Logfile for infant_recon_all Mon 16 Sep 12:53:29 BST 2024 --s sub-01 --age 18 --outdir /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/ infant_recon_all infant-dev-4a14499 fhpc-1840 Linux fhpc-1840 6.8.0-40-generic #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux INPUT FILE /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz mri_nu_correct.mni --i /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz --o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.nii.gz --n 2 /usr/bin/bc /u/j/ms2290 /usr/local/freesurfer_infant//bin/mri_nu_correct.mni --i /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz --o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.nii.gz --n 2 nIters 2 mri_nu_correct.mni infant-dev-4a14499 Linux fhpc-1840 6.8.0-40-generic #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux Mon 16 Sep 12:53:29 BST 2024 tmpdir is /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195 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 /u/j/ms2290 mri_convert /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu0.mnc -odt float mri_convert /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu0.mnc -odt float reading from /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.987392, -0.133615, -0.0848753) j_ras = (0.136201, 0.990355, 0.0254143) k_ras = (0.080661, -0.036654, 0.996067) writing to /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon 16 Sep 12:53:29 BST 2024 nu_correct -clobber /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu0.mnc /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu1.mnc -tmpdir /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/0/ [ms2290@fhpc-1840:/u/j/ms2290/] [2024-09-16 12:53:29] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/0/ /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu0.mnc /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu1.imp Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Processing:.........................................Done Number of iterations: 34 CV of field change: 0.000956133 -------------------------------------------------------- Iteration 2 Mon 16 Sep 12:53:37 BST 2024 nu_correct -clobber /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu1.mnc /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc -tmpdir /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/1/ [ms2290@fhpc-1840:/u/j/ms2290/] [2024-09-16 12:53:37] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/1/ /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu1.mnc /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.imp 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: 11 CV of field change: 0.000979352 mri_binarize --i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc --min -1 --o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz infant-dev-4a14499 cwd /u/j/ms2290 cmdline mri_binarize --i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc --min -1 --o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz sysname Linux hostname fhpc-1840 machine x86_64 user ms2290 input /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 5898240 values in range Counting number of voxels in first frame Found 5898239 voxels in final mask Writing output to /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz Count: 5898239 5898239.000000 5898240 99.999983 mri_binarize done mri_segstats --id 1 --seg /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz --i /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz --sum /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/sum.junk --avgwf /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/input.mean.dat infant-dev-4a14499 cwd cmdline mri_segstats --id 1 --seg /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz --i /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz --sum /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/sum.junk --avgwf /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/input.mean.dat sysname Linux hostname fhpc-1840 machine x86_64 user ms2290 whitesurfname white UseRobust 0 Loading /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz Loading /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/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 /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz --i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc --sum /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/sum.junk --avgwf /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/output.mean.dat infant-dev-4a14499 cwd cmdline mri_segstats --id 1 --seg /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz --i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc --sum /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/sum.junk --avgwf /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/output.mean.dat sysname Linux hostname fhpc-1840 machine x86_64 user ms2290 whitesurfname white UseRobust 0 Loading /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/ones.mgz Loading /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/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 /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/output.mean.dat mri_segstats done mris_calc -o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc mul 1.00958017327143769917 Saving result to '/data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc' (type = MINC ) [ ok ] mri_convert /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.nii.gz --like /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz --conform mri_convert /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.nii.gz --like /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz --conform reading from /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/tmp.mri_nu_correct.mni.1070195/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.987392, -0.133615, -0.0848753) j_ras = (0.136201, 0.990355, 0.0254143) k_ras = (0.080661, -0.036654, 0.996067) INFO: transform src into the like-volume: /data/ewalton/marlene/infant_FS_testsubject/input//sub-01/mprage.nii.gz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 715.631 1000, flo=0, fhi=0.999, dest_type=0 writing to /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.nii.gz... Mon 16 Sep 12:53:44 BST 2024 mri_nu_correct.mni done NU FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.nii.gz mri_convert --conform-dc /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.nii.gz mri_convert --conform-dc /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.nii.gz reading from /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.987392, -0.133615, -0.0848753) j_ras = (0.136201, 0.990355, 0.0254143) k_ras = (0.080661, -0.036654, 0.996067) keeping DC 0 2 1 ostr RAS, width 256, size 1 K --------------- -1.00000 0.00000 0.00000 208.00000; 0.00000 0.00000 -1.00000 224.00000; 0.00000 1.00000 0.00000 32.00000; 0.00000 0.00000 0.00000 1.00000; Kinv --------------- -1.00000 -0.00000 -0.00000 208.00000; -0.00000 -0.00000 1.00000 -32.00000; -0.00000 -1.00000 -0.00000 224.00000; -0.00000 -0.00000 -0.00000 1.00000; Smri --------------- 0.98739 0.13620 0.08066 -96.22322; -0.13361 0.99036 -0.03665 -76.07434; -0.08488 0.02541 0.99607 -96.53862; 0.00000 0.00000 0.00000 1.00000; Stemp --------------- -0.98739 -0.08066 0.13620 122.86398; 0.13361 0.03665 0.99036 -143.76811; 0.08488 -0.99607 0.02541 108.11315; 0.00000 0.00000 0.00000 1.00000; ---------------------- Reslicing using trilinear interpolation writing to /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.nii.gz... CONFORMED FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.nii.gz sscnn_skullstrip -i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.nii.gz -o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/sscnn -c t1w --gpu -1 2024-09-16 12:53:47.656914: 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/freesurfer_infant//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 /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/sscnn/conformed.nii.gz reading from /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.987392, 0.133615, 0.0848753) j_ras = (-0.080661, 0.036654, -0.996067) k_ras = (0.136201, 0.990355, 0.0254143) Reslicing using trilinear interpolation writing to /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/sscnn/conformed.nii.gz... [, , , , , , , , , , , ] 12 Loaded model file: /usr/local/freesurfer_infant/average/sscnn_skullstripping/cor_sscnn.h5 1.3144329896907216 Image max is :1.3144329896907216 [, , , , , , , , , , , ] 12 Loaded model file: /usr/local/freesurfer_infant/average/sscnn_skullstripping/ax_sscnn.h5 1.3144329896907216 Image max is :1.3144329896907216 [, , , , , , , , , , , ] 12 Loaded model file: /usr/local/freesurfer_infant/average/sscnn_skullstripping/sag_sscnn.h5 1.3144329896907216 Image max is :1.3144329896907216 mv /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/sscnn/sscnn_skullstrip.