12e-04 - (wLE)1.12e-05 [+ 0.795319 mm] [NiftyReg F3D] [161] Current objective function: 1.06725 = (wSIM)1.06738 - (wBE)1.15e-04 - (wLE)1.13e-05 [+ 0.452338 mm] [NiftyReg F3D] [169] Current objective function: 1.06729 = (wSIM)1.06742 - (wBE)1.19e-04 - (wLE)1.14e-05 [+ 0.576731 mm] [NiftyReg F3D] [178] Current objective function: 1.06734 = (wSIM)1.06747 - (wBE)1.24e-04 - (wLE)1.15e-05 [+ 0.656031 mm] [NiftyReg F3D] [186] Current objective function: 1.06735 = (wSIM)1.0675 - (wBE)1.33e-04 - (wLE)1.18e-05 [+ 0.656031 mm] [NiftyReg F3D] [194] Current objective function: 1.06737 = (wSIM)1.06753 - (wBE)1.42e-04 - (wLE)1.21e-05 [+ 0.656031 mm] [NiftyReg F3D] [202] Current objective function: 1.06743 = (wSIM)1.06759 - (wBE)1.50e-04 - (wLE)1.23e-05 [+ 0.656031 mm] [NiftyReg F3D] [210] Current objective function: 1.06745 = (wSIM)1.06763 - (wBE)1.62e-04 - (wLE)1.26e-05 [+ 0.656031 mm] [NiftyReg F3D] [218] Current objective function: 1.06753 = (wSIM)1.06771 - (wBE)1.68e-04 - (wLE)1.28e-05 [+ 0.656031 mm] [NiftyReg F3D] [228] Current objective function: 1.06753 = (wSIM)1.06772 - (wBE)1.78e-04 - (wLE)1.31e-05 [+ 0.725939 mm] [NiftyReg F3D] [236] Current objective function: 1.06753 = (wSIM)1.06774 - (wBE)1.88e-04 - (wLE)1.34e-05 [+ 0.725939 mm] [NiftyReg F3D] [244] Current objective function: 1.06755 = (wSIM)1.06777 - (wBE)2.00e-04 - (wLE)1.38e-05 [+ 0.725939 mm] [NiftyReg F3D] [253] Current objective function: 1.06758 = (wSIM)1.0678 - (wBE)2.13e-04 - (wLE)1.42e-05 [+ 0.750893 mm] [NiftyReg F3D] [261] Current objective function: 1.06764 = (wSIM)1.06788 - (wBE)2.23e-04 - (wLE)1.45e-05 [+ 0.750893 mm] [NiftyReg F3D] [269] Current objective function: 1.06766 = (wSIM)1.0679 - (wBE)2.30e-04 - (wLE)1.47e-05 [+ 0.375447 mm] [NiftyReg F3D] [278] Current objective function: 1.06767 = (wSIM)1.06792 - (wBE)2.35e-04 - (wLE)1.49e-05 [+ 0.319364 mm] [NiftyReg F3D] [286] Current objective function: 1.06769 = (wSIM)1.06794 - (wBE)2.38e-04 - (wLE)1.50e-05 [+ 0.341321 mm] [NiftyReg F3D] [293] Current objective function: 1.0677 = (wSIM)1.06795 - (wBE)2.40e-04 - (wLE)1.51e-05 [+ 0.17066 mm] [NiftyReg F3D] [299] Current objective function: 1.0677 = (wSIM)1.06795 - (wBE)2.41e-04 - (wLE)1.51e-05 [+ 0.0853302 mm] [NiftyReg F3D] [300] Current objective function: 1.0677 = (wSIM)1.06795 - (wBE)2.41e-04 - (wLE)1.51e-05 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 3 / 3 [NiftyReg F3D] Maximum iteration number: 150 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 55 x 55 x 55 [NiftyReg F3D] * image spacing: 5 x 5 x 5 mm [NiftyReg F3D] Initial objective function: 1.05466 = (wSIM)1.05489 - (wBE)0.000182728 - (wLE)4.84044e-05 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [11] Current objective function: 1.05491 = (wSIM)1.05522 - (wBE)2.61e-04 - (wLE)5.14e-05 [+ 2.5 mm] [NiftyReg F3D] [21] Current objective function: 1.05504 = (wSIM)1.05549 - (wBE)3.94e-04 - (wLE)5.57e-05 [+ 1.5 mm] [NiftyReg F3D] [30] Current objective function: 1.05504 = (wSIM)1.05565 - (wBE)5.50e-04 - (wLE)6.04e-05 [+ 1 mm] [NiftyReg F3D] [39] Current objective function: 1.05506 = (wSIM)1.05573 - (wBE)6.02e-04 - (wLE)6.19e-05 [+ 1 mm] [NiftyReg F3D] [47] Current objective function: 1.05506 = (wSIM)1.05573 - (wBE)6.02e-04 - (wLE)6.19e-05 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [reg_f3d] Registration performed in 0 min 33 sec [reg_f3d] Have a good day ! reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz -inter 0 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Command line: reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz -inter 0 Parameters Reference image name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm Floating image name: /usr/local/infantFS/average/CNYBCH/Template7/manualseg.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * [NiftyReg] Resampled image has been saved: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz reg_aladin -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.affine.txt -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.affine.nii.gz -voff Padding value here nan reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] Command line: [reg_f3d] reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] OpenMP is used with 32 thread(s) [NiftyReg F3D] *********************************************************** [NiftyReg F3D] INPUT PARAMETERS [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Reference image: [NiftyReg F3D] * name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38] [NiftyReg F3D] * binnining