External Email - Use Caution
Hi FreeSurfer team,
I'm trying to run the infant freesurfer (version:
freesurfer-infant-20200205 ) and get the following error:
ln: failed to create symbolic link 'brain.nii.gz': Operation not supported
The command I used was:
infant_recon_all --s 002B --age 0
I think this may have to do with the fact that my subjects_dir is located
on a server (not the computer I'm running FreeSurfer on), since when I ran
the command with the subjects_dir located on my local computer it ran fine
and completed without errors. Unfortunately for space reasons it isn't
possible for me to do that for my entire dataset.
Thanks,
Fleur
--
Fleur Warton
Logfile for infant_recon_all
Mon Sep 21 11:18:40 SAST 2020
--s 002B --age 0
$Id: infant_recon_all,v 1.00 2017/01/10 12:27:40 lzollei Exp $
buddha
Linux buddha 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
INPUT FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz
mri_nu_correct.mni --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz --n 2
/usr/bin/bc
/home/fleur
/usr/local/infantFS/bin/mri_nu_correct.mni
--i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux buddha 4.15.0-112-generic #113-Ubuntu SMP Thu Jul 9 23:41:39 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Mon Sep 21 11:18:40 SAST 2020
Found /dev/shm , will use for temp dir
tmpdir is /dev/shm/tmp.mri_nu_correct.mni.59646
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/home/fleur
mri_convert /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc -odt float
mri_convert /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc -odt float
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz...
TR=2540.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, 0)
j_ras = (0.0139622, -0, -0.999903)
k_ras = (-0.999903, -0, -0.0139622)
changing data type from short to float (noscale = 0)...
writing to /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc...
--------------------------------------------------------
Iteration 1 Mon Sep 21 11:18:40 SAST 2020
nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu1.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.59646/0/
[fleur@buddha:/home/fleur/] [2020-09-21 11:18:40] running:
/usr/local/infantFS/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /dev/shm/tmp.mri_nu_correct.mni.59646/0/ /dev/shm/tmp.mri_nu_correct.mni.59646/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu1.imp
Processing:.................................................Done
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Processing:.................................................Done
Number of iterations: 33
CV of field change: 0.000953628
--------------------------------------------------------
Iteration 2 Mon Sep 21 11:18:50 SAST 2020
nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.59646/nu1.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.59646/1/
[fleur@buddha:/home/fleur/] [2020-09-21 11:18:50] running:
/usr/local/infantFS/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /dev/shm/tmp.mri_nu_correct.mni.59646/1/ /dev/shm/tmp.mri_nu_correct.mni.59646/nu1.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.imp
Processing:.................................................Done
Processing:.................................................Done
Processing:.................................................Done
Processing:.................................................Done
Processing:.................................................Done
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Processing:.................................................Done
Processing:.................................................Done
Number of iterations: 28
CV of field change: 0.000989219
mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fleur
cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz
sysname Linux
hostname buddha
machine x86_64
user fleur
input /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 5308416 values in range
Counting number of voxels in first frame
Found 5308415 voxels in final mask
Count: 5308415 5308415.000000 5308416 99.999981
mri_binarize done
mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --sum /dev/shm/tmp.mri_nu_correct.mni.59646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.59646/input.mean.dat
$Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --sum /dev/shm/tmp.mri_nu_correct.mni.59646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.59646/input.mean.dat
sysname Linux
hostname buddha
machine x86_64
user fleur
whitesurfname white
UseRobust 0
Loading /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz
Loading /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to /dev/shm/tmp.mri_nu_correct.mni.59646/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc --sum /dev/shm/tmp.mri_nu_correct.mni.59646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.59646/output.mean.dat
$Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc --sum /dev/shm/tmp.mri_nu_correct.mni.59646/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.59646/output.mean.dat
sysname Linux
hostname buddha
machine x86_64
user fleur
whitesurfname white
UseRobust 0
Loading /dev/shm/tmp.mri_nu_correct.mni.59646/ones.mgz
Loading /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to /dev/shm/tmp.mri_nu_correct.mni.59646/output.mean.dat
mri_segstats done
mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc mul 1.01379943233959615991
Saving result to '/dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc' (type = MINC ) [ ok ]
mri_convert /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz --like /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --conform
mri_convert /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz --like /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz --conform
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /dev/shm/tmp.mri_nu_correct.mni.59646/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, 0)
j_ras = (0.0139622, -0, -0.999903)
k_ras = (-0.999903, -0, -0.0139622)
INFO: transform src into the like-volume: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/mprage.nii.gz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 0 79.2454 1000, flo=0, fhi=0.999, dest_type=0
writing to /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz...
Mon Sep 21 11:19:05 SAST 2020
mri_nu_correct.mni done
NU FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz
mri_convert --conform-dc /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz
mri_convert --conform-dc /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.nii.gz...
TR=2540.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, 0)
j_ras = (0.0139622, -0, -0.999903)
k_ras = (-0.999903, -0, -0.0139622)
keeping DC 2 1 0
ostr PIL, width 256, size 1
K ---------------
0.00000 0.00000 1.00000 56.00000;
0.00000 1.00000 0.00000 32.00000;
-1.00000 0.00000 0.00000 224.00000;
0.00000 0.00000 0.00000 1.00000;
Kinv ---------------
0.00000 0.00000 -1.00000 224.00000;
0.00000 1.00000 0.00000 -32.00000;
1.00000 0.00000 0.00000 -56.00000;
0.00000 0.00000 0.00000 1.00000;
Smri ---------------
-0.00000 0.01396 -0.99990 73.44720;
-1.00000 -0.00000 -0.00000 64.08650;
0.00000 -0.99990 -0.01396 109.13969;
0.00000 0.00000 0.00000 1.00000;
Stemp ---------------
-0.99990 0.01396 0.00000 128.99495;
0.00000 0.00000 1.00000 -159.91350;
-0.01396 -0.99990 0.00000 141.91846;
0.00000 0.00000 0.00000 1.00000;
----------------------
Reslicing using trilinear interpolation
writing to /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz...
CONFORMED FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz
sscnn_skullstrip -i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz -o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/sscnn -c t1w --gpu -1
2020-09-21 11:19:14.016922: I tensorflow/core/platform/cpu_feature_guard.cc:137] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA
Using TensorFlow backend.
/usr/local/infantFS/python/scripts/sscnn_skullstrip:93: UserWarning: The argument 'neighbors' is deprecated and will be removed in scikit-image 0.18, use 'connectivity' instead. For neighbors=8, use connectivity=3
label_img_data = skimage.measure.label(np.int8(hard_img_data), neighbors=8)
mri_convert --conform /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg/002B/work/mprage.nu.conf.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/sscnn/conformed.nii.gz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg/002B/work/mprage.nu.conf.nii.gz...
TR=2540.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999903, 0, -0.0139622)
j_ras = (0.0139622, 0, -0.999903)
k_ras = (0, 1, 0)
Reslicing using trilinear interpolation
writing to /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/sscnn/conformed.nii.gz...
[<tf.Tensor 'bnorm_D_1_00_1/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_01_1/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_10_1/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_11_1/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_20_1/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_21_1/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_30_1/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_31_1/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_40_1/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_41_1/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_50_1/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>, <tf.Tensor 'bnorm_D_1_51_1/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>]
12
Loaded model file: /usr/local/infantFS/average/sscnn_skullstripping/cor_sscnn.h5
1.3144329896907216
Image max is :1.3144329896907216
[<tf.Tensor 'bnorm_D_1_00_3/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_01_3/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_10_3/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_11_3/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_20_3/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_21_3/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_30_3/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_31_3/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_40_3/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_41_3/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_50_3/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>, <tf.Tensor 'bnorm_D_1_51_3/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>]
12
Loaded model file: /usr/local/infantFS/average/sscnn_skullstripping/ax_sscnn.h5
1.3144329896907216
Image max is :1.3144329896907216
[<tf.Tensor 'bnorm_D_1_00_5/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_01_5/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_10_5/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_11_5/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_20_5/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_21_5/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_30_5/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_31_5/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_40_5/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_41_5/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_50_5/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>, <tf.Tensor 'bnorm_D_1_51_5/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>]
12
Loaded model file: /usr/local/infantFS/average/sscnn_skullstripping/sag_sscnn.h5
1.3144329896907216
Image max is :1.3144329896907216
mv /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/sscnn/sscnn_skullstrip.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.mask.nii.gz
MASK FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.mask.nii.gz
mri_mask /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.mask.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
DoAbs = 0
MRImask(): AllowDiffGeom = 1
INFO: MRImask() using MRImaskDifferentGeometry()
Writing masked volume to /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz...done.