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.mask.nii.gz MASK FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.mask.nii.gz mri_mask /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.mask.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz DoAbs = 0 MRImask(): AllowDiffGeom = 1 INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz...done. MASKED FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz MASKED FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz find_neighbors_byAge_extended.csh --age 18 --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 /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/selectedtrainingsubjects.txt --gmwm --gmwmtrpool Template5 Template6 Template8 Template10 Template13 Template18 Template20 Template22 Template26 --gmwmtrages 18 12 0 8 18 16 12 15 0 Template5 Template24 Template18 Template25 reg_aladin -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template5/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.affine.txt -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.affine.nii.gz -voff Padding value here nan reg_f3d -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template5/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.affine.txt -cpp /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] Command line: [reg_f3d] reg_f3d -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template5/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.affine.txt -cpp /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] OpenMP is used with 20 thread(s) [NiftyReg F3D] *********************************************************** [NiftyReg F3D] INPUT PARAMETERS [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Reference image: [NiftyReg F3D] * name: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/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/freesurfer_infant//average/CNYBCH/Template5/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: 1.11609 = (wSIM)1.1161 - (wBE)5.15162e-14 - (wLE)1.26101e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [10] Current objective function: 1.1222 = (wSIM)1.12221 - (wBE)1.37e-06 - (wLE)1.41e-06 [+ 6 mm] [NiftyReg F3D] [19] Current objective function: 1.12318 = (wSIM)1.12319 - (wBE)4.40e-06 - (wLE)1.63e-06 [+ 4 mm] [NiftyReg F3D] [28] Current objective function: 1.12478 = (wSIM)1.12479 - (wBE)7.26e-06 - (wLE)1.76e-06 [+ 4 mm] [NiftyReg F3D] [37] Current objective function: 1.12513 = (wSIM)1.12514 - (wBE)1.09e-05 - (wLE)1.90e-06 [+ 4 mm] [NiftyReg F3D] [47] Current objective function: 1.12573 = (wSIM)1.12574 - (wBE)1.35e-05 - (wLE)2.02e-06 [+ 2.1375 mm] [NiftyReg F3D] [58] Current objective function: 1.12707 = (wSIM)1.12709 - (wBE)1.55e-05 - (wLE)2.12e-06 [+ 2.47182 mm] [NiftyReg F3D] [67] Current objective function: 1.12735 = (wSIM)1.12737 - (wBE)1.73e-05 - (wLE)2.20e-06 [+ 2.47182 mm] [NiftyReg F3D] [78] Current objective function: 1.12827 = (wSIM)1.12829 - (wBE)1.85e-05 - (wLE)2.21e-06 [+ 2.73522 mm] [NiftyReg F3D] [87] Current objective function: 1.12835 = (wSIM)1.12838 - (wBE)2.03e-05 - (wLE)2.22e-06 [+ 2.73522 mm] [NiftyReg F3D] [96] Current objective function: 1.1284 = (wSIM)1.12842 - (wBE)2.10e-05 - (wLE)2.24e-06 [+ 0.341903 mm] [NiftyReg F3D] [106] Current objective function: 1.12962 = (wSIM)1.12964 - (wBE)2.01e-05 - (wLE)2.23e-06 [+ 1.48438 mm] [NiftyReg F3D] [114] Current objective function: 1.1299 = (wSIM)1.12992 - (wBE)1.99e-05 - (wLE)2.24e-06 [+ 0.74219 mm] [NiftyReg F3D] [121] Current objective function: 1.12994 = (wSIM)1.12996 - (wBE)1.99e-05 - (wLE)2.24e-06 [+ 0.74219 mm] [NiftyReg F3D] [128] Current objective function: 1.1301 = (wSIM)1.13012 - (wBE)1.99e-05 - (wLE)2.24e-06 [+ 0.74219 mm] [NiftyReg F3D] [135] Current objective function: 1.13023 = (wSIM)1.13026 - (wBE)2.00e-05 - (wLE)2.24e-06 [+ 0.74219 mm] [NiftyReg F3D] [144] Current objective function: 1.13038 = (wSIM)1.1304 - (wBE)2.05e-05 - (wLE)2.26e-06 [+ 1.61473 mm] [NiftyReg F3D] [153] Current objective function: 1.13045 = (wSIM)1.13047 - (wBE)2.11e-05 - (wLE)2.28e-06 [+ 0.862869 mm] [NiftyReg F3D] [161] Current objective function: 1.1307 = (wSIM)1.13072 - (wBE)2.22e-05 - (wLE)2.31e-06 [+ 1.81203 mm] [NiftyReg F3D] [169] Current objective function: 1.13086 = (wSIM)1.13088 - (wBE)2.35e-05 - (wLE)2.34e-06 [+ 0.906013 mm] [NiftyReg F3D] [176] Current objective function: 1.13099 = (wSIM)1.13102 - (wBE)2.52e-05 - (wLE)2.40e-06 [+ 0.906013 mm] [NiftyReg F3D] [184] Current objective function: 1.13109 = (wSIM)1.13112 - (wBE)2.88e-05 - (wLE)2.51e-06 [+ 0.968301 mm] [NiftyReg F3D] [191] Current objective function: 1.13111 = (wSIM)1.13114 - (wBE)3.25e-05 - (wLE)2.63e-06 [+ 0.968301 mm] [NiftyReg F3D] [198] Current objective function: 1.13131 = (wSIM)1.13135 - (wBE)3.56e-05 - (wLE)2.73e-06 [+ 0.968301 mm] [NiftyReg F3D] [208] Current objective function: 1.13163 = (wSIM)1.13167 - (wBE)3.96e-05 - (wLE)2.85e-06 [+ 1.30781 mm] [NiftyReg F3D] [216] Current objective function: 1.13181 = (wSIM)1.13186 - (wBE)4.15e-05 - (wLE)2.90e-06 [+ 1.30781 mm] [NiftyReg F3D] [226] Current objective function: 1.13186 = (wSIM)1.1319 - (wBE)4.34e-05 - (wLE)2.95e-06 [+ 0.79327 mm] [NiftyReg F3D] [234] Current objective function: 1.13195 = (wSIM)1.132 - (wBE)4.53e-05 - (wLE)3.01e-06 [+ 0.902344 mm] [NiftyReg F3D] [241] Current objective function: 1.13199 = (wSIM)1.13204 - (wBE)4.71e-05 - (wLE)3.06e-06 [+ 0.902344 mm] [NiftyReg F3D] [249] Current objective function: 1.13209 = (wSIM)1.13214 - (wBE)4.92e-05 - (wLE)3.12e-06 [+ 1.39863 mm] [NiftyReg F3D] [257] Current objective function: 1.13211 = (wSIM)1.13216 - (wBE)5.15e-05 - (wLE)3.18e-06 [+ 0.699317 mm] [NiftyReg F3D] [265] Current objective function: 1.13233 = (wSIM)1.13239 - (wBE)5.35e-05 - (wLE)3.24e-06 [+ 1.08394 mm] [NiftyReg F3D] [274] Current objective function: 1.13247 = (wSIM)1.13253 - (wBE)5.49e-05 - (wLE)3.28e-06 [+ 1.15846 mm] [NiftyReg F3D] [283] Current objective function: 1.13257 = (wSIM)1.13263 - (wBE)5.59e-05 - (wLE)3.32e-06 [+ 0.36926 mm] [NiftyReg F3D] [290] Current objective function: 1.13269 = (wSIM)1.13275 - (wBE)5.60e-05 - (wLE)3.32e-06 [+ 0.775445 mm] [NiftyReg F3D] [297] Current objective function: 1.13269 = (wSIM)1.13275 - (wBE)5.60e-05 - (wLE)3.32e-06 [+ 0.0484653 mm] [NiftyReg F3D] [299] Current objective function: 1.13269 = (wSIM)1.13275 - (wBE)5.60e-05 - (wLE)3.32e-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: 1.1096 = (wSIM)1.10967 - (wBE)5.26255e-05 - (wLE)1.47438e-05 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [11] Current objective function: 1.11098 = (wSIM)1.11105 - (wBE)5.62e-05 - (wLE)1.49e-05 [+ 4.03125 mm] [NiftyReg F3D] [22] Current objective function: 1.11238 = (wSIM)1.11246 - (wBE)7.18e-05 - (wLE)1.55e-05 [+ 6 mm] [NiftyReg F3D] [32] Current objective function: 1.11316 = (wSIM)1.11327 - (wBE)9.57e-05 - (wLE)1.63e-05 [+ 4 mm] [NiftyReg F3D] [41] Current objective