size for timepoint 0/0: 64 [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] [NiftyReg F3D] Floating image: [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] * name: /usr/local/infantFS/average/CNYBCH/Template8/norm.nii.gz [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38] [NiftyReg F3D] * binnining size for timepoint 0/0: 64 [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] [NiftyReg F3D] Warped image padding value: nan [NiftyReg F3D] [NiftyReg F3D] Level number: 3 [NiftyReg F3D] [NiftyReg F3D] Maximum iteration number during the last level: 150 [NiftyReg F3D] [NiftyReg F3D] Final spacing in mm: -5 -5 -5 [NiftyReg F3D] [NiftyReg F3D] The NMI is used as a similarity measure. [NiftyReg F3D] Similarity measure term weight: 0.989 [NiftyReg F3D] [NiftyReg F3D] Bending energy penalty term weight: 0.001 [NiftyReg F3D] [NiftyReg F3D] Linear energy penalty term weight: 0.01 [NiftyReg F3D] [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 1 / 3 [NiftyReg F3D] Maximum iteration number: 600 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1 [NiftyReg F3D] * image spacing: 4 x 4 x 4 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1 [NiftyReg F3D] * image spacing: 4 x 4 x 4 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 16 x 16 x 16 [NiftyReg F3D] * image spacing: 20 x 20 x 20 mm [NiftyReg F3D] Initial objective function: 1.06902 = (wSIM)1.06902 - (wBE)6.60901e-14 - (wLE)5.1736e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [10] Current objective function: 1.07304 = (wSIM)1.07305 - (wBE)1.46e-06 - (wLE)5.28e-06 [+ 8 mm] [NiftyReg F3D] [19] Current objective function: 1.07379 = (wSIM)1.0738 - (wBE)3.63e-06 - (wLE)5.41e-06 [+ 4 mm] [NiftyReg F3D] [28] Current objective function: 1.07416 = (wSIM)1.07417 - (wBE)5.10e-06 - (wLE)5.46e-06 [+ 2 mm] [NiftyReg F3D] [37] Current objective function: 1.0756 = (wSIM)1.07561 - (wBE)5.76e-06 - (wLE)5.40e-06 [+ 4.2 mm] [NiftyReg F3D] [47] Current objective function: 1.0763 = (wSIM)1.07631 - (wBE)6.47e-06 - (wLE)5.37e-06 [+ 2.06875 mm] [NiftyReg F3D] [56] Current objective function: 1.07741 = (wSIM)1.07742 - (wBE)6.65e-06 - (wLE)5.38e-06 [+ 3.20656 mm] [NiftyReg F3D] [64] Current objective function: 1.07741 = (wSIM)1.07742 - (wBE)6.65e-06 - (wLE)5.38e-06 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 2 / 3 [NiftyReg F3D] Maximum iteration number: 300 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1 [NiftyReg F3D] * image spacing: 2 x 2 x 2 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1 [NiftyReg F3D] * image spacing: 2 x 2 x 2 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 29 x 29 x 29 [NiftyReg F3D] * image spacing: 10 x 10 x 10 mm [NiftyReg F3D] Initial objective function: 1.06224 = (wSIM)1.06227 - (wBE)6.72245e-06 - (wLE)1.97996e-05 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [11] Current objective function: 1.06359 = (wSIM)1.06361 - (wBE)7.71e-06 - (wLE)1.97e-05 [+ 3.06875 mm] [NiftyReg F3D] [22] Current objective function: 1.06437 = (wSIM)1.06441 - (wBE)1.16e-05 - (wLE)1.97e-05 [+ 5 mm] [NiftyReg F3D] [33] Current objective function: 1.06484 = (wSIM)1.06488 - (wBE)1.94e-05 - (wLE)1.99e-05 [+ 2.6375 mm] [NiftyReg F3D] [43] Current objective function: 1.06538 = (wSIM)1.06543 - (wBE)2.88e-05 - (wLE)2.01e-05 [+ 2.25 mm] [NiftyReg F3D] [53] Current objective function: 1.06589 = (wSIM)1.06595 - (wBE)3.61e-05 - (wLE)2.03e-05 [+ 3 mm] [NiftyReg F3D] [62] Current objective function: 1.06615 = (wSIM)1.06622 - (wBE)4.56e-05 - (wLE)2.06e-05 [+ 2 mm] [NiftyReg F3D] [71] Current objective function: 1.06624 = (wSIM)1.06632 - (wBE)6.16e-05 - (wLE)2.11e-05 [+ 2 mm] [NiftyReg F3D] [80] Current objective function: 1.06634 = (wSIM)1.06645 - (wBE)8.24e-05 - (wLE)2.16e-05 [+ 2 mm] [NiftyReg F3D] [90] Current objective function: 1.0668 = (wSIM)1.06693 - (wBE)1.03e-04 - (wLE)2.21e-05 [+ 2.5 mm] [NiftyReg F3D] [99] Current objective function: 1.06697 = (wSIM)1.06711 - (wBE)1.20e-04 - (wLE)2.25e-05 [+ 2 mm] [NiftyReg F3D] [108] Current objective function: 1.06705 = (wSIM)1.06721 - (wBE)1.34e-04 - (wLE)2.28e-05 [+ 1 mm] [NiftyReg F3D] [117] Current objective function: 1.0673 = (wSIM)1.06746 - (wBE)1.39e-04 - (wLE)2.30e-05 [+ 1.275 mm] [NiftyReg F3D] [128] Current objective function: 1.06737 = (wSIM)1.06754 - (wBE)1.44e-04 - (wLE)2.31e-05 [+ 0.705434 mm] [NiftyReg F3D] [137] Current objective function: 1.06747 = (wSIM)1.06764 - (wBE)1.48e-04 - (wLE)2.32e-05 [+ 0.802431 mm] [NiftyReg F3D] [146] Current objective function: 1.06756 = (wSIM)1.06773 - (wBE)1.54e-04 - (wLE)2.33e-05 [+ 1.24377 mm] [NiftyReg F3D] [155] Current objective function: 1.06757 = (wSIM)1.06776 - (wBE)1.64e-04 - (wLE)2.36e-05 [+ 1.24377 mm] [NiftyReg F3D] [165] Current objective function: 1.06763 = (wSIM)1.06783 - (wBE)1.79e-04 - (wLE)2.40e-05 [+ 1.26514 mm] [NiftyReg F3D] [174] Current objective function: 1.06775 = (wSIM)1.06797 - (wBE)1.89e-04 - (wLE)2.42e-05 [+ 1.26514 mm] [NiftyReg F3D] [183] Current objective function: 1.06778 = (wSIM)1.06799 - (wBE)1.94e-04 - (wLE)2.44e-05 [+ 0.316286 mm] [NiftyReg F3D] [192] Current objective function: 1.06784 = (wSIM)1.06806 - (wBE)1.98e-04 - (wLE)2.45e-05 [+ 0.514163 mm] [NiftyReg F3D] [199] Current objective function: 1.06786 = (wSIM)1.06808 - (wBE)2.00e-04 - (wLE)2.46e-05 [+ 0.514163 mm] [NiftyReg F3D] [206] Current objective function: 1.06786 = (wSIM)1.06808 - (wBE)2.02e-04 - (wLE)2.46e-05 [+ 0.128541 mm] [NiftyReg F3D] [212] Current objective function: 1.06787 = (wSIM)1.0681 - (wBE)2.02e-04 - (wLE)2.46e-05 [+ 0.163889 mm] [NiftyReg F3D] [217] Current objective function: 1.06787 = (wSIM)1.0681 - (wBE)2.02e-04 - (wLE)2.46e-05 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 3 / 3 [NiftyReg F3D] Maximum iteration number: 150 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 55 x 55 x 55 [NiftyReg F3D] * image spacing: 5 x 5 x 5 mm [NiftyReg F3D] Initial objective function: 1.05542 = (wSIM)1.05566 - (wBE)0.000155494 - (wLE)8.18335e-05 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [11] Current objective function: 1.0557 = (wSIM)1.05601 - (wBE)2.32e-04 - (wLE)8.47e-05 [+ 2.25 mm] [NiftyReg F3D] [21] Current objective function: 1.05581 = (wSIM)1.05626 - (wBE)3.58e-04 - (wLE)8.87e-05 [+ 1.5 mm] [NiftyReg F3D] [30] Current objective function: 1.05584 = (wSIM)1.05641 - (wBE)4.80e-04 - (wLE)9.23e-05 [+ 1 mm] [NiftyReg F3D] [39] Current objective function: 1.05586 = (wSIM)1.05648 - (wBE)5.23e-04 - (wLE)9.36e-05 [+ 0.5 mm] [NiftyReg F3D] [46] Current objective function: 1.05586 = (wSIM)1.05648 - (wBE)5.23e-04 - (wLE)9.36e-05 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [reg_f3d] Registration performed in 0 min 27 sec [reg_f3d] Have a good day ! reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz -inter 0 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Command line: reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz -inter 0 Parameters Reference image name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm Floating image name: /usr/local/infantFS/average/CNYBCH/Template8/manualseg.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * [NiftyReg] Resampled image has been saved: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz reg_aladin -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.affine.txt -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.affine.nii.gz -voff Padding value here nan reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] Command line: [reg_f3d] reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] OpenMP is used with 32 thread(s) [NiftyReg F3D] *********************************************************** [NiftyReg F3D] INPUT PARAMETERS [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Reference image: [NiftyReg F3D] * name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38] [NiftyReg F3D] * binnining size for timepoint 0/0: 64 [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] [NiftyReg F3D] Floating image: [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] * name: /usr/local/infantFS/average/CNYBCH/Template19/norm.nii.gz [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38] [NiftyReg F3D] * binnining size for timepoint 0/0: 64 [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] [NiftyReg F3D] Warped image padding value: nan [NiftyReg F3D] [NiftyReg F3D] Level number: 3 [NiftyReg F3D] [NiftyReg F3D] Maximum iteration number during the last level: 150 [NiftyReg F3D] [NiftyReg F3D] Final spacing in mm: -5 -5 -5 [NiftyReg F3D] [NiftyReg F3D] The NMI is used as a similarity measure. [NiftyReg F3D] Similarity measure term weight: 0.989 [NiftyReg F3D] [NiftyReg F3D] Bending energy penalty term weight: 0.001 [NiftyReg F3D] [NiftyReg F3D] Linear energy penalty term weight: 0.01 [NiftyReg F3D] [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 1 / 3 [NiftyReg F3D] Maximum iteration number: 600 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1 [NiftyReg F3D] * image spacing: 4 x 4 x 4 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1 [NiftyReg