MASKED FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
MASKED FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
find_neighbors_byAge_extended.csh --age 0 --trages 9 7 6 5 18 12 0 0 3 8 10 10 18 4 2 14 3 16 0 12 0 15 5 17 16 0 --trpool Template1 Template2 Template3 Template4 Template5 Template6 Template7 Template8 Template9 Template10 Template11 Template12 Template13 Template14 Template15 Template16 Template17 Template18 Template19 Template20 Template21 Template22 Template23 Template24 Template25 Template26 --k 4 --outfile /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/selectedtrainingsubjects.txt --gmwm --gmwmtrpool Template5 Template6 Template8 Template10 Template13 Template18 Template20 Template22 Template26 --gmwmtrages 18 12 0 8 18 16 12 15 0
Template7 Template8 Template19 Template21
reg_aladin -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.affine.txt -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.affine.nii.gz -voff
Padding value here nan
reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.nii.gz
[reg_f3d]
[reg_f3d] Command line:
[reg_f3d] reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.nii.gz
[reg_f3d]
[reg_f3d] OpenMP is used with 32 thread(s)
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] INPUT PARAMETERS
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Reference image:
[NiftyReg F3D] * name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38]
[NiftyReg F3D] * binnining size for timepoint 0/0: 64
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D]
[NiftyReg F3D] Floating image:
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D] * name: /usr/local/infantFS/average/CNYBCH/Template7/norm.nii.gz
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38]
[NiftyReg F3D] * binnining size for timepoint 0/0: 64
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D]
[NiftyReg F3D] Warped image padding value: nan
[NiftyReg F3D]
[NiftyReg F3D] Level number: 3
[NiftyReg F3D]
[NiftyReg F3D] Maximum iteration number during the last level: 150
[NiftyReg F3D]
[NiftyReg F3D] Final spacing in mm: -5 -5 -5
[NiftyReg F3D]
[NiftyReg F3D] The NMI is used as a similarity measure.
[NiftyReg F3D] Similarity measure term weight: 0.989
[NiftyReg F3D]
[NiftyReg F3D] Bending energy penalty term weight: 0.001
[NiftyReg F3D]
[NiftyReg F3D] Linear energy penalty term weight: 0.01
[NiftyReg F3D]
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 1 / 3
[NiftyReg F3D] Maximum iteration number: 600
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1
[NiftyReg F3D] * image spacing: 4 x 4 x 4 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1
[NiftyReg F3D] * image spacing: 4 x 4 x 4 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 16 x 16 x 16
[NiftyReg F3D] * image spacing: 20 x 20 x 20 mm
[NiftyReg F3D] Initial objective function: 1.07208 = (wSIM)1.07208 - (wBE)5.57221e-14 - (wLE)1.60795e-06 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [10] Current objective function: 1.07621 = (wSIM)1.07621 - (wBE)5.02e-07 - (wLE)1.67e-06 [+ 6 mm]
[NiftyReg F3D] [19] Current objective function: 1.07649 = (wSIM)1.07649 - (wBE)1.17e-06 - (wLE)1.73e-06 [+ 2 mm]
[NiftyReg F3D] [28] Current objective function: 1.07727 = (wSIM)1.07727 - (wBE)1.57e-06 - (wLE)1.75e-06 [+ 2.06875 mm]
[NiftyReg F3D] [36] Current objective function: 1.07772 = (wSIM)1.07773 - (wBE)1.78e-06 - (wLE)1.75e-06 [+ 2.06875 mm]
[NiftyReg F3D] [44] Current objective function: 1.07784 = (wSIM)1.07784 - (wBE)2.13e-06 - (wLE)1.76e-06 [+ 1.03437 mm]
[NiftyReg F3D] [54] Current objective function: 1.07836 = (wSIM)1.07836 - (wBE)2.74e-06 - (wLE)1.80e-06 [+ 1.75973 mm]
[NiftyReg F3D] [64] Current objective function: 1.07854 = (wSIM)1.07854 - (wBE)3.52e-06 - (wLE)1.83e-06 [+ 1.18837 mm]
[NiftyReg F3D] [73] Current objective function: 1.079 = (wSIM)1.07901 - (wBE)4.56e-06 - (wLE)1.87e-06 [+ 1.27007 mm]
[NiftyReg F3D] [82] Current objective function: 1.07941 = (wSIM)1.07942 - (wBE)5.29e-06 - (wLE)1.89e-06 [+ 1.35739 mm]
[NiftyReg F3D] [90] Current objective function: 1.07954 = (wSIM)1.07954 - (wBE)5.70e-06 - (wLE)1.91e-06 [+ 0.678693 mm]
[NiftyReg F3D] [97] Current objective function: 1.07962 = (wSIM)1.07962 - (wBE)6.24e-06 - (wLE)1.93e-06 [+ 0.678693 mm]
[NiftyReg F3D] [106] Current objective function: 1.07974 = (wSIM)1.07975 - (wBE)6.80e-06 - (wLE)1.96e-06 [+ 1.1033 mm]
[NiftyReg F3D] [113] Current objective function: 1.07981 = (wSIM)1.07982 - (wBE)7.17e-06 - (wLE)1.97e-06 [+ 0.55165 mm]
[NiftyReg F3D] [119] Current objective function: 1.07989 = (wSIM)1.0799 - (wBE)7.52e-06 - (wLE)1.99e-06 [+ 0.55165 mm]
[NiftyReg F3D] [128] Current objective function: 1.08004 = (wSIM)1.08005 - (wBE)8.03e-06 - (wLE)2.01e-06 [+ 0.938495 mm]
[NiftyReg F3D] [135] Current objective function: 1.08009 = (wSIM)1.0801 - (wBE)8.63e-06 - (wLE)2.03e-06 [+ 0.938495 mm]
[NiftyReg F3D] [142] Current objective function: 1.08012 = (wSIM)1.08013 - (wBE)9.24e-06 - (wLE)2.05e-06 [+ 0.469247 mm]
[NiftyReg F3D] [149] Current objective function: 1.08026 = (wSIM)1.08027 - (wBE)9.60e-06 - (wLE)2.06e-06 [+ 0.985419 mm]
[NiftyReg F3D] [156] Current objective function: 1.08026 = (wSIM)1.08027 - (wBE)9.96e-06 - (wLE)2.07e-06 [+ 0.49271 mm]
[NiftyReg F3D] [162] Current objective function: 1.08044 = (wSIM)1.08045 - (wBE)1.02e-05 - (wLE)2.08e-06 [+ 0.49271 mm]
[NiftyReg F3D] [168] Current objective function: 1.08045 = (wSIM)1.08046 - (wBE)1.04e-05 - (wLE)2.09e-06 [+ 0.49271 mm]
[NiftyReg F3D] [174] Current objective function: 1.08047 = (wSIM)1.08048 - (wBE)1.05e-05 - (wLE)2.09e-06 [+ 0.246355 mm]
[NiftyReg F3D] [180] Current objective function: 1.08052 = (wSIM)1.08053 - (wBE)1.06e-05 - (wLE)2.10e-06 [+ 0.38185 mm]
[NiftyReg F3D] [185] Current objective function: 1.08052 = (wSIM)1.08053 - (wBE)1.06e-05 - (wLE)2.10e-06 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 2 / 3
[NiftyReg F3D] Maximum iteration number: 300
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1
[NiftyReg F3D] * image spacing: 2 x 2 x 2 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1
[NiftyReg F3D] * image spacing: 2 x 2 x 2 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 29 x 29 x 29
[NiftyReg F3D] * image spacing: 10 x 10 x 10 mm
[NiftyReg F3D] Initial objective function: 1.06405 = (wSIM)1.06406 - (wBE)1.02817e-05 - (wLE)8.06882e-06 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [10] Current objective function: 1.06482 = (wSIM)1.06484 - (wBE)1.24e-05 - (wLE)8.13e-06 [+ 3 mm]
[NiftyReg F3D] [19] Current objective function: 1.06525 = (wSIM)1.06528 - (wBE)1.84e-05 - (wLE)8.36e-06 [+ 2 mm]
[NiftyReg F3D] [29] Current objective function: 1.06571 = (wSIM)1.06574 - (wBE)2.41e-05 - (wLE)8.59e-06 [+ 2.25 mm]
[NiftyReg F3D] [38] Current objective function: 1.06579 = (wSIM)1.06584 - (wBE)3.29e-05 - (wLE)8.92e-06 [+ 2 mm]