function: 1.11346 = (wSIM)1.1136 - (wBE)1.23e-04 - (wLE)1.72e-05 [+ 1 mm] [NiftyReg F3D] [53] Current objective function: 1.1144 = (wSIM)1.11455 - (wBE)1.37e-04 - (wLE)1.77e-05 [+ 2.15861 mm] [NiftyReg F3D] [62] Current objective function: 1.115 = (wSIM)1.11517 - (wBE)1.50e-04 - (wLE)1.81e-05 [+ 2 mm] [NiftyReg F3D] [71] Current objective function: 1.11543 = (wSIM)1.11562 - (wBE)1.70e-04 - (wLE)1.88e-05 [+ 2 mm] [NiftyReg F3D] [82] Current objective function: 1.11595 = (wSIM)1.11616 - (wBE)1.89e-04 - (wLE)1.94e-05 [+ 2.56875 mm] [NiftyReg F3D] [93] Current objective function: 1.11634 = (wSIM)1.11657 - (wBE)2.15e-04 - (wLE)2.03e-05 [+ 2.28437 mm] [NiftyReg F3D] [102] Current objective function: 1.11636 = (wSIM)1.11665 - (wBE)2.71e-04 - (wLE)2.23e-05 [+ 2 mm] [NiftyReg F3D] [112] Current objective function: 1.11689 = (wSIM)1.11724 - (wBE)3.26e-04 - (wLE)2.43e-05 [+ 2.5 mm] [NiftyReg F3D] [121] Current objective function: 1.117 = (wSIM)1.11743 - (wBE)4.01e-04 - (wLE)2.69e-05 [+ 2 mm] [NiftyReg F3D] [131] Current objective function: 1.11752 = (wSIM)1.11799 - (wBE)4.44e-04 - (wLE)2.84e-05 [+ 2.03125 mm] [NiftyReg F3D] [140] Current objective function: 1.11766 = (wSIM)1.11816 - (wBE)4.68e-04 - (wLE)2.93e-05 [+ 0.5 mm] [NiftyReg F3D] [151] Current objective function: 1.11795 = (wSIM)1.11845 - (wBE)4.70e-04 - (wLE)2.94e-05 [+ 1.14642 mm] [NiftyReg F3D] [159] Current objective function: 1.11811 = (wSIM)1.11861 - (wBE)4.71e-04 - (wLE)2.95e-05 [+ 1.14642 mm] [NiftyReg F3D] [170] Current objective function: 1.11825 = (wSIM)1.11875 - (wBE)4.72e-04 - (wLE)2.96e-05 [+ 1.50504 mm] [NiftyReg F3D] [179] Current objective function: 1.11831 = (wSIM)1.11881 - (wBE)4.76e-04 - (wLE)2.99e-05 [+ 1.50504 mm] [NiftyReg F3D] [188] Current objective function: 1.11847 = (wSIM)1.11898 - (wBE)4.80e-04 - (wLE)3.02e-05 [+ 1.50504 mm] [NiftyReg F3D] [197] Current objective function: 1.11857 = (wSIM)1.11908 - (wBE)4.84e-04 - (wLE)3.05e-05 [+ 1.50504 mm] [NiftyReg F3D] [206] Current objective function: 1.11865 = (wSIM)1.11917 - (wBE)4.92e-04 - (wLE)3.10e-05 [+ 0.752518 mm] [NiftyReg F3D] [214] Current objective function: 1.11874 = (wSIM)1.11927 - (wBE)4.97e-04 - (wLE)3.13e-05 [+ 0.752518 mm] [NiftyReg F3D] [224] Current objective function: 1.1188 = (wSIM)1.11934 - (wBE)5.04e-04 - (wLE)3.18e-05 [+ 1.07328 mm] [NiftyReg F3D] [232] Current objective function: 1.11884 = (wSIM)1.11939 - (wBE)5.19e-04 - (wLE)3.26e-05 [+ 1.07328 mm] [NiftyReg F3D] [243] Current objective function: 1.11895 = (wSIM)1.11952 - (wBE)5.33e-04 - (wLE)3.35e-05 [+ 1.13047 mm] [NiftyReg F3D] [253] Current objective function: 1.11902 = (wSIM)1.11961 - (wBE)5.47e-04 - (wLE)3.43e-05 [+ 1.16932 mm] [NiftyReg F3D] [262] Current objective function: 1.11906 = (wSIM)1.11967 - (wBE)5.71e-04 - (wLE)3.57e-05 [+ 1.16932 mm] [NiftyReg F3D] [271] Current objective function: 1.11912 = (wSIM)1.11975 - (wBE)5.94e-04 - (wLE)3.71e-05 [+ 1.16932 mm] [NiftyReg F3D] [280] Current objective function: 1.1192 = (wSIM)1.11985 - (wBE)6.13e-04 - (wLE)3.82e-05 [+ 1.16932 mm] [NiftyReg F3D] [290] Current objective function: 1.11925 = (wSIM)1.11991 - (wBE)6.31e-04 - (wLE)3.93e-05 [+ 0.60476 mm] [NiftyReg F3D] [298] Current objective function: 1.11929 = (wSIM)1.11997 - (wBE)6.47e-04 - (wLE)4.04e-05 [+ 0.60476 mm] [NiftyReg F3D] [300] Current objective function: 1.11936 = (wSIM)1.12006 - (wBE)6.55e-04 - (wLE)4.09e-05 [+ 0.60476 mm] [NiftyReg WARNING] The current level reached the maximum number of iteration [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: 1.10109 = (wSIM)1.10181 - (wBE)0.000566778 - (wLE)0.000148443 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [13] Current objective function: 1.10206 = (wSIM)1.10287 - (wBE)6.53e-04 - (wLE)1.53e-04 [+ 3.58766 mm] [NiftyReg F3D] [24] Current objective function: 1.10275 = (wSIM)1.10366 - (wBE)7.50e-04 - (wLE)1.57e-04 [+ 2.5 mm] [NiftyReg F3D] [35] Current objective function: 1.10323 = (wSIM)1.10428 - (wBE)8.81e-04 - (wLE)1.62e-04 [+ 2.03125 mm] [NiftyReg F3D] [45] Current objective function: 1.10351 = (wSIM)1.10463 - (wBE)9.55e-04 - (wLE)1.65e-04 [+ 2 mm] [NiftyReg F3D] [57] Current objective function: 1.10374 = (wSIM)1.10498 - (wBE)1.08e-03 - (wLE)1.70e-04 [+ 2.26719 mm] [NiftyReg F3D] [67] Current objective function: 1.10393 = (wSIM)1.10531 - (wBE)1.21e-03 - (wLE)1.75e-04 [+ 1.5 mm] [NiftyReg F3D] [77] Current objective function: 1.10407 = (wSIM)1.10552 - (wBE)1.27e-03 - (wLE)1.78e-04 [+ 1.25 mm] [NiftyReg F3D] [86] Current objective function: 1.10412 = (wSIM)1.1057 - (wBE)1.40e-03 - (wLE)1.83e-04 [+ 1 mm] [NiftyReg F3D] [95] Current objective function: 1.10423 = (wSIM)1.10585 - (wBE)1.43e-03 - (wLE)1.85e-04 [+ 1 mm] [NiftyReg F3D] [104] Current objective function: 1.10424 = (wSIM)1.10595 - (wBE)1.52e-03 - (wLE)1.88e-04 [+ 1 mm] [NiftyReg F3D] [113] Current objective function: 1.10431 = (wSIM)1.10609 - (wBE)1.59e-03 - (wLE)1.91e-04 [+ 1 mm] [NiftyReg F3D] [123] Current objective function: 1.10435 = (wSIM)1.1062 - (wBE)1.65e-03 - (wLE)1.94e-04 [+ 1.01562 mm] [NiftyReg F3D] [132] Current objective function: 1.10438 = (wSIM)1.10631 - (wBE)1.73e-03 - (wLE)1.98e-04 [+ 0.5 mm] [NiftyReg F3D] [141] Current objective function: 1.10443 = (wSIM)1.10639 - (wBE)1.76e-03 - (wLE)1.99e-04 [+ 0.534375 mm] [NiftyReg F3D] [149] Current objective function: 1.10443 = (wSIM)1.10644 - (wBE)1.81e-03 - (wLE)2.02e-04 [+ 0.534375 mm] [NiftyReg F3D] [150] Current objective function: 1.10443 = (wSIM)1.10644 - (wBE)1.81e-03 - (wLE)2.02e-04 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [reg_f3d] Registration performed in 0 min 52 sec [reg_f3d] Have a good day ! reg_resample -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template5/manualseg.nii.gz -trans /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template5-2-sub-01.NIFTYREG.nii.gz -inter 0 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Command line: reg_resample -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template5/manualseg.nii.gz -trans /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template5-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template5-2-sub-01.NIFTYREG.nii.gz -inter 0 Parameters Reference image name: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm Floating image name: /usr/local/freesurfer_infant//average/CNYBCH/Template5/manualseg.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * [NiftyReg] Resampled image has been saved: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template5-2-sub-01.NIFTYREG.nii.gz reg_aladin -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template24/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.affine.txt -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.affine.nii.gz -voff Padding value here nan reg_f3d -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template24/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.affine.txt -cpp /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] Command line: [reg_f3d] reg_f3d -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template24/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.affine.txt -cpp /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] OpenMP is used with 20 thread(s) [NiftyReg F3D] *********************************************************** [NiftyReg F3D] INPUT PARAMETERS [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Reference image: [NiftyReg F3D] * name: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/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/freesurfer_infant//average/CNYBCH/Template24/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: 1.11565 = (wSIM)1.11565 - (wBE)5.88132e-14 - (wLE)2.23369e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [11] Current objective function: 1.1263 = (wSIM)1.1263 - (wBE)2.41e-06 - (wLE)2.54e-06 [+ 12 mm] [NiftyReg F3D] [21] Current objective function: 1.12758 = (wSIM)1.12759 - (wBE)4.24e-06 - (wLE)2.74e-06 [+ 2.1375 mm] [NiftyReg F3D] [33] Current objective function: 1.13089 = (wSIM)1.1309 - (wBE)5.29e-06 - (wLE)2.74e-06 [+ 4.98986 mm] [NiftyReg F3D] [42] Current objective function: 1.13129 = (wSIM)1.1313 - (wBE)6.78e-06 - (wLE)2.79e-06 [+ 2 mm] [NiftyReg F3D] [51] Current objective function: 1.13225 = (wSIM)1.13226 - (wBE)9.19e-06 - (wLE)2.93e-06 [+ 4.2 mm] [NiftyReg F3D] [60] Current objective function: 1.13235 = (wSIM)1.13236 - (wBE)1.21e-05 - (wLE)3.08e-06 [+ 2 mm] [NiftyReg F3D] [69] Current objective function: 1.13303 = (wSIM)1.13305 - (wBE)1.46e-05 - (wLE)3.16e-06 [+ 2.06875 mm] [NiftyReg F3D] [77] Current objective function: 1.13409 = (wSIM)1.13411 - (wBE)1.60e-05 - (wLE)3.17e-06 [+ 2.06875 mm] [NiftyReg F3D] [85] Current objective function: 1.13457 = (wSIM)1.13459 - (wBE)1.71e-05 - (wLE)3.19e-06 [+ 1.03437 mm] [NiftyReg F3D] [93] Current objective function: 1.13518 = (wSIM)1.1352 - (wBE)1.76e-05 - (wLE)3.21e-06 [+ 2.17219 mm] [NiftyReg F3D] [104] Current objective function: 1.13523 = (wSIM)1.13525 - (wBE)1.81e-05 - (wLE)3.22e-06 [+ 0.658784 mm] [NiftyReg F3D] [112] Current objective function: 1.13551 = (wSIM)1.13553 - (wBE)1.80e-05 - (wLE)3.21e-06 [+ 1.38345 mm] [NiftyReg F3D] [120] Current objective function: 1.13554 = (wSIM)1.13556 - (wBE)1.80e-05 - (wLE)3.21e-06 [+ 0.691723 mm] [NiftyReg F3D] [129] Current objective function: 1.13555 = (wSIM)1.13557 - (wBE)1.82e-05 - (wLE)3.21e-06 [+ 0.934258 mm] [NiftyReg F3D] [136] Current objective function: 1.13565 = (wSIM)1.13567 - (wBE)1.87e-05 - (wLE)3.21e-06 [+ 0.934258 mm] [NiftyReg F3D] [144] Current objective function: 1.13584 = (wSIM)1.13586 - (wBE)1.93e-05 - (wLE)3.22e-06 [+ 1.4481 mm] [NiftyReg F3D] [153] Current objective function: 1.13588 = (wSIM)1.1359 - (wBE)2.01e-05 - (wLE)3.24e-06 [+ 0.823607 mm] [NiftyReg F3D] [160] Current objective function: 1.13596 = (wSIM)1.13598 - (wBE)2.07e-05 - (wLE)3.24e-06 [+ 0.823607 mm] [NiftyReg F3D] [167] Current objective function: 1.13601 = (wSIM)1.13604 - (wBE)2.16e-05 - (wLE)3.25e-06 [+ 0.411804 mm] [NiftyReg F3D] [175] Current objective function: 1.13625 = (wSIM)1.13628 - (wBE)2.24e-05 - (wLE)3.26e-06 [+ 0.989358 mm] [NiftyReg F3D] [182] Current objective function: 1.13631 = (wSIM)1.13634 - (wBE)2.39e-05 - (wLE)3.29e-06 [+ 0.989358 mm] [NiftyReg F3D] [190] Current objective function: 1.13643 = (wSIM)1.13646 - (wBE)2.69e-05 - (wLE)3.35e-06 [+ 1.05738 mm] [NiftyReg F3D] [198] Current objective function: 1.13672 = (wSIM)1.13675 - (wBE)3.11e-05 - (wLE)3.42e-06 [+ 1.63893 mm] [NiftyReg F3D] [206] Current objective function: 1.13696 = (wSIM)1.137 - (wBE)3.36e-05 - (wLE)3.48e-06 [+ 1.63893 mm] [NiftyReg F3D] [214] Current objective function: 1.13705 = (wSIM)1.13709 - (wBE)3.60e-05 - (wLE)3.55e-06 [+ 0.819467 mm] [NiftyReg F3D] [222] Current objective function: 1.13714 = (wSIM)1.13718 - (wBE)3.74e-05 - (wLE)3.61e-06 [+ 0.932143 mm] [NiftyReg F3D] [229] Current objective function: 1.13726 = (wSIM)1.1373 - (wBE)3.81e-05 - (wLE)3.62e-06 [+ 0.932143 mm] [NiftyReg F3D] [237] Current objective function: 1.13727 = (wSIM)1.13731 - (wBE)3.83e-05 - (wLE)3.63e-06 [+ 0.180603 mm] [NiftyReg F3D] [243] Current objective function: 1.13731 = (wSIM)1.13736 - (wBE)3.87e-05 - (wLE)3.63e-06 [+ 0.379266 mm] [NiftyReg F3D] [250] Current objective function: 1.13735 = (wSIM)1.13739 - (wBE)3.92e-05 - (wLE)3.64e-06 [+ 0.796458 mm] [NiftyReg F3D] [257] Current objective function: 1.13737 = (wSIM)1.13741 - (wBE)3.93e-05 - (wLE)3.65e-06 [+ 0.0995573 mm] [NiftyReg F3D] [261] Current objective function: 1.13739 = (wSIM)1.13744 - (wBE)3.93e-05 - (wLE)3.65e-06 [+ 0.0995573 mm] [NiftyReg F3D] [264] Current objective function: 1.13739 = (wSIM)1.13744 - (wBE)3.93e-05 - (wLE)3.65e-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: 1.11297 = (wSIM)1.11302 - (wBE)3.7717e-05 - (wLE)1.51712e-05 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [10] Current objective function: 1.11473 = (wSIM)1.11479 - (wBE)4.48e-05 - (wLE)1.55e-05 [+ 4 mm] [NiftyReg F3D] [21] Current objective function: 1.11621 = (wSIM)1.1163 - (wBE)7.29e-05 - (wLE)1.65e-05 [+ 4.03125 mm] [NiftyReg F3D] [31] Current objective function: 1.11712 = (wSIM)1.11723 - (wBE)9.56e-05 - (wLE)1.72e-05 [+ 2.25 mm] [NiftyReg F3D] [42] Current objective function: 1.11806 = (wSIM)1.11819 - (wBE)1.10e-04 - (wLE)1.77e-05 [+ 2.31875 mm] [NiftyReg F3D] [52] Current objective function: 1.11866 = (wSIM)1.11879 - (wBE)1.19e-04 - (wLE)1.80e-05 [+ 3 mm] [NiftyReg F3D] [63] Current objective function: 1.11908 = (wSIM)1.11922 - (wBE)1.31e-04 - (wLE)1.83e-05 [+ 2.6375 mm] [NiftyReg F3D] [72] Current objective function: 1.1193 = (wSIM)1.11946 - (wBE)1.47e-04 - (wLE)1.87e-05 [+ 1 mm] [NiftyReg F3D] [81] Current objective function: 1.11971 = (wSIM)1.11989 - (wBE)1.58e-04 - (wLE)1.90e-05 [+ 2.1 mm] [NiftyReg F3D] [91] Current objective function: 1.12 = (wSIM)1.12019 - (wBE)1.67e-04 - (wLE)1.93e-05 [+ 2.125 mm] [NiftyReg F3D] [100] Current objective function: 1.12001 = (wSIM)1.12022 - (wBE)1.90e-04 - (wLE)2.01e-05 [+ 2 mm] [NiftyReg F3D] [110] Current objective function: 1.12043 = (wSIM)1.12066 - (wBE)2.08e-04 - (wLE)2.07e-05 [+ 2.125 mm] [NiftyReg F3D] [119] Current objective function: 1.12065 = (wSIM)1.1209 - (wBE)2.31e-04 - (wLE)2.14e-05 [+ 2 mm] [NiftyReg F3D] [128] Current objective function: 1.12092 = (wSIM)1.1212 - (wBE)2.54e-04 - (wLE)2.22e-05 [+ 2 mm] [NiftyReg F3D] [141] Current objective function: 1.12128 = (wSIM)1.12157 - (wBE)2.72e-04 - (wLE)2.28e-05 [+ 2.69611 mm] [NiftyReg F3D] [151] Current objective function: 1.1214 = (wSIM)1.12171 - (wBE)2.88e-04 - (wLE)2.34e-05 [+ 1.06875 mm] [NiftyReg F3D] [161] Current objective function: 1.12162 = (wSIM)1.12194 - (wBE)2.94e-04 - (wLE)2.36e-05 [+ 1.65656 mm] [NiftyReg F3D] [170] Current objective function: 1.1217 = (wSIM)1.12203 - (wBE)3.02e-04 - (wLE)2.39e-05 [+ 1.65656 mm] [NiftyReg F3D] [179] Current objective function: 1.12178 = (wSIM)1.12211 - (wBE)3.12e-04 - (wLE)2.42e-05 [+ 0.828281 mm] [NiftyReg F3D] [189] Current objective function: 1.12191 = (wSIM)1.12225 - (wBE)3.18e-04 - (wLE)2.45e-05 [+ 1.77071 mm] [NiftyReg F3D] [198] Current objective function: 1.12194 = (wSIM)1.1223 - (wBE)3.29e-04 - (wLE)2.49e-05 [+ 1.77071 mm] [NiftyReg F3D] [208] Current objective function: 1.12202 = (wSIM)1.12239 - (wBE)3.42e-04 - (wLE)2.55e-05 [+ 1.00709 mm] [NiftyReg F3D] [219] Current objective function: 1.12222 = (wSIM)1.1226 - (wBE)3.58e-04 - (wLE)2.61e-05 [+ 1.3602 mm] [NiftyReg F3D] [228] Current objective function: 1.12229 = (wSIM)1.12269 - (wBE)3.79e-04 - (wLE)2.69e-05 [+ 0.680101 mm] [NiftyReg F3D] [237] Current objective function: 1.12246 = (wSIM)1.12287 - (wBE)3.85e-04 - (wLE)2.72e-05 [+ 1.05416 mm] [NiftyReg F3D] [246] Current objective function: 1.12251 = (wSIM)1.12293 - (wBE)3.90e-04 - (wLE)2.74e-05 [+ 1.1991 mm] [NiftyReg F3D] [255] Current objective function: 1.12251 = (wSIM)1.12293 - (wBE)3.91e-04 - (wLE)2.75e-05 [+ 0.037472 mm] [NiftyReg F3D] [268] Current objective function: 1.12256 = (wSIM)1.12298 - (wBE)3.93e-04 - (wLE)2.76e-05 [+ 0.597207 mm] [NiftyReg F3D] [276] Current objective function: 1.12257 = (wSIM)1.123 - (wBE)3.96e-04 - (wLE)2.77e-05 [+ 0.597207 mm] [NiftyReg F3D] [284] Current objective function: 1.12259 = (wSIM)1.12302 - (wBE)4.01e-04 - (wLE)2.80e-05 [+ 0.298604 mm] [NiftyReg F3D] [292] Current objective function: 1.12263 = (wSIM)1.12306 - (wBE)4.04e-04 - (wLE)2.81e-05 [+ 0.627067 mm] [NiftyReg F3D] [300] Current objective function: 1.12266 = (wSIM)1.1231 - (wBE)4.11e-04 - (wLE)2.84e-05 [+ 0.799511 mm] [NiftyReg WARNING] The current level reached the maximum number of iteration [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: 1.10309 = (wSIM)1.10355 - (wBE)0.000354152 - (wLE)0.000104703 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [11] Current objective function: 1.10409 = (wSIM)1.1046 - (wBE)4.09e-04 - (wLE)1.07e-04 [+ 3 mm] [NiftyReg