F3D] * image spacing: 4 x 4 x 4 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 16 x 16 x 16 [NiftyReg F3D] * image spacing: 20 x 20 x 20 mm [NiftyReg F3D] Initial objective function: 1.0692 = (wSIM)1.0692 - (wBE)5.59997e-14 - (wLE)1.328e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [10] Current objective function: 1.07174 = (wSIM)1.07174 - (wBE)3.57e-07 - (wLE)1.36e-06 [+ 5 mm] [NiftyReg F3D] [20] Current objective function: 1.07186 = (wSIM)1.07186 - (wBE)1.03e-06 - (wLE)1.41e-06 [+ 2.1375 mm] [NiftyReg F3D] [30] Current objective function: 1.07248 = (wSIM)1.07249 - (wBE)1.61e-06 - (wLE)1.42e-06 [+ 2.43141 mm] [NiftyReg F3D] [39] Current objective function: 1.07311 = (wSIM)1.07311 - (wBE)2.05e-06 - (wLE)1.43e-06 [+ 2.43141 mm] [NiftyReg F3D] [48] Current objective function: 1.07315 = (wSIM)1.07315 - (wBE)2.32e-06 - (wLE)1.44e-06 [+ 0.607852 mm] [NiftyReg F3D] [56] Current objective function: 1.07351 = (wSIM)1.07351 - (wBE)2.68e-06 - (wLE)1.45e-06 [+ 0.94217 mm] [NiftyReg F3D] [64] Current objective function: 1.07381 = (wSIM)1.07381 - (wBE)2.92e-06 - (wLE)1.46e-06 [+ 1.20127 mm] [NiftyReg F3D] [72] Current objective function: 1.07386 = (wSIM)1.07387 - (wBE)3.22e-06 - (wLE)1.48e-06 [+ 1.20127 mm] [NiftyReg F3D] [80] Current objective function: 1.07387 = (wSIM)1.07387 - (wBE)3.74e-06 - (wLE)1.50e-06 [+ 1.20127 mm] [NiftyReg F3D] [88] Current objective function: 1.07397 = (wSIM)1.07397 - (wBE)4.57e-06 - (wLE)1.53e-06 [+ 1.20127 mm] [NiftyReg F3D] [96] Current objective function: 1.07398 = (wSIM)1.07399 - (wBE)5.95e-06 - (wLE)1.58e-06 [+ 1.20127 mm] [NiftyReg F3D] [105] Current objective function: 1.07428 = (wSIM)1.07429 - (wBE)7.33e-06 - (wLE)1.63e-06 [+ 1.28385 mm] [NiftyReg F3D] [114] Current objective function: 1.07438 = (wSIM)1.07439 - (wBE)8.43e-06 - (wLE)1.68e-06 [+ 0.730192 mm] [NiftyReg F3D] [121] Current objective function: 1.07465 = (wSIM)1.07467 - (wBE)9.18e-06 - (wLE)1.71e-06 [+ 0.730192 mm] [NiftyReg F3D] [129] Current objective function: 1.07473 = (wSIM)1.07474 - (wBE)9.23e-06 - (wLE)1.71e-06 [+ 0.830593 mm] [NiftyReg F3D] [137] Current objective function: 1.07475 = (wSIM)1.07476 - (wBE)9.25e-06 - (wLE)1.71e-06 [+ 0.264752 mm] [NiftyReg F3D] [145] Current objective function: 1.07483 = (wSIM)1.07484 - (wBE)9.20e-06 - (wLE)1.71e-06 [+ 0.716153 mm] [NiftyReg F3D] [151] Current objective function: 1.07483 = (wSIM)1.07484 - (wBE)9.20e-06 - (wLE)1.71e-06 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 2 / 3 [NiftyReg F3D] Maximum iteration number: 300 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1 [NiftyReg F3D] * image spacing: 2 x 2 x 2 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1 [NiftyReg F3D] * image spacing: 2 x 2 x 2 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 29 x 29 x 29 [NiftyReg F3D] * image spacing: 10 x 10 x 10 mm [NiftyReg F3D] Initial objective function: 1.05985 = (wSIM)1.05987 - (wBE)8.91417e-06 - (wLE)6.62404e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [10] Current objective function: 1.06056 = (wSIM)1.06058 - (wBE)9.48e-06 - (wLE)6.62e-06 [+ 2.125 mm] [NiftyReg F3D] [19] Current objective function: 1.06089 = (wSIM)1.06091 - (wBE)1.31e-05 - (wLE)6.71e-06 [+ 2 mm] [NiftyReg F3D] [29] Current objective function: 1.06141 = (wSIM)1.06144 - (wBE)1.76e-05 - (wLE)6.85e-06 [+ 2.5 mm] [NiftyReg F3D] [38] Current objective function: 1.06167 = (wSIM)1.0617 - (wBE)2.46e-05 - (wLE)7.11e-06 [+ 2 mm] [NiftyReg F3D] [47] Current objective function: 1.06185 = (wSIM)1.06189 - (wBE)3.22e-05 - (wLE)7.40e-06 [+ 1 mm] [NiftyReg F3D] [56] Current objective function: 1.06216 = (wSIM)1.06221 - (wBE)3.80e-05 - (wLE)7.56e-06 [+ 2.1 mm] [NiftyReg F3D] [65] Current objective function: 1.06231 = (wSIM)1.06236 - (wBE)4.54e-05 - (wLE)7.82e-06 [+ 2 mm] [NiftyReg F3D] [78] Current objective function: 1.06246 = (wSIM)1.06252 - (wBE)5.38e-05 - (wLE)8.09e-06 [+ 1.12736 mm] [NiftyReg F3D] [86] Current objective function: 1.0627 = (wSIM)1.06277 - (wBE)5.71e-05 - (wLE)8.19e-06 [+ 1.12736 mm] [NiftyReg F3D] [94] Current objective function: 1.06277 = (wSIM)1.06284 - (wBE)6.12e-05 - (wLE)8.34e-06 [+ 0.56368 mm] [NiftyReg F3D] [103] Current objective function: 1.06288 = (wSIM)1.06295 - (wBE)6.27e-05 - (wLE)8.40e-06 [+ 0.873704 mm] [NiftyReg F3D] [111] Current objective function: 1.0629 = (wSIM)1.06297 - (wBE)6.47e-05 - (wLE)8.47e-06 [+ 0.436852 mm] [NiftyReg F3D] [120] Current objective function: 1.06299 = (wSIM)1.06306 - (wBE)6.63e-05 - (wLE)8.51e-06 [+ 0.710157 mm] [NiftyReg F3D] [128] Current