[NiftyReg F3D] [49] Current objective function: 1.06618 = (wSIM)1.06623 - (wBE)3.98e-05 - (wLE)9.13e-06 [+ 2.15937 mm]
[NiftyReg F3D] [58] Current objective function: 1.06643 = (wSIM)1.06648 - (wBE)4.94e-05 - (wLE)9.42e-06 [+ 2 mm]
[NiftyReg F3D] [67] Current objective function: 1.06646 = (wSIM)1.06654 - (wBE)6.44e-05 - (wLE)9.91e-06 [+ 2 mm]
[NiftyReg F3D] [77] Current objective function: 1.06674 = (wSIM)1.06682 - (wBE)7.47e-05 - (wLE)1.02e-05 [+ 2.25 mm]
[NiftyReg F3D] [86] Current objective function: 1.06684 = (wSIM)1.06693 - (wBE)8.23e-05 - (wLE)1.04e-05 [+ 1 mm]
[NiftyReg F3D] [94] Current objective function: 1.06693 = (wSIM)1.06703 - (wBE)8.70e-05 - (wLE)1.05e-05 [+ 1 mm]
[NiftyReg F3D] [102] Current objective function: 1.06694 = (wSIM)1.06705 - (wBE)9.46e-05 - (wLE)1.08e-05 [+ 1 mm]
[NiftyReg F3D] [113] Current objective function: 1.06709 = (wSIM)1.0672 - (wBE)9.68e-05 - (wLE)1.08e-05 [+ 1.62562 mm]
[NiftyReg F3D] [123] Current objective function: 1.06711 = (wSIM)1.06722 - (wBE)9.94e-05 - (wLE)1.09e-05 [+ 0.462287 mm]
[NiftyReg F3D] [131] Current objective function: 1.06717 = (wSIM)1.06729 - (wBE)1.03e-04 - (wLE)1.10e-05 [+ 0.970803 mm]
[NiftyReg F3D] [142] Current objective function: 1.06718 = (wSIM)1.0673 - (wBE)1.09e-04 - (wLE)1.11e-05 [+ 0.588853 mm]
[NiftyReg F3D] [152] Current objective function: 1.06724 = (wSIM)1.06737 - (wBE)1.12e-04 - (wLE)1.12e-05 [+ 0.795319 mm]
[NiftyReg F3D] [161] Current objective function: 1.06725 = (wSIM)1.06738 - (wBE)1.15e-04 - (wLE)1.13e-05 [+ 0.452338 mm]
[NiftyReg F3D] [169] Current objective function: 1.06729 = (wSIM)1.06742 - (wBE)1.19e-04 - (wLE)1.14e-05 [+ 0.576731 mm]
[NiftyReg F3D] [178] Current objective function: 1.06734 = (wSIM)1.06747 - (wBE)1.24e-04 - (wLE)1.15e-05 [+ 0.656031 mm]
[NiftyReg F3D] [186] Current objective function: 1.06735 = (wSIM)1.0675 - (wBE)1.33e-04 - (wLE)1.18e-05 [+ 0.656031 mm]
[NiftyReg F3D] [194] Current objective function: 1.06737 = (wSIM)1.06753 - (wBE)1.42e-04 - (wLE)1.21e-05 [+ 0.656031 mm]
[NiftyReg F3D] [202] Current objective function: 1.06743 = (wSIM)1.06759 - (wBE)1.50e-04 - (wLE)1.23e-05 [+ 0.656031 mm]
[NiftyReg F3D] [210] Current objective function: 1.06745 = (wSIM)1.06763 - (wBE)1.62e-04 - (wLE)1.26e-05 [+ 0.656031 mm]
[NiftyReg F3D] [218] Current objective function: 1.06753 = (wSIM)1.06771 - (wBE)1.68e-04 - (wLE)1.28e-05 [+ 0.656031 mm]
[NiftyReg F3D] [228] Current objective function: 1.06753 = (wSIM)1.06772 - (wBE)1.78e-04 - (wLE)1.31e-05 [+ 0.725939 mm]
[NiftyReg F3D] [236] Current objective function: 1.06753 = (wSIM)1.06774 - (wBE)1.88e-04 - (wLE)1.34e-05 [+ 0.725939 mm]
[NiftyReg F3D] [244] Current objective function: 1.06755 = (wSIM)1.06777 - (wBE)2.00e-04 - (wLE)1.38e-05 [+ 0.725939 mm]
[NiftyReg F3D] [253] Current objective function: 1.06758 = (wSIM)1.0678 - (wBE)2.13e-04 - (wLE)1.42e-05 [+ 0.750893 mm]
[NiftyReg F3D] [261] Current objective function: 1.06764 = (wSIM)1.06788 - (wBE)2.23e-04 - (wLE)1.45e-05 [+ 0.750893 mm]
[NiftyReg F3D] [269] Current objective function: 1.06766 = (wSIM)1.0679 - (wBE)2.30e-04 - (wLE)1.47e-05 [+ 0.375447 mm]
[NiftyReg F3D] [278] Current objective function: 1.06767 = (wSIM)1.06792 - (wBE)2.35e-04 - (wLE)1.49e-05 [+ 0.319364 mm]
[NiftyReg F3D] [286] Current objective function: 1.06769 = (wSIM)1.06794 - (wBE)2.38e-04 - (wLE)1.50e-05 [+ 0.341321 mm]
[NiftyReg F3D] [293] Current objective function: 1.0677 = (wSIM)1.06795 - (wBE)2.40e-04 - (wLE)1.51e-05 [+ 0.17066 mm]
[NiftyReg F3D] [299] Current objective function: 1.0677 = (wSIM)1.06795 - (wBE)2.41e-04 - (wLE)1.51e-05 [+ 0.0853302 mm]
[NiftyReg F3D] [300] Current objective function: 1.0677 = (wSIM)1.06795 - (wBE)2.41e-04 - (wLE)1.51e-05 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 3 / 3
[NiftyReg F3D] Maximum iteration number: 150
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 55 x 55 x 55
[NiftyReg F3D] * image spacing: 5 x 5 x 5 mm
[NiftyReg F3D] Initial objective function: 1.05466 = (wSIM)1.05489 - (wBE)0.000182728 - (wLE)4.84044e-05 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [11] Current objective function: 1.05491 = (wSIM)1.05522 - (wBE)2.61e-04 - (wLE)5.14e-05 [+ 2.5 mm]
[NiftyReg F3D] [21] Current objective function: 1.05504 = (wSIM)1.05549 - (wBE)3.94e-04 - (wLE)5.57e-05 [+ 1.5 mm]
[NiftyReg F3D] [30] Current objective function: 1.05504 = (wSIM)1.05565 - (wBE)5.50e-04 - (wLE)6.04e-05 [+ 1 mm]
[NiftyReg F3D] [39] Current objective function: 1.05506 = (wSIM)1.05573 - (wBE)6.02e-04 - (wLE)6.19e-05 [+ 1 mm]
[NiftyReg F3D] [47] Current objective function: 1.05506 = (wSIM)1.05573 - (wBE)6.02e-04 - (wLE)6.19e-05 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[reg_f3d] Registration performed in 0 min 33 sec
[reg_f3d] Have a good day !
reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz -inter 0
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Command line:
reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template7/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template7-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz -inter 0
Parameters
Reference image name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
256x256x256 voxels, 1 volumes
1x1x1 mm
Floating image name: /usr/local/infantFS/average/CNYBCH/Template7/manualseg.nii.gz
256x256x256 voxels, 1 volumes
1x1x1 mm
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[NiftyReg] Resampled image has been saved: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz
reg_aladin -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.affine.txt -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.affine.nii.gz -voff
Padding value here nan
reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.nii.gz
[reg_f3d]
[reg_f3d] Command line:
[reg_f3d] reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.nii.gz
[reg_f3d]
[reg_f3d] OpenMP is used with 32 thread(s)
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] INPUT PARAMETERS
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Reference image:
[NiftyReg F3D] * name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38]
[NiftyReg F3D] * binnining size for timepoint 0/0: 64
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D]
[NiftyReg F3D] Floating image:
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D] * name: /usr/local/infantFS/average/CNYBCH/Template8/norm.nii.gz
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38]
[NiftyReg F3D] * binnining size for timepoint 0/0: 64
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D]
[NiftyReg F3D] Warped image padding value: nan
[NiftyReg F3D]
[NiftyReg F3D] Level number: 3
[NiftyReg F3D]
[NiftyReg F3D] Maximum iteration number during the last level: 150
[NiftyReg F3D]
[NiftyReg F3D] Final spacing in mm: -5 -5 -5
[NiftyReg F3D]
[NiftyReg F3D] The NMI is used as a similarity measure.