F3D] [23] Current objective function: 1.10477 = (wSIM)1.10534 - (wBE)4.61e-04 - (wLE)1.10e-04 [+ 3.01562 mm] [NiftyReg F3D] [36] Current objective function: 1.10533 = (wSIM)1.10602 - (wBE)5.77e-04 - (wLE)1.14e-04 [+ 3.33766 mm] [NiftyReg F3D] [47] Current objective function: 1.10578 = (wSIM)1.10659 - (wBE)6.91e-04 - (wLE)1.18e-04 [+ 3 mm] [NiftyReg F3D] [59] Current objective function: 1.10611 = (wSIM)1.10704 - (wBE)8.00e-04 - (wLE)1.22e-04 [+ 2.26719 mm] [NiftyReg F3D] [69] Current objective function: 1.10636 = (wSIM)1.10743 - (wBE)9.41e-04 - (wLE)1.27e-04 [+ 2 mm] [NiftyReg F3D] [80] Current objective function: 1.10656 = (wSIM)1.10774 - (wBE)1.05e-03 - (wLE)1.31e-04 [+ 1.28437 mm] [NiftyReg F3D] [89] Current objective function: 1.10667 = (wSIM)1.1079 - (wBE)1.10e-03 - (wLE)1.33e-04 [+ 1 mm] [NiftyReg F3D] [100] Current objective function: 1.10676 = (wSIM)1.10804 - (wBE)1.14e-03 - (wLE)1.35e-04 [+ 1.15937 mm] [NiftyReg F3D] [109] Current objective function: 1.10683 = (wSIM)1.10817 - (wBE)1.20e-03 - (wLE)1.37e-04 [+ 1 mm] [NiftyReg F3D] [119] Current objective function: 1.1069 = (wSIM)1.1083 - (wBE)1.26e-03 - (wLE)1.40e-04 [+ 1.0625 mm] [NiftyReg F3D] [128] Current objective function: 1.10696 = (wSIM)1.1084 - (wBE)1.31e-03 - (wLE)1.42e-04 [+ 1 mm] [NiftyReg F3D] [137] Current objective function: 1.10699 = (wSIM)1.10852 - (wBE)1.39e-03 - (wLE)1.45e-04 [+ 1 mm] [NiftyReg F3D] [146] Current objective function: 1.10704 = (wSIM)1.10862 - (wBE)1.44e-03 - (wLE)1.47e-04 [+ 1 mm] [NiftyReg F3D] [150] Current objective function: 1.1071 = (wSIM)1.10873 - (wBE)1.48e-03 - (wLE)1.49e-04 [+ 1 mm] [NiftyReg WARNING] The current level reached the maximum number of iteration [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [reg_f3d] Registration performed in 0 min 52 sec [reg_f3d] Have a good day ! reg_resample -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template24/manualseg.nii.gz -trans /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template24-2-sub-01.NIFTYREG.nii.gz -inter 0 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Command line: reg_resample -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template24/manualseg.nii.gz -trans /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template24-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template24-2-sub-01.NIFTYREG.nii.gz -inter 0 Parameters Reference image name: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm Floating image name: /usr/local/freesurfer_infant//average/CNYBCH/Template24/manualseg.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * [NiftyReg] Resampled image has been saved: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template24-2-sub-01.NIFTYREG.nii.gz reg_aladin -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template18/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.affine.txt -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.affine.nii.gz -voff Padding value here nan reg_f3d -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template18/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.affine.txt -cpp /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] Command line: [reg_f3d] reg_f3d -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template18/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.affine.txt -cpp /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] OpenMP is used with 20 thread(s) [NiftyReg F3D] *********************************************************** [NiftyReg F3D] INPUT PARAMETERS [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Reference image: [NiftyReg F3D] * name: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/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/freesurfer_infant//average/CNYBCH/Template18/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: 1.10967 = (wSIM)1.10968 - (wBE)5.07933e-14 - (wLE)1.51829e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [11] Current objective function: 1.11715 = (wSIM)1.11715 - (wBE)2.03e-06 - (wLE)1.74e-06 [+ 12 mm] [NiftyReg F3D] [20] Current objective function: 1.1177 = (wSIM)1.11771 - (wBE)4.34e-06 - (wLE)1.93e-06 [+ 4 mm] [NiftyReg F3D] [29] Current objective function: 1.11794 = (wSIM)1.11795 - (wBE)7.39e-06 - (wLE)2.11e-06 [+ 4 mm] [NiftyReg F3D] [38] Current objective function: 1.11796 = (wSIM)1.11798 - (wBE)1.05e-05 - (wLE)2.28e-06 [+ 2 mm] [NiftyReg F3D] [47] Current objective function: 1.12032 = (wSIM)1.12033 - (wBE)1.15e-05 - (wLE)2.28e-06 [+ 4.2 mm] [NiftyReg F3D] [57] Current objective function: 1.12094 = (wSIM)1.12096 - (wBE)1.20e-05 - (wLE)2.28e-06 [+ 2.275 mm] [NiftyReg F3D] [65] Current objective function: 1.12211 = (wSIM)1.12212 - (wBE)1.28e-05 - (wLE)2.28e-06 [+ 2.275 mm] [NiftyReg F3D] [76] Current objective function: 1.12305 = (wSIM)1.12307 - (wBE)1.37e-05 - (wLE)2.31e-06 [+ 3.61227 mm] [NiftyReg F3D] [86] Current objective function: 1.12315 = (wSIM)1.12317 - (wBE)1.46e-05 - (wLE)2.35e-06 [+ 1.02724 mm] [NiftyReg F3D] [97] Current objective function: 1.12348 = (wSIM)1.1235 - (wBE)1.53e-05 - (wLE)2.39e-06 [+ 1.71263 mm] [NiftyReg F3D] [105] Current objective function: 1.12367 = (wSIM)1.12369 - (wBE)1.59e-05 - (wLE)2.42e-06 [+ 0.856317 mm] [NiftyReg F3D] [115] Current objective function: 1.12404 = (wSIM)1.12406 - (wBE)1.64e-05 - (wLE)2.43e-06 [+ 2.12854 mm] [NiftyReg F3D] [123] Current objective function: 1.12406 = (wSIM)1.12408 - (wBE)1.68e-05 - (wLE)2.44e-06 [+ 0.532134 mm] [NiftyReg F3D] [131] Current objective function: 1.12426 = (wSIM)1.12427 - (wBE)1.68e-05 - (wLE)2.45e-06 [+ 1.11748 mm] [NiftyReg F3D] [137] Current objective function: 1.12426 = (wSIM)1.12427 - (wBE)1.68e-05 - (wLE)2.45e-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: 1.10359 = (wSIM)1.10362 - (wBE)1.63301e-05 - (wLE)9.68331e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [12] Current objective function: 1.10597 = (wSIM)1.106 - (wBE)2.31e-05 - (wLE)9.96e-06 [+ 5.03438 mm] [NiftyReg F3D] [24] Current objective function: 1.10765 = (wSIM)1.10771 - (wBE)4.75e-05 - (wLE)1.11e-05 [+ 6.03125 mm] [NiftyReg F3D] [34] Current objective function: 1.10843 = (wSIM)1.10851 - (wBE)7.42e-05 - (wLE)1.22e-05 [+ 2.25 mm] [NiftyReg F3D] [44] Current objective function: 1.10958 = (wSIM)1.10969 - (wBE)1.01e-04 - (wLE)1.31e-05 [+ 2.5 mm] [NiftyReg F3D] [55] Current objective function: 1.11043 = (wSIM)1.11056 - (wBE)1.17e-04 - (wLE)1.37e-05 [+ 2.6375 mm] [NiftyReg F3D] [65] Current objective function: 1.1111 = (wSIM)1.11124 - (wBE)1.26e-04 - (wLE)1.40e-05 [+ 4 mm] [NiftyReg F3D] [74] Current objective function: 1.11134 = (wSIM)1.1115 - (wBE)1.42e-04 - (wLE)1.46e-05 [+ 2 mm] [NiftyReg F3D] [84] Current objective function: 1.11202 = (wSIM)1.11218 - (wBE)1.54e-04 - (wLE)1.50e-05 [+ 2.5 mm] [NiftyReg F3D] [93] Current objective function: 1.11212 = (wSIM)1.11231 - (wBE)1.67e-04 - (wLE)1.54e-05 [+ 1 mm] [NiftyReg F3D] [105] Current objective function: 1.11255 = (wSIM)1.11274 - (wBE)1.70e-04 - (wLE)1.55e-05 [+ 2.27205 mm] [NiftyReg F3D] [115] Current objective function: 1.11259 = (wSIM)1.11278 - (wBE)1.72e-04 - (wLE)1.56e-05 [+ 0.284375 mm] [NiftyReg F3D] [125] Current objective function: 1.1127 = (wSIM)1.11289 - (wBE)1.74e-04 - (wLE)1.57e-05 [+ 1.31978 mm] [NiftyReg F3D] [134] Current objective function: 1.1127 = (wSIM)1.11289 - (wBE)1.75e-04 - (wLE)1.57e-05 [+ 0.164973 mm] [NiftyReg F3D] [144] Current objective function: 1.11279 = (wSIM)1.11298 - (wBE)1.76e-04 - (wLE)1.58e-05 [+ 0.716235 mm] [NiftyReg F3D] [151] Current objective function: 1.11279 = (wSIM)1.11298 - (wBE)1.76e-04 - (wLE)1.58e-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: 1.09656 = (wSIM)1.09677 - (wBE)0.000152706 - (wLE)5.67771e-05 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [13] Current objective function: 1.09771 = (wSIM)1.09801 - (wBE)2.41e-04 - (wLE)5.99e-05 [+ 4.04844 mm] [NiftyReg F3D] [24] Current objective function: 1.0985 = (wSIM)1.09898 - (wBE)4.13e-04 - (wLE)6.49e-05 [+ 3 mm] [NiftyReg F3D] [35] Current objective function: 1.09903 = (wSIM)1.09964 - (wBE)5.39e-04 - (wLE)6.84e-05 [+ 2.125 mm] [NiftyReg F3D] [45] Current objective function: 1.09938 = (wSIM)1.1002 - (wBE)7.52e-04 - (wLE)7.42e-05 [+ 2 mm] [NiftyReg F3D] [55] Current objective function: 1.09959 = (wSIM)1.10052 - (wBE)8.57e-04 - (wLE)7.71e-05 [+ 1.25 mm] [NiftyReg F3D] [65] Current objective function: 1.09972 = (wSIM)1.10075 - (wBE)9.54e-04 - (wLE)7.99e-05 [+ 1.125 mm] [NiftyReg F3D] [74] Current objective function: 1.09981 = (wSIM)1.10096 - (wBE)1.07e-03 - (wLE)8.32e-05 [+ 1 mm] [NiftyReg F3D] [83] Current objective function: 1.09987 = (wSIM)1.10114 - (wBE)1.18e-03 - (wLE)8.65e-05 [+ 1 mm] [NiftyReg F3D] [92] Current objective function: 1.09994 = (wSIM)1.10125 - (wBE)1.22e-03 - (wLE)8.78e-05 [+ 1 mm] [NiftyReg F3D] [101] Current objective function: 1.09994 = (wSIM)1.10128 - (wBE)1.25e-03 - (wLE)8.86e-05 [+ 0.125 mm] [NiftyReg F3D] [111] Current objective function: 1.09998 = (wSIM)1.10135 - (wBE)1.27e-03 - (wLE)8.94e-05 [+ 0.455344 mm] [NiftyReg F3D] [120] Current objective function: 1.09999 = (wSIM)1.1014 - (wBE)1.31e-03 - (wLE)9.06e-05 [+ 0.243324 mm] [NiftyReg F3D] [128] Current objective function: 1.10002 = (wSIM)1.10143 - (wBE)1.33e-03 - (wLE)9.12e-05 [+ 0.377153 mm] [NiftyReg F3D] [136] Current objective function: 1.10002 = (wSIM)1.10145 - (wBE)1.34e-03 - (wLE)9.16e-05 [+ 0.0471441 mm] [NiftyReg F3D] [143] Current objective function: 1.10003 = (wSIM)1.10148 - (wBE)1.35e-03 - (wLE)9.20e-05 [+ 0.156047 mm] [NiftyReg F3D] [150] Current objective function: 1.10004 = (wSIM)1.10151 - (wBE)1.38e-03 - (wLE)9.27e-05 [+ 0.166775 mm] [NiftyReg WARNING] The current level reached the maximum number of iteration [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [reg_f3d] Registration performed in 0 min 43 sec [reg_f3d] Have a good day ! reg_resample -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template18/manualseg.nii.gz -trans /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template18-2-sub-01.NIFTYREG.nii.gz -inter 0 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Command line: reg_resample -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template18/manualseg.nii.gz -trans /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template18-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template18-2-sub-01.NIFTYREG.nii.gz -inter 0 Parameters Reference image name: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm Floating image name: /usr/local/freesurfer_infant//average/CNYBCH/Template18/manualseg.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * [NiftyReg] Resampled image has been saved: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template18-2-sub-01.NIFTYREG.nii.gz reg_aladin -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template25/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.affine.txt -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.affine.nii.gz -voff Padding value here nan reg_f3d -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template25/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.affine.txt -cpp /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] Command line: [reg_f3d] reg_f3d -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template25/norm.nii.gz -aff /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.affine.txt -cpp /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.nii.gz [reg_f3d] [reg_f3d] OpenMP is used with 20 thread(s) [NiftyReg F3D] *********************************************************** [NiftyReg F3D] INPUT PARAMETERS [NiftyReg F3D] *********************************************************** [NiftyReg F3D] Reference image: [NiftyReg F3D] * name: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/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/freesurfer_infant//average/CNYBCH/Template25/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: 1.1178 = (wSIM)1.1178 - (wBE)5.69367e-14 - (wLE)6.95452e-07 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [10] Current objective function: 1.12602 = (wSIM)1.12602 - (wBE)1.40e-06 - (wLE)8.53e-07 [+ 5 mm] [NiftyReg F3D] [19] Current objective function: 1.12704 = (wSIM)1.12704 - (wBE)3.72e-06 - (wLE)1.06e-06 [+ 4 mm] [NiftyReg F3D] [28] Current objective function: 1.12714 = (wSIM)1.12715 - (wBE)6.86e-06 - (wLE)1.23e-06 [+ 4 mm] [NiftyReg F3D] [37] Current objective function: 1.12898 = (wSIM)1.12899 - (wBE)8.61e-06 - (wLE)1.26e-06 [+ 4 mm] [NiftyReg F3D] [46] Current objective function: 1.12917 = (wSIM)1.12918 - (wBE)9.34e-06 - (wLE)1.27e-06 [+ 0.5 mm] [NiftyReg F3D] [57] Current objective function: 1.13092 = (wSIM)1.13093 - (wBE)8.74e-06 - (wLE)1.24e-06 [+ 2.36625 mm] [NiftyReg F3D] [66] Current objective function: 1.13104 = (wSIM)1.13105 - (wBE)8.40e-06 - (wLE)1.21e-06 [+ 2.36625 mm] [NiftyReg F3D] [75] Current objective function: 1.13107 = (wSIM)1.13108 - (wBE)9.14e-06 - (wLE)1.20e-06 [+ 2.36625 mm] [NiftyReg F3D] [84] Current objective function: 1.13138 = (wSIM)1.13139 - (wBE)1.09e-05 - (wLE)1.22e-06 [+ 2.36625 mm] [NiftyReg F3D] [93] Current objective function: 1.13146 = (wSIM)1.13147 - (wBE)1.24e-05 - (wLE)1.26e-06 [+ 0.591563 mm] [NiftyReg F3D] [102] Current objective function: 1.13281 = (wSIM)1.13282 - (wBE)1.29e-05 - (wLE)1.32e-06 [+ 1.95807 mm] [NiftyReg F3D] [110] Current objective function: 1.13317 = (wSIM)1.13319 - (wBE)1.37e-05 - (wLE)1.37e-06 [+ 0.979037 mm] [NiftyReg F3D] [118] Current objective function: 1.13355 = (wSIM)1.13356 - (wBE)1.43e-05 - (wLE)1.38e-06 [+ 1.11365 mm] [NiftyReg F3D] [127] Current objective function: 1.13368 = (wSIM)1.1337 - (wBE)1.51e-05 - (wLE)1.41e-06 [+ 0.633391 mm] [NiftyReg F3D] [135] Current objective function: 1.13383 = (wSIM)1.13385 - (wBE)1.61e-05 - (wLE)1.45e-06 [+ 1.33012 mm] [NiftyReg F3D] [143] Current objective function: 1.13389 = (wSIM)1.1339 - (wBE)1.66e-05 - (wLE)1.47e-06 [+ 0.33253 mm] [NiftyReg F3D] [151] Current objective function: 1.13404 = (wSIM)1.13406 - (wBE)1.73e-05 - (wLE)1.48e-06 [+ 0.748609 mm] [NiftyReg F3D] [158] Current objective function: 1.1341 = (wSIM)1.13412 - (wBE)1.83e-05 - (wLE)1.51e-06 [+ 0.748609 mm] [NiftyReg F3D] [165] Current objective function: 1.13416 = (wSIM)1.13418 - (wBE)1.98e-05 - (wLE)1.55e-06 [+ 0.748609 mm] [NiftyReg F3D] [172] Current objective function: 1.13435 = (wSIM)1.13437 - (wBE)2.15e-05 - (wLE)1.60e-06 [+ 0.748609 mm] [NiftyReg F3D] [179] Current objective function: 1.13452 = (wSIM)1.13454 - (wBE)2.30e-05 - (wLE)1.64e-06 [+ 0.748609 mm] [NiftyReg F3D] [187] Current objective function: 1.13464 = (wSIM)1.13467 - (wBE)2.55e-05 - (wLE)1.71e-06 [+ 0.954477 mm] [NiftyReg F3D] [194] Current objective function: 1.13482 = (wSIM)1.13485 - (wBE)2.86e-05 - (wLE)1.80e-06 [+ 0.954477 mm] [NiftyReg F3D] [202] Current objective function: 1.13499 = (wSIM)1.13503 - (wBE)3.17e-05 - (wLE)1.89e-06 [+ 1.0201 mm] [NiftyReg F3D] [209] Current objective function: 1.13507 = (wSIM)1.13511 - (wBE)3.46e-05 - (wLE)1.97e-06 [+ 0.510048 mm] [NiftyReg F3D] [218] Current objective function: 1.13529 = (wSIM)1.13533 - (wBE)3.59e-05 - (wLE)2.00e-06 [+ 0.86772 mm] [NiftyReg F3D] [225] Current objective function: 1.13534 = (wSIM)1.13538 - (wBE)3.72e-05 - (wLE)2.04e-06 [+ 0.86772 mm] [NiftyReg F3D] [232] Current objective function: 1.13538 = (wSIM)1.13543 - (wBE)3.85e-05 - (wLE)2.07e-06 [+ 0.43386 mm] [NiftyReg F3D] [239] Current objective function: 1.13549 = (wSIM)1.13553 - (wBE)3.93e-05 - (wLE)2.08e-06 [+ 0.493516 mm] [NiftyReg F3D] [245] Current objective function: 1.13554 = (wSIM)1.13559 - (wBE)3.99e-05 - (wLE)2.10e-06 [+ 0.493516 mm] [NiftyReg F3D] [252] Current objective function: 1.13563 = (wSIM)1.13567 - (wBE)4.04e-05 - (wLE)2.11e-06 [+ 0.629233 mm] [NiftyReg F3D] [259] Current objective function: 1.13563 = (wSIM)1.13568 - (wBE)4.06e-05 - (wLE)2.11e-06 [+ 0.157308 mm] [NiftyReg