objective function: 1.063 = (wSIM)1.06307 - (wBE)6.76e-05 - (wLE)8.55e-06 [+ 0.177539 mm] [NiftyReg F3D] [135] Current objective function: 1.06303 = (wSIM)1.0631 - (wBE)6.82e-05 - (wLE)8.57e-06 [+ 0.372833 mm] [NiftyReg F3D] [142] Current objective function: 1.06303 = (wSIM)1.0631 - (wBE)6.84e-05 - (wLE)8.58e-06 [+ 0.0466041 mm] [NiftyReg F3D] [145] Current objective function: 1.06303 = (wSIM)1.0631 - (wBE)6.84e-05 - (wLE)8.58e-06 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 3 / 3 [NiftyReg F3D] Maximum iteration number: 150 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 55 x 55 x 55 [NiftyReg F3D] * image spacing: 5 x 5 x 5 mm [NiftyReg F3D] Initial objective function: 1.05125 = (wSIM)1.05134 - (wBE)5.67949e-05 - (wLE)2.94078e-05 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [13] Current objective function: 1.05151 = (wSIM)1.05164 - (wBE)9.52e-05 - (wLE)3.08e-05 [+ 3.31875 mm] [NiftyReg F3D] [23] Current objective function: 1.05169 = (wSIM)1.05195 - (wBE)2.31e-04 - (wLE)3.46e-05 [+ 2 mm] [NiftyReg F3D] [32] Current objective function: 1.05179 = (wSIM)1.05214 - (wBE)3.14e-04 - (wLE)3.67e-05 [+ 1 mm] [NiftyReg F3D] [41] Current objective function: 1.0518 = (wSIM)1.05223 - (wBE)3.88e-04 - (wLE)3.87e-05 [+ 1 mm] [NiftyReg F3D] [50] Current objective function: 1.05181 = (wSIM)1.05231 - (wBE)4.57e-04 - (wLE)4.05e-05 [+ 1 mm] [NiftyReg F3D] [59] Current objective function: 1.05183 = (wSIM)1.05235 - (wBE)4.81e-04 - (wLE)4.12e-05 [+ 0.5 mm] [NiftyReg F3D] [67] Current objective function: 1.05183 = (wSIM)1.05236 - (wBE)4.93e-04 - (wLE)4.15e-05 [+ 0.0625 mm] [NiftyReg F3D] [72] Current objective function: 1.05183 = (wSIM)1.05237 - (wBE)5.02e-04 - (wLE)4.17e-05 [+ 0.0625 mm] [NiftyReg F3D] [77] Current objective function: 1.05183 = (wSIM)1.05238 - (wBE)5.04e-04 - (wLE)4.18e-05 [+ 0.015625 mm] [NiftyReg F3D] [79] Current objective function: 1.05183 = (wSIM)1.05238 - (wBE)5.04e-04 - (wLE)4.18e-05 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [reg_f3d] Registration performed in 0 min 36 sec [reg_f3d] Have a good day ! reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz -inter 0 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Command line: reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz -inter 0 Parameters Reference image name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm Floating image name: /usr/local/infantFS/average/CNYBCH/Template19/manualseg.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * [NiftyReg] Resampled image has been saved: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz reg_aladin -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.affine.txt -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.affine.nii.gz -voff Padding value here nan reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] Command line: [reg_f3d] reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] OpenMP is used with 32 thread(s) [NiftyReg F3D] *********************************************************** [NiftyReg F3D] INPUT PARAMETERS [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Reference image: [NiftyReg F3D] * name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38] [NiftyReg F3D] * binnining size for timepoint 0/0: 64 [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] [NiftyReg F3D] Floating image: [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] * name: /usr/local/infantFS/average/CNYBCH/Template21/norm.nii.gz [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38] [NiftyReg F3D] * binnining size for timepoint 0/0: 64 [NiftyReg F3D] * gaussian smoothing sigma: 0 [NiftyReg F3D] [NiftyReg F3D] Warped image padding value: nan [NiftyReg F3D] [NiftyReg F3D] Level number: 3 [NiftyReg F3D] [NiftyReg F3D] Maximum iteration number during the last level: 150 [NiftyReg F3D] [NiftyReg F3D] Final spacing in mm: -5 -5 -5 [NiftyReg F3D] [NiftyReg F3D] The NMI is used as a similarity measure. [NiftyReg F3D] Similarity measure term weight: 0.989 [NiftyReg F3D] [NiftyReg F3D] Bending energy penalty term weight: 0.001 [NiftyReg F3D] [NiftyReg F3D] Linear energy penalty term weight: 0.01 [NiftyReg F3D] [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 1 / 3 [NiftyReg F3D] Maximum iteration number: 600 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1 [NiftyReg F3D] * image spacing: 4 x 4 x 4 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1 [NiftyReg F3D] * image spacing: 4 x 4 x 4 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 16 x 16 