[NiftyReg F3D] Similarity measure term weight: 0.989
[NiftyReg F3D]
[NiftyReg F3D] Bending energy penalty term weight: 0.001
[NiftyReg F3D]
[NiftyReg F3D] Linear energy penalty term weight: 0.01
[NiftyReg F3D]
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 1 / 3
[NiftyReg F3D] Maximum iteration number: 600
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1
[NiftyReg F3D] * image spacing: 4 x 4 x 4 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1
[NiftyReg F3D] * image spacing: 4 x 4 x 4 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 16 x 16 x 16
[NiftyReg F3D] * image spacing: 20 x 20 x 20 mm
[NiftyReg F3D] Initial objective function: 1.06902 = (wSIM)1.06902 - (wBE)6.60901e-14 - (wLE)5.1736e-06 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [10] Current objective function: 1.07304 = (wSIM)1.07305 - (wBE)1.46e-06 - (wLE)5.28e-06 [+ 8 mm]
[NiftyReg F3D] [19] Current objective function: 1.07379 = (wSIM)1.0738 - (wBE)3.63e-06 - (wLE)5.41e-06 [+ 4 mm]
[NiftyReg F3D] [28] Current objective function: 1.07416 = (wSIM)1.07417 - (wBE)5.10e-06 - (wLE)5.46e-06 [+ 2 mm]
[NiftyReg F3D] [37] Current objective function: 1.0756 = (wSIM)1.07561 - (wBE)5.76e-06 - (wLE)5.40e-06 [+ 4.2 mm]
[NiftyReg F3D] [47] Current objective function: 1.0763 = (wSIM)1.07631 - (wBE)6.47e-06 - (wLE)5.37e-06 [+ 2.06875 mm]
[NiftyReg F3D] [56] Current objective function: 1.07741 = (wSIM)1.07742 - (wBE)6.65e-06 - (wLE)5.38e-06 [+ 3.20656 mm]
[NiftyReg F3D] [64] Current objective function: 1.07741 = (wSIM)1.07742 - (wBE)6.65e-06 - (wLE)5.38e-06 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 2 / 3
[NiftyReg F3D] Maximum iteration number: 300
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1
[NiftyReg F3D] * image spacing: 2 x 2 x 2 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1
[NiftyReg F3D] * image spacing: 2 x 2 x 2 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 29 x 29 x 29
[NiftyReg F3D] * image spacing: 10 x 10 x 10 mm
[NiftyReg F3D] Initial objective function: 1.06224 = (wSIM)1.06227 - (wBE)6.72245e-06 - (wLE)1.97996e-05 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [11] Current objective function: 1.06359 = (wSIM)1.06361 - (wBE)7.71e-06 - (wLE)1.97e-05 [+ 3.06875 mm]
[NiftyReg F3D] [22] Current objective function: 1.06437 = (wSIM)1.06441 - (wBE)1.16e-05 - (wLE)1.97e-05 [+ 5 mm]
[NiftyReg F3D] [33] Current objective function: 1.06484 = (wSIM)1.06488 - (wBE)1.94e-05 - (wLE)1.99e-05 [+ 2.6375 mm]
[NiftyReg F3D] [43] Current objective function: 1.06538 = (wSIM)1.06543 - (wBE)2.88e-05 - (wLE)2.01e-05 [+ 2.25 mm]
[NiftyReg F3D] [53] Current objective function: 1.06589 = (wSIM)1.06595 - (wBE)3.61e-05 - (wLE)2.03e-05 [+ 3 mm]
[NiftyReg F3D] [62] Current objective function: 1.06615 = (wSIM)1.06622 - (wBE)4.56e-05 - (wLE)2.06e-05 [+ 2 mm]
[NiftyReg F3D] [71] Current objective function: 1.06624 = (wSIM)1.06632 - (wBE)6.16e-05 - (wLE)2.11e-05 [+ 2 mm]
[NiftyReg F3D] [80] Current objective function: 1.06634 = (wSIM)1.06645 - (wBE)8.24e-05 - (wLE)2.16e-05 [+ 2 mm]
[NiftyReg F3D] [90] Current objective function: 1.0668 = (wSIM)1.06693 - (wBE)1.03e-04 - (wLE)2.21e-05 [+ 2.5 mm]
[NiftyReg F3D] [99] Current objective function: 1.06697 = (wSIM)1.06711 - (wBE)1.20e-04 - (wLE)2.25e-05 [+ 2 mm]
[NiftyReg F3D] [108] Current objective function: 1.06705 = (wSIM)1.06721 - (wBE)1.34e-04 - (wLE)2.28e-05 [+ 1 mm]
[NiftyReg F3D] [117] Current objective function: 1.0673 = (wSIM)1.06746 - (wBE)1.39e-04 - (wLE)2.30e-05 [+ 1.275 mm]
[NiftyReg F3D] [128] Current objective function: 1.06737 = (wSIM)1.06754 - (wBE)1.44e-04 - (wLE)2.31e-05 [+ 0.705434 mm]
[NiftyReg F3D] [137] Current objective function: 1.06747 = (wSIM)1.06764 - (wBE)1.48e-04 - (wLE)2.32e-05 [+ 0.802431 mm]
[NiftyReg F3D] [146] Current objective function: 1.06756 = (wSIM)1.06773 - (wBE)1.54e-04 - (wLE)2.33e-05 [+ 1.24377 mm]
[NiftyReg F3D] [155] Current objective function: 1.06757 = (wSIM)1.06776 - (wBE)1.64e-04 - (wLE)2.36e-05 [+ 1.24377 mm]
[NiftyReg F3D] [165] Current objective function: 1.06763 = (wSIM)1.06783 - (wBE)1.79e-04 - (wLE)2.40e-05 [+ 1.26514 mm]
[NiftyReg F3D] [174] Current objective function: 1.06775 = (wSIM)1.06797 - (wBE)1.89e-04 - (wLE)2.42e-05 [+ 1.26514 mm]
[NiftyReg F3D] [183] Current objective function: 1.06778 = (wSIM)1.06799 - (wBE)1.94e-04 - (wLE)2.44e-05 [+ 0.316286 mm]
[NiftyReg F3D] [192] Current objective function: 1.06784 = (wSIM)1.06806 - (wBE)1.98e-04 - (wLE)2.45e-05 [+ 0.514163 mm]
[NiftyReg F3D] [199] Current objective function: 1.06786 = (wSIM)1.06808 - (wBE)2.00e-04 - (wLE)2.46e-05 [+ 0.514163 mm]
[NiftyReg F3D] [206] Current objective function: 1.06786 = (wSIM)1.06808 - (wBE)2.02e-04 - (wLE)2.46e-05 [+ 0.128541 mm]
[NiftyReg F3D] [212] Current objective function: 1.06787 = (wSIM)1.0681 - (wBE)2.02e-04 - (wLE)2.46e-05 [+ 0.163889 mm]
[NiftyReg F3D] [217] Current objective function: 1.06787 = (wSIM)1.0681 - (wBE)2.02e-04 - (wLE)2.46e-05 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 3 / 3
[NiftyReg F3D] Maximum iteration number: 150
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 55 x 55 x 55
[NiftyReg F3D] * image spacing: 5 x 5 x 5 mm
[NiftyReg F3D] Initial objective function: 1.05542 = (wSIM)1.05566 - (wBE)0.000155494 - (wLE)8.18335e-05 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [11] Current objective function: 1.0557 = (wSIM)1.05601 - (wBE)2.32e-04 - (wLE)8.47e-05 [+ 2.25 mm]
[NiftyReg F3D] [21] Current objective function: 1.05581 = (wSIM)1.05626 - (wBE)3.58e-04 - (wLE)8.87e-05 [+ 1.5 mm]
[NiftyReg F3D] [30] Current objective function: 1.05584 = (wSIM)1.05641 - (wBE)4.80e-04 - (wLE)9.23e-05 [+ 1 mm]
[NiftyReg F3D] [39] Current objective function: 1.05586 = (wSIM)1.05648 - (wBE)5.23e-04 - (wLE)9.36e-05 [+ 0.5 mm]
[NiftyReg F3D] [46] Current objective function: 1.05586 = (wSIM)1.05648 - (wBE)5.23e-04 - (wLE)9.36e-05 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[reg_f3d] Registration performed in 0 min 27 sec
[reg_f3d] Have a good day !
reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz -inter 0
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Command line:
reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template8/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template8-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz -inter 0
Parameters
Reference image name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
256x256x256 voxels, 1 volumes
1x1x1 mm
Floating image name: /usr/local/infantFS/average/CNYBCH/Template8/manualseg.nii.gz
256x256x256 voxels, 1 volumes
1x1x1 mm
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[NiftyReg] Resampled image has been saved: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz
reg_aladin -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.affine.txt -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.affine.nii.gz -voff
Padding value here nan
reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.nii.gz
[reg_f3d]
[reg_f3d] Command line:
[reg_f3d] reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.nii.gz
[reg_f3d]
[reg_f3d] OpenMP is used with 32 thread(s)
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] INPUT PARAMETERS
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Reference image:
[NiftyReg F3D] * name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38]
[NiftyReg F3D] * binnining size for timepoint 0/0: 64
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D]
[NiftyReg F3D] Floating image:
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D] * name: /usr/local/infantFS/average/CNYBCH/Template19/norm.nii.gz
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38]
[NiftyReg F3D] * binnining size for timepoint 0/0: 64
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D]
[NiftyReg F3D] Warped image padding value: nan
[NiftyReg F3D]
[NiftyReg F3D] Level number: 3
[NiftyReg F3D]
[NiftyReg F3D] Maximum iteration number during the last level: 150
[NiftyReg F3D]
[NiftyReg F3D] Final spacing in mm: -5 -5 -5
[NiftyReg F3D]
[NiftyReg F3D] The NMI is used as a similarity measure.
[NiftyReg F3D] Similarity measure term weight: 0.989
[NiftyReg F3D]
[NiftyReg F3D] Bending energy penalty term weight: 0.001
[NiftyReg F3D]
[NiftyReg F3D] Linear energy penalty term weight: 0.01
[NiftyReg F3D]
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 1 / 3
[NiftyReg F3D] Maximum iteration number: 600
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1
[NiftyReg F3D] * image spacing: 4 x 4 x 4 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1
[NiftyReg F3D] * image spacing: 4 x 4 x 4 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 16 x 16 x 16
[NiftyReg F3D] * image spacing: 20 x 20 x 20 mm
[NiftyReg F3D] Initial objective function: 1.0692 = (wSIM)1.0692 - (wBE)5.59997e-14 - (wLE)1.328e-06 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [10] Current objective function: 1.07174 = (wSIM)1.07174 - (wBE)3.57e-07 - (wLE)1.36e-06 [+ 5 mm]
[NiftyReg F3D] [20] Current objective function: 1.07186 = (wSIM)1.07186 - (wBE)1.03e-06 - (wLE)1.41e-06 [+ 2.1375 mm]
[NiftyReg F3D] [30] Current objective function: 1.07248 = (wSIM)1.07249 - (wBE)1.61e-06 - (wLE)1.42e-06 [+ 2.43141 mm]
[NiftyReg F3D] [39] Current objective function: 1.07311 = (wSIM)1.07311 - (wBE)2.05e-06 - (wLE)1.43e-06 [+ 2.43141 mm]
[NiftyReg F3D] [48] Current objective function: 1.07315 = (wSIM)1.07315 - (wBE)2.32e-06 - (wLE)1.44e-06 [+ 0.607852 mm]
[NiftyReg F3D] [56] Current objective function: 1.07351 = (wSIM)1.07351 - (wBE)2.68e-06 - (wLE)1.45e-06 [+ 0.94217 mm]
[NiftyReg F3D] [64] Current objective function: 1.07381 = (wSIM)1.07381 - (wBE)2.92e-06 - (wLE)1.46e-06 [+ 1.20127 mm]
[NiftyReg F3D] [72] Current objective function: 1.07386 = (wSIM)1.07387 - (wBE)3.22e-06 - (wLE)1.48e-06 [+ 1.20127 mm]
[NiftyReg F3D] [80] Current objective function: 1.07387 = (wSIM)1.07387 - (wBE)3.74e-06 - (wLE)1.50e-06 [+ 1.20127 mm]
[NiftyReg F3D] [88] Current objective function: 1.07397 = (wSIM)1.07397 - (wBE)4.57e-06 - (wLE)1.53e-06 [+ 1.20127 mm]
[NiftyReg F3D] [96] Current objective function: 1.07398 = (wSIM)1.07399 - (wBE)5.95e-06 - (wLE)1.58e-06 [+ 1.20127 mm]
[NiftyReg F3D] [105] Current objective function: 1.07428 = (wSIM)1.07429 - (wBE)7.33e-06 - (wLE)1.63e-06 [+ 1.28385 mm]
[NiftyReg F3D] [114] Current objective function: 1.07438 = (wSIM)1.07439 - (wBE)8.43e-06 - (wLE)1.68e-06 [+ 0.730192 mm]
[NiftyReg F3D] [121] Current objective function: 1.07465 = (wSIM)1.07467 - (wBE)9.18e-06 - (wLE)1.71e-06 [+ 0.730192 mm]
[NiftyReg F3D] [129] Current objective function: 1.07473 = (wSIM)1.07474 - (wBE)9.23e-06 - (wLE)1.71e-06 [+ 0.830593 mm]
[NiftyReg F3D] [137] Current objective function: 1.07475 = (wSIM)1.07476 - (wBE)9.25e-06 - (wLE)1.71e-06 [+ 0.264752 mm]
[NiftyReg F3D] [145] Current objective function: 1.07483 = (wSIM)1.07484 - (wBE)9.20e-06 - (wLE)1.71e-06 [+ 0.716153 mm]
[NiftyReg F3D] [151] Current objective function: 1.07483 = (wSIM)1.07484 - (wBE)9.20e-06 - (wLE)1.71e-06 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 2 / 3
[NiftyReg F3D] Maximum iteration number: 300
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1
[NiftyReg F3D] * image spacing: 2 x 2 x 2 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1
[NiftyReg F3D] * image spacing: 2 x 2 x 2 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 29 x 29 x 29
[NiftyReg F3D] * image spacing: 10 x 10 x 10 mm
[NiftyReg F3D] Initial objective function: 1.05985 = (wSIM)1.05987 - (wBE)8.91417e-06 - (wLE)6.62404e-06 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [10] Current objective function: 1.06056 = (wSIM)1.06058 - (wBE)9.48e-06 - (wLE)6.62e-06 [+ 2.125 mm]
[NiftyReg F3D] [19] Current objective function: 1.06089 = (wSIM)1.06091 - (wBE)1.31e-05 - (wLE)6.71e-06 [+ 2 mm]
[NiftyReg F3D] [29] Current objective function: 1.06141 = (wSIM)1.06144 - (wBE)1.76e-05 - (wLE)6.85e-06 [+ 2.5 mm]
[NiftyReg F3D] [38] Current objective function: 1.06167 = (wSIM)1.0617 - (wBE)2.46e-05 - (wLE)7.11e-06 [+ 2 mm]
[NiftyReg F3D] [47] Current objective function: 1.06185 = (wSIM)1.06189 - (wBE)3.22e-05 - (wLE)7.40e-06 [+ 1 mm]
[NiftyReg F3D] [56] Current objective function: 1.06216 = (wSIM)1.06221 - (wBE)3.80e-05 - (wLE)7.56e-06 [+ 2.1 mm]
[NiftyReg F3D] [65] Current objective function: 1.06231 = (wSIM)1.06236 - (wBE)4.54e-05 - (wLE)7.82e-06 [+ 2 mm]
[NiftyReg F3D] [78] Current objective function: 1.06246 = (wSIM)1.06252 - (wBE)5.38e-05 - (wLE)8.09e-06 [+ 1.12736 mm]
[NiftyReg F3D] [86] Current objective function: 1.0627 = (wSIM)1.06277 - (wBE)5.71e-05 - (wLE)8.19e-06 [+ 1.12736 mm]
[NiftyReg F3D] [94] Current objective function: 1.06277 = (wSIM)1.06284 - (wBE)6.12e-05 - (wLE)8.34e-06 [+ 0.56368 mm]