F3D] [262] Current objective function: 1.13563 = (wSIM)1.13568 - (wBE)4.06e-05 - (wLE)2.11e-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: 1.11161 = (wSIM)1.11166 - (wBE)3.87301e-05 - (wLE)9.57219e-06 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [11] Current objective function: 1.11314 = (wSIM)1.11319 - (wBE)4.19e-05 - (wLE)9.59e-06 [+ 3.06875 mm] [NiftyReg F3D] [21] Current objective function: 1.11471 = (wSIM)1.11478 - (wBE)6.37e-05 - (wLE)1.05e-05 [+ 4 mm] [NiftyReg F3D] [31] Current objective function: 1.11574 = (wSIM)1.11584 - (wBE)9.09e-05 - (wLE)1.14e-05 [+ 4 mm] [NiftyReg F3D] [40] Current objective function: 1.11625 = (wSIM)1.11639 - (wBE)1.22e-04 - (wLE)1.24e-05 [+ 2 mm] [NiftyReg F3D] [49] Current objective function: 1.11712 = (wSIM)1.11727 - (wBE)1.40e-04 - (wLE)1.29e-05 [+ 2 mm] [NiftyReg F3D] [59] Current objective function: 1.1178 = (wSIM)1.11796 - (wBE)1.49e-04 - (wLE)1.32e-05 [+ 3 mm] [NiftyReg F3D] [69] Current objective function: 1.1183 = (wSIM)1.11848 - (wBE)1.63e-04 - (wLE)1.37e-05 [+ 2.25 mm] [NiftyReg F3D] [78] Current objective function: 1.11869 = (wSIM)1.11887 - (wBE)1.70e-04 - (wLE)1.40e-05 [+ 2 mm] [NiftyReg F3D] [89] Current objective function: 1.11904 = (wSIM)1.11923 - (wBE)1.81e-04 - (wLE)1.43e-05 [+ 2.19375 mm] [NiftyReg F3D] [98] Current objective function: 1.11907 = (wSIM)1.1193 - (wBE)2.14e-04 - (wLE)1.55e-05 [+ 2 mm] [NiftyReg F3D] [108] Current objective function: 1.11968 = (wSIM)1.11994 - (wBE)2.40e-04 - (wLE)1.63e-05 [+ 3 mm] [NiftyReg F3D] [117] Current objective function: 1.11973 = (wSIM)1.12003 - (wBE)2.78e-04 - (wLE)1.76e-05 [+ 2 mm] [NiftyReg F3D] [126] Current objective function: 1.1202 = (wSIM)1.12053 - (wBE)3.09e-04 - (wLE)1.86e-05 [+ 2 mm] [NiftyReg F3D] [135] Current objective function: 1.12022 = (wSIM)1.12059 - (wBE)3.56e-04 - (wLE)2.01e-05 [+ 2 mm] [NiftyReg F3D] [144] Current objective function: 1.12055 = (wSIM)1.12097 - (wBE)3.98e-04 - (wLE)2.15e-05 [+ 2 mm] [NiftyReg F3D] [153] Current objective function: 1.12078 = (wSIM)1.12124 - (wBE)4.35e-04 - (wLE)2.27e-05 [+ 2 mm] [NiftyReg F3D] [162] Current objective function: 1.12094 = (wSIM)1.12143 - (wBE)4.67e-04 - (wLE)2.38e-05 [+ 1 mm] [NiftyReg F3D] [170] Current objective function: 1.12125 = (wSIM)1.12176 - (wBE)4.90e-04 - (wLE)2.46e-05 [+ 1 mm] [NiftyReg F3D] [179] Current objective function: 1.12148 = (wSIM)1.12201 - (wBE)5.07e-04 - (wLE)2.53e-05 [+ 1.1375 mm] [NiftyReg F3D] [187] Current objective function: 1.12157 = (wSIM)1.12213 - (wBE)5.26e-04 - (wLE)2.60e-05 [+ 1.1375 mm] [NiftyReg F3D] [195] Current objective function: 1.12173 = (wSIM)1.12231 - (wBE)5.49e-04 - (wLE)2.70e-05 [+ 1.1375 mm] [NiftyReg F3D] [205] Current objective function: 1.12189 = (wSIM)1.12248 - (wBE)5.60e-04 - (wLE)2.75e-05 [+ 1.29391 mm] [NiftyReg F3D] [214] Current objective function: 1.12194 = (wSIM)1.12254 - (wBE)5.73e-04 - (wLE)2.81e-05 [+ 1.29391 mm] [NiftyReg F3D] [224] Current objective function: 1.12204 = (wSIM)1.12265 - (wBE)5.88e-04 - (wLE)2.88e-05 [+ 1.31615 mm] [NiftyReg F3D] [233] Current objective function: 1.12211 = (wSIM)1.12274 - (wBE)5.99e-04 - (wLE)2.93e-05 [+ 1.31615 mm] [NiftyReg F3D] [243] Current objective function: 1.12217 = (wSIM)1.12281 - (wBE)6.12e-04 - (wLE)3.00e-05 [+ 1.36139 mm] [NiftyReg F3D] [252] Current objective function: 1.12223 = (wSIM)1.1229 - (wBE)6.41e-04 - (wLE)3.14e-05 [+ 1.36139 mm] [NiftyReg F3D] [261] Current objective function: 1.12224 = (wSIM)1.12296 - (wBE)6.81e-04 - (wLE)3.34e-05 [+ 1.36139 mm] [NiftyReg F3D] [270] Current objective function: 1.12231 = (wSIM)1.12306 - (wBE)7.17e-04 - (wLE)3.53e-05 [+ 1.36139 mm] [NiftyReg F3D] [280] Current objective function: 1.12241 = (wSIM)1.12318 - (wBE)7.38e-04 - (wLE)3.65e-05 [+ 1.40819 mm] [NiftyReg F3D] [289] Current objective function: 1.12245 = (wSIM)1.12324 - (wBE)7.56e-04 - (wLE)3.75e-05 [+ 1.40819 mm] [NiftyReg F3D] [298] Current objective function: 1.12246 = (wSIM)1.12329 - (wBE)7.83e-04 - (wLE)3.90e-05 [+ 1.40819 mm] [NiftyReg F3D] [300] Current objective function: 1.12246 = (wSIM)1.12329 - (wBE)7.83e-04 - (wLE)3.90e-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: 1.10322 = (wSIM)1.10401 - (wBE)0.000655631 - (wLE)0.000137704 - (wJAC)0 - (wLAN)0 [NiftyReg F3D] [13] Current objective function: 1.1041 = (wSIM)1.105 - (wBE)7.59e-04 - (wLE)1.43e-04 [+ 3.56875 mm] [NiftyReg F3D] [24] Current objective function: 1.10467 = (wSIM)1.10572 - (wBE)9.00e-04 - (wLE)1.49e-04 [+ 2.5 mm] [NiftyReg F3D] [34] Current objective function: 1.10506 = (wSIM)1.10626 - (wBE)1.05e-03 - (wLE)1.55e-04 [+ 2 mm] [NiftyReg F3D] [44] Current objective function: 1.10529 = (wSIM)1.10665 - (wBE)1.20e-03 - (wLE)1.61e-04 [+ 2 mm] [NiftyReg F3D] [55] Current objective function: 1.10547 = (wSIM)1.10695 - (wBE)1.31e-03 - (wLE)1.66e-04 [+ 1.31875 mm] [NiftyReg F3D] [64] Current objective function: 1.10557 = (wSIM)1.10717 - (wBE)1.43e-03 - (wLE)1.70e-04 [+ 1 mm] [NiftyReg F3D] [73] Current objective function: 1.10561 = (wSIM)1.10736 - (wBE)1.57e-03 - (wLE)1.76e-04 [+ 1 mm] [NiftyReg F3D] [82] Current objective function: 1.10563 = (wSIM)1.1075 - (wBE)1.69e-03 - (wLE)1.81e-04 [+ 1 mm] [NiftyReg F3D] [91] Current objective function: 1.10569 = (wSIM)1.10762 - (wBE)1.75e-03 - (wLE)1.83e-04 [+ 1 mm] [NiftyReg F3D] [100] Current objective function: 1.1057 = (wSIM)1.10767 - (wBE)1.79e-03 - (wLE)1.85e-04 [+ 0.25 mm] [NiftyReg F3D] [107] Current objective function: 1.10573 = (wSIM)1.10774 - (wBE)1.83e-03 - (wLE)1.87e-04 [+ 0.25 mm] [NiftyReg F3D] [114] Current objective function: 1.10573 = (wSIM)1.10777 - (wBE)1.85e-03 - (wLE)1.88e-04 [+ 0.125 mm] [NiftyReg F3D] [120] Current objective function: 1.10573 = (wSIM)1.1078 - (wBE)1.88e-03 - (wLE)1.89e-04 [+ 0.125 mm] [NiftyReg F3D] [127] Current objective function: 1.10574 = (wSIM)1.10782 - (wBE)1.90e-03 - (wLE)1.90e-04 [+ 0.142188 mm] [NiftyReg F3D] [133] Current objective function: 1.10574 = (wSIM)1.10786 - (wBE)1.93e-03 - (wLE)1.91e-04 [+ 0.142188 mm] [NiftyReg F3D] [141] Current objective function: 1.10574 = (wSIM)1.10789 - (wBE)1.96e-03 - (wLE)1.92e-04 [+ 0.220391 mm] [NiftyReg F3D] [148] Current objective function: 1.10574 = (wSIM)1.1079 - (wBE)1.97e-03 - (wLE)1.93e-04 [+ 0.110195 mm] [NiftyReg F3D] [150] Current objective function: 1.10574 = (wSIM)1.1079 - (wBE)1.97e-03 - (wLE)1.93e-04 [+ 0 mm] [NiftyReg F3D] Current registration level done [NiftyReg F3D] *********************************************************** [reg_f3d] Registration performed in 0 min 54 sec [reg_f3d] Have a good day ! reg_resample -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template25/manualseg.nii.gz -trans /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template25-2-sub-01.NIFTYREG.nii.gz -inter 0 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Command line: reg_resample -ref /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/freesurfer_infant//average/CNYBCH/Template25/manualseg.nii.gz -trans /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/Template25-2-sub-01.NIFTYREG.field.nii.gz -res /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template25-2-sub-01.NIFTYREG.nii.gz -inter 0 Parameters Reference image name: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm Floating image name: /usr/local/freesurfer_infant//average/CNYBCH/Template25/manualseg.nii.gz 256x256x256 voxels, 1 volumes 1x1x1 mm * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * [NiftyReg] Resampled image has been saved: /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template25-2-sub-01.NIFTYREG.nii.gz TRAINING SUBJECTS LABELFUSION Template5 Template24 Template18 Template25 run_label_fusion.csh --subj sub-01 --regtype NIFTYREG --ts Template5 Template24 Template18 Template25 ARG Template5 Template24 Template18 Template25 ARG COUNT 4 TRAINING SUBJECTS Template5 Template24 Template18 Template25 CHECKING THE INPUTS... NUMBER OF NEIGHBORS 4 TRAINING SUBJECTS Template5 Template24 Template18 Template25 MOVED SEG FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template5-2-sub-01.NIFTYREG.nii.gz MOVED SEG FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template24-2-sub-01.NIFTYREG.nii.gz MOVED SEG FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template18-2-sub-01.NIFTYREG.nii.gz MOVED SEG FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template25-2-sub-01.NIFTYREG.nii.gz TRAININGDATA /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template5-2-sub-01.NIFTYREG.