x 16 [NiftyReg F3D] * image spacing: 20 x 20 x 20 mm [NiftyReg F3D] Initial objective function: 1.06731 = (wSIM)1.06731 - (wBE)5.27054e-14 - (wLE)1.5447e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [11] Current objective function: 1.07087 = (wSIM)1.07087 - (wBE)9.66e-07 - (wLE)1.62e-06 [+ 6.1375 mm] [NiftyReg F3D] [20] Current objective function: 1.0713 = (wSIM)1.0713 - (wBE)2.17e-06 - (wLE)1.70e-06 [+ 2 mm] [NiftyReg F3D] [28] Current objective function: 1.07139 = (wSIM)1.0714 - (wBE)2.75e-06 - (wLE)1.73e-06 [+ 1 mm] [NiftyReg F3D] [36] Current objective function: 1.07282 = (wSIM)1.07283 - (wBE)3.20e-06 - (wLE)1.71e-06 [+ 2.1 mm] [NiftyReg F3D] [44] Current objective function: 1.07368 = (wSIM)1.07369 - (wBE)3.43e-06 - (wLE)1.70e-06 [+ 2.1 mm] [NiftyReg F3D] [52] Current objective function: 1.07402 = (wSIM)1.07403 - (wBE)3.83e-06 - (wLE)1.71e-06 [+ 2.1 mm] [NiftyReg F3D] [60] Current objective function: 1.07413 = (wSIM)1.07413 - (wBE)4.34e-06 - (wLE)1.72e-06 [+ 1.05 mm] [NiftyReg F3D] [67] Current objective function: 1.07421 = (wSIM)1.07422 - (wBE)5.39e-06 - (wLE)1.75e-06 [+ 1.05 mm] [NiftyReg F3D] [75] Current objective function: 1.07438 = (wSIM)1.07439 - (wBE)6.60e-06 - (wLE)1.78e-06 [+ 0.669375 mm] [NiftyReg F3D] [85] Current objective function: 1.07494 = (wSIM)1.07495 - (wBE)7.73e-06 - (wLE)1.81e-06 [+ 1.86634 mm] [NiftyReg F3D] [93] Current objective function: 1.07495 = (wSIM)1.07496 - (wBE)9.13e-06 - (wLE)1.85e-06 [+ 1.86634 mm] [NiftyReg F3D] [101] Current objective function: 1.07502 = (wSIM)1.07504 - (wBE)9.77e-06 - (wLE)1.87e-06 [+ 0.933171 mm] [NiftyReg F3D] [109] Current objective function: 1.07537 = (wSIM)1.07538 - (wBE)1.01e-05 - (wLE)1.87e-06 [+ 1.18979 mm] [NiftyReg F3D] [117] Current objective function: 1.07559 = (wSIM)1.0756 - (wBE)1.03e-05 - (wLE)1.87e-06 [+ 1.18979 mm] [NiftyReg F3D] [125] Current objective function: 1.07562 = (wSIM)1.07563 - (wBE)1.05e-05 - (wLE)1.87e-06 [+ 0.594897 mm] [NiftyReg F3D] [135] Current objective function: 1.07582 = (wSIM)1.07583 - (wBE)1.06e-05 - (wLE)1.87e-06 [+ 1.06156 mm] [NiftyReg F3D] [142] Current objective function: 1.07589 = (wSIM)1.0759 - (wBE)1.10e-05 - (wLE)1.87e-06 [+ 1.06156 mm] [NiftyReg F3D] [149] Current objective function: 1.07596 = (wSIM)1.07597 - (wBE)1.13e-05 - (wLE)1.88e-06 [+ 0.530778 mm] [NiftyReg F3D] [157] Current objective function: 1.07614 = (wSIM)1.07615 - (wBE)1.16e-05 - (wLE)1.88e-06 [+ 0.822706 mm] [NiftyReg F3D] [164] Current objective function: 1.07625 = (wSIM)1.07626 - (wBE)1.18e-05 - (wLE)1.89e-06 [+ 0.822706 mm] [NiftyReg F3D] [171] Current objective function: 1.07628 = (wSIM)1.0763 - (wBE)1.19e-05 - (wLE)1.89e-06 [+ 0.205676 mm] [NiftyReg F3D] [179] Current objective function: 1.07634 = (wSIM)1.07635 - (wBE)1.19e-05 - (wLE)1.89e-06 [+ 0.624794 mm] [NiftyReg F3D] [186] Current objective function: 1.07634 = (wSIM)1.07635 - (wBE)1.20e-05 - (wLE)1.89e-06 [+ 0.624794 mm] [NiftyReg F3D] [193] Current objective function: 1.07634 = (wSIM)1.07635 - (wBE)1.21e-05 - (wLE)1.89e-06 [+ 0.624794 mm] [NiftyReg F3D] [198] Current objective function: 1.07634 = (wSIM)1.07635 - (wBE)1.21e-05 - (wLE)1.89e-06 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 2 / 3 [NiftyReg F3D] Maximum iteration number: 300 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1 [NiftyReg F3D] * image spacing: 2 x 2 x 2 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1 [NiftyReg F3D] * image spacing: 2 x 2 x 2 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 29 x 29 x 29 [NiftyReg F3D] * image spacing: 10 x 10 x 10 mm [NiftyReg F3D] Initial objective function: 1.06109 = (wSIM)1.06111 - (wBE)1.16436e-05 - (wLE)7.43262e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [10] Current objective function: 1.06173 = (wSIM)1.06175 - (wBE)1.45e-05 - (wLE)7.53e-06 [+ 4 mm] [NiftyReg F3D] [20] Current objective function: 1.06238 = (wSIM)1.06242 - (wBE)2.46e-05 - (wLE)7.84e-06 [+ 3 mm] [NiftyReg F3D] [29] Current objective function: 1.06273 = (wSIM)1.06277 - (wBE)3.50e-05 - (wLE)8.15e-06 [+ 2 mm] [NiftyReg F3D] [38] Current objective function: 1.06314 = (wSIM)1.06319 - (wBE)4.38e-05 - (wLE)8.40e-06 [+ 2 mm] [NiftyReg F3D] [47] Current objective function: 1.06343 = (wSIM)1.06349 - (wBE)5.26e-05 - (wLE)8.63e-06 [+ 2 mm] [NiftyReg F3D] [56] Current objective function: 1.06369 = (wSIM)1.06376 - (wBE)6.60e-05 - (wLE)8.97e-06 [+ 2 mm] [NiftyReg F3D] [65] Current objective function: 1.06384 = (wSIM)1.06393 - (wBE)8.09e-05 - (wLE)9.39e-06 [+ 2 mm] [NiftyReg F3D] [74] Current