[NiftyReg F3D] [103] Current objective function: 1.06288 = (wSIM)1.06295 - (wBE)6.27e-05 - (wLE)8.40e-06 [+ 0.873704 mm]
[NiftyReg F3D] [111] Current objective function: 1.0629 = (wSIM)1.06297 - (wBE)6.47e-05 - (wLE)8.47e-06 [+ 0.436852 mm]
[NiftyReg F3D] [120] Current objective function: 1.06299 = (wSIM)1.06306 - (wBE)6.63e-05 - (wLE)8.51e-06 [+ 0.710157 mm]
[NiftyReg F3D] [128] Current objective function: 1.063 = (wSIM)1.06307 - (wBE)6.76e-05 - (wLE)8.55e-06 [+ 0.177539 mm]
[NiftyReg F3D] [135] Current objective function: 1.06303 = (wSIM)1.0631 - (wBE)6.82e-05 - (wLE)8.57e-06 [+ 0.372833 mm]
[NiftyReg F3D] [142] Current objective function: 1.06303 = (wSIM)1.0631 - (wBE)6.84e-05 - (wLE)8.58e-06 [+ 0.0466041 mm]
[NiftyReg F3D] [145] Current objective function: 1.06303 = (wSIM)1.0631 - (wBE)6.84e-05 - (wLE)8.58e-06 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 3 / 3
[NiftyReg F3D] Maximum iteration number: 150
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 55 x 55 x 55
[NiftyReg F3D] * image spacing: 5 x 5 x 5 mm
[NiftyReg F3D] Initial objective function: 1.05125 = (wSIM)1.05134 - (wBE)5.67949e-05 - (wLE)2.94078e-05 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [13] Current objective function: 1.05151 = (wSIM)1.05164 - (wBE)9.52e-05 - (wLE)3.08e-05 [+ 3.31875 mm]
[NiftyReg F3D] [23] Current objective function: 1.05169 = (wSIM)1.05195 - (wBE)2.31e-04 - (wLE)3.46e-05 [+ 2 mm]
[NiftyReg F3D] [32] Current objective function: 1.05179 = (wSIM)1.05214 - (wBE)3.14e-04 - (wLE)3.67e-05 [+ 1 mm]
[NiftyReg F3D] [41] Current objective function: 1.0518 = (wSIM)1.05223 - (wBE)3.88e-04 - (wLE)3.87e-05 [+ 1 mm]
[NiftyReg F3D] [50] Current objective function: 1.05181 = (wSIM)1.05231 - (wBE)4.57e-04 - (wLE)4.05e-05 [+ 1 mm]
[NiftyReg F3D] [59] Current objective function: 1.05183 = (wSIM)1.05235 - (wBE)4.81e-04 - (wLE)4.12e-05 [+ 0.5 mm]
[NiftyReg F3D] [67] Current objective function: 1.05183 = (wSIM)1.05236 - (wBE)4.93e-04 - (wLE)4.15e-05 [+ 0.0625 mm]
[NiftyReg F3D] [72] Current objective function: 1.05183 = (wSIM)1.05237 - (wBE)5.02e-04 - (wLE)4.17e-05 [+ 0.0625 mm]
[NiftyReg F3D] [77] Current objective function: 1.05183 = (wSIM)1.05238 - (wBE)5.04e-04 - (wLE)4.18e-05 [+ 0.015625 mm]
[NiftyReg F3D] [79] Current objective function: 1.05183 = (wSIM)1.05238 - (wBE)5.04e-04 - (wLE)4.18e-05 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[reg_f3d] Registration performed in 0 min 36 sec
[reg_f3d] Have a good day !
reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz -inter 0
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Command line:
reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template19/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template19-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz -inter 0
Parameters
Reference image name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
256x256x256 voxels, 1 volumes
1x1x1 mm
Floating image name: /usr/local/infantFS/average/CNYBCH/Template19/manualseg.nii.gz
256x256x256 voxels, 1 volumes
1x1x1 mm
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[NiftyReg] Resampled image has been saved: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz
reg_aladin -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.affine.txt -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.affine.nii.gz -voff
Padding value here nan
reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.nii.gz
[reg_f3d]
[reg_f3d] Command line:
[reg_f3d] reg_f3d -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/norm.nii.gz -aff /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.affine.txt -cpp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.nii.gz
[reg_f3d]
[reg_f3d] OpenMP is used with 32 thread(s)
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] INPUT PARAMETERS
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Reference image:
[NiftyReg F3D] * name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38]
[NiftyReg F3D] * binnining size for timepoint 0/0: 64
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D]
[NiftyReg F3D] Floating image:
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D] * name: /usr/local/infantFS/average/CNYBCH/Template21/norm.nii.gz
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] * intensity threshold for timepoint 0/0: [-3.4e+38 3.4e+38]
[NiftyReg F3D] * binnining size for timepoint 0/0: 64
[NiftyReg F3D] * gaussian smoothing sigma: 0
[NiftyReg F3D]
[NiftyReg F3D] Warped image padding value: nan
[NiftyReg F3D]
[NiftyReg F3D] Level number: 3
[NiftyReg F3D]
[NiftyReg F3D] Maximum iteration number during the last level: 150
[NiftyReg F3D]
[NiftyReg F3D] Final spacing in mm: -5 -5 -5
[NiftyReg F3D]
[NiftyReg F3D] The NMI is used as a similarity measure.
[NiftyReg F3D] Similarity measure term weight: 0.989
[NiftyReg F3D]
[NiftyReg F3D] Bending energy penalty term weight: 0.001
[NiftyReg F3D]
[NiftyReg F3D] Linear energy penalty term weight: 0.01
[NiftyReg F3D]
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 1 / 3
[NiftyReg F3D] Maximum iteration number: 600
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1
[NiftyReg F3D] * image spacing: 4 x 4 x 4 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 64 x 64 x 64 x 1
[NiftyReg F3D] * image spacing: 4 x 4 x 4 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 16 x 16 x 16
[NiftyReg F3D] * image spacing: 20 x 20 x 20 mm
[NiftyReg F3D] Initial objective function: 1.06731 = (wSIM)1.06731 - (wBE)5.27054e-14 - (wLE)1.5447e-06 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [11] Current objective function: 1.07087 = (wSIM)1.07087 - (wBE)9.66e-07 - (wLE)1.62e-06 [+ 6.1375 mm]
[NiftyReg F3D] [20] Current objective function: 1.0713 = (wSIM)1.0713 - (wBE)2.17e-06 - (wLE)1.70e-06 [+ 2 mm]
[NiftyReg F3D] [28] Current objective function: 1.07139 = (wSIM)1.0714 - (wBE)2.75e-06 - (wLE)1.73e-06 [+ 1 mm]
[NiftyReg F3D] [36] Current objective function: 1.07282 = (wSIM)1.07283 - (wBE)3.20e-06 - (wLE)1.71e-06 [+ 2.1 mm]
[NiftyReg F3D] [44] Current objective function: 1.07368 = (wSIM)1.07369 - (wBE)3.43e-06 - (wLE)1.70e-06 [+ 2.1 mm]
[NiftyReg F3D] [52] Current objective function: 1.07402 = (wSIM)1.07403 - (wBE)3.83e-06 - (wLE)1.71e-06 [+ 2.1 mm]
[NiftyReg F3D] [60] Current objective function: 1.07413 = (wSIM)1.07413 - (wBE)4.34e-06 - (wLE)1.72e-06 [+ 1.05 mm]
[NiftyReg F3D] [67] Current objective function: 1.07421 = (wSIM)1.07422 - (wBE)5.39e-06 - (wLE)1.75e-06 [+ 1.05 mm]
[NiftyReg F3D] [75] Current objective function: 1.07438 = (wSIM)1.07439 - (wBE)6.60e-06 - (wLE)1.78e-06 [+ 0.669375 mm]
[NiftyReg F3D] [85] Current objective function: 1.07494 = (wSIM)1.07495 - (wBE)7.73e-06 - (wLE)1.81e-06 [+ 1.86634 mm]