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template24-2-sub-01.NIFTYREG.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template18-2-sub-01.NIFTYREG.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template25-2-sub-01.NIFTYREG.nii.gz OUTPUT FILE /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/sub-01-BETA0.3-RHO.70.labels.mrf.nii.gz LABELFUSION CMD mri_label_fusion -i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/mprage.nu.conf.masked.nii.gz -s /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template5-2-sub-01.NIFTYREG.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template24-2-sub-01.NIFTYREG.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template18-2-sub-01.NIFTYREG.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template25-2-sub-01.NIFTYREG.nii.gz -o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/sub-01-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 33 unique labels computing distance maps and prior label probabilities 1) processing /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template5-2-sub-01.NIFTYREG.nii.gz 2) processing /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template24-2-sub-01.NIFTYREG.nii.gz note: label 2 not found in volume note: label 7 not found in volume note: label 26 not found in volume note: label 41 not found in volume note: label 46 not found in volume note: label 58 not found in volume 3) processing /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template18-2-sub-01.NIFTYREG.nii.gz 4) processing /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/manseg-Template25-2-sub-01.NIFTYREG.nii.gz note: label 2 not found in volume note: label 7 not found in volume note: label 26 not found in volume note: label 41 not found in volume note: label 46 not found in volume note: label 58 not found in volume optimizing for intensity parameters and Q (E-step) running iteration 1 mean Q increment: 0.021064 mean Q increment: 0.010224 mean Q increment: 0.006251 mean Q increment: 0.004163 mean Q increment: 0.002904 mean Q increment: 0.002091 mean Q increment: 0.001541 mean Q increment: 0.001156 mean Q increment: 0.000880 mean Q increment: 0.000678 max change: 145.20 running iteration 2 mean Q increment: 0.008275 mean Q increment: 0.003421 mean Q increment: 0.001846 mean Q increment: 0.001154 mean Q increment: 0.000772 mean Q increment: 0.000541 mean Q increment: 0.000390 mean Q increment: 0.000288 mean Q increment: 0.000216 mean Q increment: 0.000165 max change: 95.52 running iteration 3 mean Q increment: 0.005336 mean Q increment: 0.002115 mean Q increment: 0.001091 mean Q increment: 0.000663 mean Q increment: 0.000436 mean Q increment: 0.000302 mean Q increment: 0.000216 mean Q increment: 0.000158 mean Q increment: 0.000118 mean Q increment: 0.000089 max change: 56.49 running iteration 4 mean Q increment: 0.003237 mean Q increment: 0.001287 mean Q increment: 0.000658 mean Q increment: 0.000398 mean Q increment: 0.000262 mean Q increment: 0.000181 mean Q increment: 0.000130 mean Q increment: 0.000095 max change: 45.00 running iteration 5 mean Q increment: 0.001789 mean Q increment: 0.000738 mean Q increment: 0.000387 mean Q increment: 0.000239 mean Q increment: 0.000160 mean Q increment: 0.000112 mean Q increment: 0.000081 max change: 32.54 running iteration 6 mean Q increment: 0.000917 mean Q increment: 0.000391 mean Q increment: 0.000210 mean Q increment: 0.000132 mean Q increment: 0.000090 max change: 21.71 running iteration 7 mean Q increment: 0.000478 mean Q increment: 0.000217 mean Q increment: 0.000125 mean Q increment: 0.000082 max change: 17.27 running iteration 8 mean Q increment: 0.000278 mean Q increment: 0.000137 mean Q increment: 0.000083 max change: 15.25 running iteration 9 mean Q increment: 0.000192 mean Q increment: 0.000099 max change: 13.08 running iteration 10 mean Q increment: 0.000167 mean Q increment: 0.000090 max change: 11.11 running iteration 11 mean Q increment: 0.000148 mean Q increment: 0.000081 max change: 9.62 running iteration 12 mean Q increment: 0.000140 mean Q increment: 0.000076 max change: 8.52 running iteration 13 mean Q increment: 0.000132 mean Q increment: 0.000072 max change: 8.74 running iteration 14 mean Q increment: 0.000128 mean Q increment: 0.000070 max change: 8.87 running iteration 15 mean Q increment: 0.000127 mean Q increment: 0.000068 max change: 8.96 running iteration 16 mean Q increment: 0.000132 mean Q increment: 0.000071 max change: 9.00 running iteration 17 mean Q increment: 0.000151 mean Q increment: 0.000077 max change: 9.07 running iteration 18 mean Q increment: 0.000142 mean Q increment: 0.000076 max change: 9.15 running iteration 19 mean Q increment: 0.000144 mean Q increment: 0.000079 max change: 9.26 running iteration 20 mean Q increment: 0.000145 mean Q increment: 0.000080 max change: 9.42 collecting label contributions from each atlas performing markov random field label-smoothing mri_binarize --match 2 41 --count /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/sub-01-BETA0.3-RHO.70.labels.mrf.count.txt --i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/sub-01-BETA0.3-RHO.70.labels.mrf.nii.gz --noverbose niiRead(): detected input as 64 bit double, reading in as 32 bit float Starting parallel 1 cp /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/sub-01-BETA0.3-RHO.70.labels.mrf.nii.gz /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz mri_binarize --i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz --replace 48 49 --replace 9 10 --o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz infant-dev-4a14499 cwd /u/j/ms2290 cmdline mri_binarize --i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz --replace 48 49 --replace 9 10 --o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz sysname Linux hostname fhpc-1840 machine x86_64 user ms2290 input /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz Binarizing based on threshold min -infinity 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 Replacing 2 1: 48 49 2: 9 10 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Writing output to /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz Count: -1 -1.000000 16777216 -0.000006 mri_binarize done mri_binarize --i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz --o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/alllabelmask.nii.gz --min 1 infant-dev-4a14499 cwd /u/j/ms2290 cmdline mri_binarize --i /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz --o /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/alllabelmask.nii.gz --min 1 sysname Linux hostname fhpc-1840 machine x86_64 user ms2290 input /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/aseg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/alllabelmask.nii.gz Binarizing based on threshold min 1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 875775 values in range Counting number of voxels in first frame Found 875774 voxels in final mask Writing output to /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/alllabelmask.nii.gz Count: 875774 875774.000000 16777216 5.220020 mri_binarize done mri_distance_transform /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/alllabelmask.nii.gz 1 3 3 /data/ewalton/marlene/infant_FS_testsubject/output/sub-01_infantseparate/work/alllabelmask.distmap.nii.gz mri_distance_transform