objective function: 1.06403 = (wSIM)1.06414 - (wBE)1.02e-04 - (wLE)9.95e-06 [+ 2 mm] [NiftyReg F3D] [83] Current objective function: 1.06429 = (wSIM)1.06442 - (wBE)1.22e-04 - (wLE)1.05e-05 [+ 2 mm] [NiftyReg F3D] [92] Current objective function: 1.0644 = (wSIM)1.06455 - (wBE)1.42e-04 - (wLE)1.10e-05 [+ 1 mm] [NiftyReg F3D] [104] Current objective function: 1.06458 = (wSIM)1.06473 - (wBE)1.45e-04 - (wLE)1.11e-05 [+ 1.64642 mm] [NiftyReg F3D] [113] Current objective function: 1.06459 = (wSIM)1.06475 - (wBE)1.50e-04 - (wLE)1.12e-05 [+ 1.64642 mm] [NiftyReg F3D] [122] Current objective function: 1.06463 = (wSIM)1.0648 - (wBE)1.57e-04 - (wLE)1.14e-05 [+ 1.64642 mm] [NiftyReg F3D] [131] Current objective function: 1.06469 = (wSIM)1.06487 - (wBE)1.67e-04 - (wLE)1.17e-05 [+ 1.64642 mm] [NiftyReg F3D] [140] Current objective function: 1.06475 = (wSIM)1.06494 - (wBE)1.80e-04 - (wLE)1.20e-05 [+ 1.64642 mm] [NiftyReg F3D] [150] Current objective function: 1.06481 = (wSIM)1.06501 - (wBE)1.92e-04 - (wLE)1.24e-05 [+ 0.851509 mm] [NiftyReg F3D] [158] Current objective function: 1.06488 = (wSIM)1.06509 - (wBE)2.00e-04 - (wLE)1.26e-05 [+ 0.851509 mm] [NiftyReg F3D] [167] Current objective function: 1.06491 = (wSIM)1.06513 - (wBE)2.09e-04 - (wLE)1.29e-05 [+ 0.968591 mm] [NiftyReg F3D] [175] Current objective function: 1.06493 = (wSIM)1.06516 - (wBE)2.17e-04 - (wLE)1.31e-05 [+ 0.968591 mm] [NiftyReg F3D] [184] Current objective function: 1.06497 = (wSIM)1.06521 - (wBE)2.24e-04 - (wLE)1.33e-05 [+ 1.03518 mm] [NiftyReg F3D] [192] Current objective function: 1.06498 = (wSIM)1.06522 - (wBE)2.29e-04 - (wLE)1.35e-05 [+ 0.258795 mm] [NiftyReg F3D] [201] Current objective function: 1.06503 = (wSIM)1.06527 - (wBE)2.30e-04 - (wLE)1.35e-05 [+ 0.621756 mm] [NiftyReg F3D] [207] Current objective function: 1.06503 = (wSIM)1.06527 - (wBE)2.30e-04 - (wLE)1.35e-05 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Current level: 3 / 3 [NiftyReg F3D] Maximum iteration number: 150 [NiftyReg F3D] Current reference image [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] Current floating image [NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1 [NiftyReg F3D] * image spacing: 1 x 1 x 1 mm [NiftyReg F3D] Current control point image [NiftyReg F3D] * image dimension: 55 x 55 x 55 [NiftyReg F3D] * image spacing: 5 x 5 x 5 mm [NiftyReg F3D] Initial objective function: 1.05223 = (wSIM)1.05245 - (wBE)0.000172216 - (wLE)4.2218e-05 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [12] Current objective function: 1.05242 = (wSIM)1.05272 - (wBE)2.53e-04 - (wLE)4.52e-05 [+ 2.26719 mm] [NiftyReg F3D] [22] Current objective function: 1.05249 = (wSIM)1.05286 - (wBE)3.28e-04 - (wLE)4.77e-05 [+ 1.125 mm] [NiftyReg F3D] [31] Current objective function: 1.05249 = (wSIM)1.05298 - (wBE)4.35e-04 - (wLE)5.11e-05 [+ 1 mm] [NiftyReg F3D] [40] Current objective function: 1.05251 = (wSIM)1.05304 - (wBE)4.75e-04 - (wLE)5.23e-05 [+ 1 mm] [NiftyReg F3D] [49] Current objective function: 1.05252 = (wSIM)1.05308 - (wBE)5.04e-04 - (wLE)5.31e-05 [+ 0.25 mm] [NiftyReg F3D] [57] Current objective function: 1.05252 = (wSIM)1.05309 - (wBE)5.16e-04 - (wLE)5.35e-05 [+ 0.0796875 mm] [NiftyReg F3D] [61] Current objective function: 1.05252 = (wSIM)1.05309 - (wBE)5.16e-04 - (wLE)5.35e-05 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [reg_f3d] Registration performed in 0 min 35 sec [reg_f3d] Have a good day ! reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz -inter 0 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Command line: reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz -inter 0 Parameters Reference image name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm Floating image name: /usr/local/infantFS/average/CNYBCH/Template21/manualseg.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * [NiftyReg] Resampled image has been saved: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz TRAINING SUBJECTS LABELFUSION Template7 Template8 Template19 Template21 run_label_fusion.csh --subj 002B --regtype NIFTYREG --ts Template7 Template8 Template19 Template21 ARG Template7 Template8 Template19 Template21 ARG COUNT 4 TRAINING SUBJECTS Template7 Template8 Template19 Template21 CHECKING THE INPUTS... NUMBER OF NEIGHBORS 4 TRAINING SUBJECTS Template7 Template8 Template19 Template21 MOVED SEG FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz MOVED SEG FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz MOVED SEG FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz MOVED SEG FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz TRAININGDATA /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz OUTPUT FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.nii.gz LABELFUSION CMD mri_label_fusion -i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -s /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz -o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.nii.gz --smooth --rho .70 --beta 0.3 --bf-order 4 --max-lab 3 --unary-weight 5 --verbose -e 2 41 3 42 -e 7 46 8 47 -e 12 51 13 52 found 31 unique labels computing distance maps and prior label probabilities 1) processing /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz note: label 2 not found in volume note: label 41 not found in volume 2) processing /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz 3) processing /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz note: label 2 not found in volume note: label 41 not found in volume 4) processing /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz note: label 2 not found in volume note: label 41 not found in volume optimizing for intensity parameters and Q (E-step) running iteration 1 mean Q increment: 0.017570 mean Q increment: 0.005664 mean Q increment: 0.002564 mean Q increment: 0.001244 mean Q increment: 0.000662 mean Q increment: 0.000364 mean Q increment: 0.000209 mean Q increment: 0.000122 mean Q increment: 0.000074 max change: 84.33 running iteration 2 mean Q increment: 0.001837 mean Q increment: 0.000553 mean Q increment: 0.000233 mean Q increment: 0.000112 mean Q increment: 0.000057 max change: 61.74 running iteration 3 mean Q increment: 0.000891 mean Q increment: 0.000269 mean Q increment: 0.000115 mean Q increment: 0.000055 max change: 48.81 running iteration 4 mean Q increment: 0.000505 mean Q increment: 0.000157 mean Q increment: 0.000068 max change: 47.34 running iteration 5 mean Q increment: 0.000327 mean Q increment: 0.000105 mean Q increment: 0.000046 max change: 41.24 running iteration 6 mean Q increment: 0.000225 mean Q increment: 0.000072 max change: 32.62 running iteration 7 mean Q increment: 0.000178 mean Q increment: 0.000060 max change: 24.91 running iteration 8 mean Q increment: 0.000138 mean Q increment: 0.000047 max change: 18.96 running iteration 9 mean Q increment: 0.000110 mean Q increment: 0.000038 max change: 14.41 running iteration 10 mean Q increment: 0.000090 max change: 10.86 running iteration 11 mean Q increment: 0.000088 max change: 7.96 running iteration 12 mean Q increment: 0.000081 max change: 6.75 running iteration 13 mean Q increment: 0.000080 max change: 6.87 running iteration 14 mean Q increment: 0.000071 max change: 6.49 running iteration 15 mean Q increment: 0.000067 max change: 6.79 running iteration 16 mean Q increment: 0.000061 max change: 6.89 running iteration 17 mean Q increment: 0.000073 max change: 7.96 running iteration 18 mean Q increment: 0.000066 max change: 6.71 running iteration 19 mean Q increment: 0.000066 max change: 6.95 running iteration 20 mean Q increment: 0.000066 max change: 6.74 collecting label contributions from each atlas performing markov random field label-smoothing mri_binarize --match 2 41 --count /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.count.txt --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.nii.gz --noverbose niiRead(): detected input as 64 bit double, reading in as 32 bit float cp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.nii.gz mri_binarize --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.nii.gz --o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.nii.gz --min 1 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/fleur cmdline mri_binarize --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.nii.gz --o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.nii.gz --min 1 sysname Linux hostname buddha machine x86_64 user fleur input /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.nii.gz Binarizing based on threshold min 1 max +infinity binval 1 binvalnot 0 niiRead(): detected input as 64 bit double, reading in as 32 bit float fstart = 0, fend = 0, nframes = 1 Found 313677 values in range Counting number of voxels in first frame Found 313676 voxels in final mask Count: 313676 313676.000000 16777216 1.869655 mri_binarize done mri_distance_transform /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.nii.gz 1 3 3 /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.distmap.nii.gz mri_distance_transform