[NiftyReg F3D] [93] Current objective function: 1.07495 = (wSIM)1.07496 - (wBE)9.13e-06 - (wLE)1.85e-06 [+ 1.86634 mm]
[NiftyReg F3D] [101] Current objective function: 1.07502 = (wSIM)1.07504 - (wBE)9.77e-06 - (wLE)1.87e-06 [+ 0.933171 mm]
[NiftyReg F3D] [109] Current objective function: 1.07537 = (wSIM)1.07538 - (wBE)1.01e-05 - (wLE)1.87e-06 [+ 1.18979 mm]
[NiftyReg F3D] [117] Current objective function: 1.07559 = (wSIM)1.0756 - (wBE)1.03e-05 - (wLE)1.87e-06 [+ 1.18979 mm]
[NiftyReg F3D] [125] Current objective function: 1.07562 = (wSIM)1.07563 - (wBE)1.05e-05 - (wLE)1.87e-06 [+ 0.594897 mm]
[NiftyReg F3D] [135] Current objective function: 1.07582 = (wSIM)1.07583 - (wBE)1.06e-05 - (wLE)1.87e-06 [+ 1.06156 mm]
[NiftyReg F3D] [142] Current objective function: 1.07589 = (wSIM)1.0759 - (wBE)1.10e-05 - (wLE)1.87e-06 [+ 1.06156 mm]
[NiftyReg F3D] [149] Current objective function: 1.07596 = (wSIM)1.07597 - (wBE)1.13e-05 - (wLE)1.88e-06 [+ 0.530778 mm]
[NiftyReg F3D] [157] Current objective function: 1.07614 = (wSIM)1.07615 - (wBE)1.16e-05 - (wLE)1.88e-06 [+ 0.822706 mm]
[NiftyReg F3D] [164] Current objective function: 1.07625 = (wSIM)1.07626 - (wBE)1.18e-05 - (wLE)1.89e-06 [+ 0.822706 mm]
[NiftyReg F3D] [171] Current objective function: 1.07628 = (wSIM)1.0763 - (wBE)1.19e-05 - (wLE)1.89e-06 [+ 0.205676 mm]
[NiftyReg F3D] [179] Current objective function: 1.07634 = (wSIM)1.07635 - (wBE)1.19e-05 - (wLE)1.89e-06 [+ 0.624794 mm]
[NiftyReg F3D] [186] Current objective function: 1.07634 = (wSIM)1.07635 - (wBE)1.20e-05 - (wLE)1.89e-06 [+ 0.624794 mm]
[NiftyReg F3D] [193] Current objective function: 1.07634 = (wSIM)1.07635 - (wBE)1.21e-05 - (wLE)1.89e-06 [+ 0.624794 mm]
[NiftyReg F3D] [198] Current objective function: 1.07634 = (wSIM)1.07635 - (wBE)1.21e-05 - (wLE)1.89e-06 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 2 / 3
[NiftyReg F3D] Maximum iteration number: 300
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1
[NiftyReg F3D] * image spacing: 2 x 2 x 2 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 128 x 128 x 128 x 1
[NiftyReg F3D] * image spacing: 2 x 2 x 2 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 29 x 29 x 29
[NiftyReg F3D] * image spacing: 10 x 10 x 10 mm
[NiftyReg F3D] Initial objective function: 1.06109 = (wSIM)1.06111 - (wBE)1.16436e-05 - (wLE)7.43262e-06 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [10] Current objective function: 1.06173 = (wSIM)1.06175 - (wBE)1.45e-05 - (wLE)7.53e-06 [+ 4 mm]
[NiftyReg F3D] [20] Current objective function: 1.06238 = (wSIM)1.06242 - (wBE)2.46e-05 - (wLE)7.84e-06 [+ 3 mm]
[NiftyReg F3D] [29] Current objective function: 1.06273 = (wSIM)1.06277 - (wBE)3.50e-05 - (wLE)8.15e-06 [+ 2 mm]
[NiftyReg F3D] [38] Current objective function: 1.06314 = (wSIM)1.06319 - (wBE)4.38e-05 - (wLE)8.40e-06 [+ 2 mm]
[NiftyReg F3D] [47] Current objective function: 1.06343 = (wSIM)1.06349 - (wBE)5.26e-05 - (wLE)8.63e-06 [+ 2 mm]
[NiftyReg F3D] [56] Current objective function: 1.06369 = (wSIM)1.06376 - (wBE)6.60e-05 - (wLE)8.97e-06 [+ 2 mm]
[NiftyReg F3D] [65] Current objective function: 1.06384 = (wSIM)1.06393 - (wBE)8.09e-05 - (wLE)9.39e-06 [+ 2 mm]
[NiftyReg F3D] [74] Current objective function: 1.06403 = (wSIM)1.06414 - (wBE)1.02e-04 - (wLE)9.95e-06 [+ 2 mm]
[NiftyReg F3D] [83] Current objective function: 1.06429 = (wSIM)1.06442 - (wBE)1.22e-04 - (wLE)1.05e-05 [+ 2 mm]
[NiftyReg F3D] [92] Current objective function: 1.0644 = (wSIM)1.06455 - (wBE)1.42e-04 - (wLE)1.10e-05 [+ 1 mm]
[NiftyReg F3D] [104] Current objective function: 1.06458 = (wSIM)1.06473 - (wBE)1.45e-04 - (wLE)1.11e-05 [+ 1.64642 mm]
[NiftyReg F3D] [113] Current objective function: 1.06459 = (wSIM)1.06475 - (wBE)1.50e-04 - (wLE)1.12e-05 [+ 1.64642 mm]
[NiftyReg F3D] [122] Current objective function: 1.06463 = (wSIM)1.0648 - (wBE)1.57e-04 - (wLE)1.14e-05 [+ 1.64642 mm]
[NiftyReg F3D] [131] Current objective function: 1.06469 = (wSIM)1.06487 - (wBE)1.67e-04 - (wLE)1.17e-05 [+ 1.64642 mm]
[NiftyReg F3D] [140] Current objective function: 1.06475 = (wSIM)1.06494 - (wBE)1.80e-04 - (wLE)1.20e-05 [+ 1.64642 mm]
[NiftyReg F3D] [150] Current objective function: 1.06481 = (wSIM)1.06501 - (wBE)1.92e-04 - (wLE)1.24e-05 [+ 0.851509 mm]
[NiftyReg F3D] [158] Current objective function: 1.06488 = (wSIM)1.06509 - (wBE)2.00e-04 - (wLE)1.26e-05 [+ 0.851509 mm]
[NiftyReg F3D] [167] Current objective function: 1.06491 = (wSIM)1.06513 - (wBE)2.09e-04 - (wLE)1.29e-05 [+ 0.968591 mm]
[NiftyReg F3D] [175] Current objective function: 1.06493 = (wSIM)1.06516 - (wBE)2.17e-04 - (wLE)1.31e-05 [+ 0.968591 mm]
[NiftyReg F3D] [184] Current objective function: 1.06497 = (wSIM)1.06521 - (wBE)2.24e-04 - (wLE)1.33e-05 [+ 1.03518 mm]
[NiftyReg F3D] [192] Current objective function: 1.06498 = (wSIM)1.06522 - (wBE)2.29e-04 - (wLE)1.35e-05 [+ 0.258795 mm]
[NiftyReg F3D] [201] Current objective function: 1.06503 = (wSIM)1.06527 - (wBE)2.30e-04 - (wLE)1.35e-05 [+ 0.621756 mm]
[NiftyReg F3D] [207] Current objective function: 1.06503 = (wSIM)1.06527 - (wBE)2.30e-04 - (wLE)1.35e-05 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[NiftyReg F3D] Current level: 3 / 3
[NiftyReg F3D] Maximum iteration number: 150
[NiftyReg F3D] Current reference image
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] Current floating image
[NiftyReg F3D] * image dimension: 256 x 256 x 256 x 1
[NiftyReg F3D] * image spacing: 1 x 1 x 1 mm
[NiftyReg F3D] Current control point image
[NiftyReg F3D] * image dimension: 55 x 55 x 55
[NiftyReg F3D] * image spacing: 5 x 5 x 5 mm
[NiftyReg F3D] Initial objective function: 1.05223 = (wSIM)1.05245 - (wBE)0.000172216 - (wLE)4.2218e-05 - (wJAC)0 - (wLAN)0
[NiftyReg F3D] [12] Current objective function: 1.05242 = (wSIM)1.05272 - (wBE)2.53e-04 - (wLE)4.52e-05 [+ 2.26719 mm]
[NiftyReg F3D] [22] Current objective function: 1.05249 = (wSIM)1.05286 - (wBE)3.28e-04 - (wLE)4.77e-05 [+ 1.125 mm]
[NiftyReg F3D] [31] Current objective function: 1.05249 = (wSIM)1.05298 - (wBE)4.35e-04 - (wLE)5.11e-05 [+ 1 mm]
[NiftyReg F3D] [40] Current objective function: 1.05251 = (wSIM)1.05304 - (wBE)4.75e-04 - (wLE)5.23e-05 [+ 1 mm]
[NiftyReg F3D] [49] Current objective function: 1.05252 = (wSIM)1.05308 - (wBE)5.04e-04 - (wLE)5.31e-05 [+ 0.25 mm]
[NiftyReg F3D] [57] Current objective function: 1.05252 = (wSIM)1.05309 - (wBE)5.16e-04 - (wLE)5.35e-05 [+ 0.0796875 mm]
[NiftyReg F3D] [61] Current objective function: 1.05252 = (wSIM)1.05309 - (wBE)5.16e-04 - (wLE)5.35e-05 [+ 0 mm]
[NiftyReg F3D] Current registration level done
[NiftyReg F3D] ***********************************************************
[reg_f3d] Registration performed in 0 min 35 sec
[reg_f3d] Have a good day !
reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz -inter 0
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Command line:
reg_resample -ref /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -flo /usr/local/infantFS/average/CNYBCH/Template21/manualseg.nii.gz -trans /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/Template21-2-002B.NIFTYREG.field.nii.gz -res /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz -inter 0
Parameters
Reference image name: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz
256x256x256 voxels, 1 volumes
1x1x1 mm
Floating image name: /usr/local/infantFS/average/CNYBCH/Template21/manualseg.nii.gz
256x256x256 voxels, 1 volumes
1x1x1 mm
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
[NiftyReg] Resampled image has been saved: /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz
TRAINING SUBJECTS LABELFUSION Template7 Template8 Template19 Template21
run_label_fusion.csh --subj 002B --regtype NIFTYREG --ts Template7 Template8 Template19 Template21
ARG Template7 Template8 Template19 Template21
ARG COUNT 4
TRAINING SUBJECTS Template7 Template8 Template19 Template21
CHECKING THE INPUTS...
NUMBER OF NEIGHBORS 4
TRAINING SUBJECTS Template7 Template8 Template19 Template21
MOVED SEG FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz
MOVED SEG FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz
MOVED SEG FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz
MOVED SEG FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz
TRAININGDATA /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz
OUTPUT FILE /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.nii.gz
LABELFUSION CMD mri_label_fusion -i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz -s /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz -o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.nii.gz --smooth --rho .70 --beta 0.3 --bf-order 4 --max-lab 3 --unary-weight 5 --verbose -e 2 41 3 42 -e 7 46 8 47 -e 12 51 13 52
found 31 unique labels
computing distance maps and prior label probabilities
1) processing /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template7-2-002B.NIFTYREG.nii.gz
note: label 2 not found in volume
note: label 41 not found in volume
2) processing /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template8-2-002B.NIFTYREG.nii.gz
3) processing /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template19-2-002B.NIFTYREG.nii.gz
note: label 2 not found in volume
note: label 41 not found in volume
4) processing /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/manseg-Template21-2-002B.NIFTYREG.nii.gz
note: label 2 not found in volume
note: label 41 not found in volume
optimizing for intensity parameters and Q (E-step)
running iteration 1
mean Q increment: 0.017570
mean Q increment: 0.005664
mean Q increment: 0.002564
mean Q increment: 0.001244
mean Q increment: 0.000662
mean Q increment: 0.000364
mean Q increment: 0.000209
mean Q increment: 0.000122
mean Q increment: 0.000074
max change: 84.33
running iteration 2
mean Q increment: 0.001837
mean Q increment: 0.000553
mean Q increment: 0.000233
mean Q increment: 0.000112
mean Q increment: 0.000057
max change: 61.74
running iteration 3
mean Q increment: 0.000891
mean Q increment: 0.000269
mean Q increment: 0.000115
mean Q increment: 0.000055
max change: 48.81
running iteration 4
mean Q increment: 0.000505
mean Q increment: 0.000157
mean Q increment: 0.000068
max change: 47.34
running iteration 5
mean Q increment: 0.000327
mean Q increment: 0.000105
mean Q increment: 0.000046
max change: 41.24
running iteration 6
mean Q increment: 0.000225
mean Q increment: 0.000072
max change: 32.62
running iteration 7
mean Q increment: 0.000178
mean Q increment: 0.000060
max change: 24.91
running iteration 8
mean Q increment: 0.000138
mean Q increment: 0.000047
max change: 18.96
running iteration 9
mean Q increment: 0.000110
mean Q increment: 0.000038
max change: 14.41
running iteration 10
mean Q increment: 0.000090
max change: 10.86
running iteration 11
mean Q increment: 0.000088
max change: 7.96
running iteration 12
mean Q increment: 0.000081
max change: 6.75
running iteration 13
mean Q increment: 0.000080
max change: 6.87
running iteration 14
mean Q increment: 0.000071
max change: 6.49
running iteration 15
mean Q increment: 0.000067
max change: 6.79
running iteration 16
mean Q increment: 0.000061
max change: 6.89
running iteration 17
mean Q increment: 0.000073
max change: 7.96
running iteration 18
mean Q increment: 0.000066
max change: 6.71
running iteration 19
mean Q increment: 0.000066
max change: 6.95
running iteration 20
mean Q increment: 0.000066
max change: 6.74
collecting label contributions from each atlas
performing markov random field label-smoothing
mri_binarize --match 2 41 --count /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.count.txt --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.nii.gz --noverbose
niiRead(): detected input as 64 bit double, reading in as 32 bit float
cp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/002B-BETA0.3-RHO.70.labels.mrf.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.nii.gz
mri_binarize --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.nii.gz --o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.nii.gz --min 1
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/fleur
cmdline mri_binarize --i /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.nii.gz --o /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.nii.gz --min 1
sysname Linux
hostname buddha
machine x86_64
user fleur
input /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.nii.gz
Binarizing based on threshold
min 1
max +infinity
binval 1
binvalnot 0
niiRead(): detected input as 64 bit double, reading in as 32 bit float
fstart = 0, fend = 0, nframes = 1
Found 313677 values in range
Counting number of voxels in first frame
Found 313676 voxels in final mask
Count: 313676 313676.000000 16777216 1.869655
mri_binarize done
mri_distance_transform /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.nii.gz 1 3 3 /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/alllabelmask.distmap.nii.gz
mri_distance_transform <input volume> <label> <max_distance> <mode[=1]> <output volume>
mode : 1 = outside , mode : 2 = inside , mode : 3 = both, mode : 4 = both unsigned
label=1 distance=3 mode=3
cp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.GMWM.nii.gz
mri_correct_segmentations /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.GMWM.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.GMWM.edited.nii.gz
processing 2 input files
processing 2 input files
processing segmentation input volume /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.GMWM.nii.gz
niiRead(): detected input as 64 bit double, reading in as 32 bit float
output fname /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.GMWM.edited.nii.gz
writing output to /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.GMWM.edited.nii.gz
cp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/aseg.GMWM.edited.nii.gz /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/finalaseg.nii.gz
mkdir -p /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work//002B/mri/transforms
mkdir -p /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work//002B/surf
mkdir -p /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work//002B/label
mkdir -p /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work//002B/stats
cp /home/fleur/researchdata/UserFolders/FleurWarton/hbs_FS_seg//002B/work/mprage.nu.conf.masked.nii.gz norm.nii.gz
mri_convert norm.nii.gz norm.mgz
mri_convert norm.nii.gz norm.mgz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from norm.nii.gz...
TR=2540.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999903, 0, -0.0139622)
j_ras = (0.0139622, 0, -0.999903)
k_ras = (0, 1, 0)
writing to norm.mgz...
ln -s norm.nii.gz brain.nii.gz
ln: failed to create symbolic link 'brain.nii.gz': Operation not supported
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