Sorry, sir. I understand you now and thanks for your suggestion.
The output in the terminal and in out.txt after running the commands posted as follows:
siying@siying-vbox:~$ cd /home/siying/population_template-tmp-WZ4837/
siying@siying-vbox:~/population_template-tmp-WZ4837$ mrinfo /home/siying/sharefolder/study/template/fod_input/1.mif average_header.mif
************************************************
Image: "/home/siying/sharefolder/study/template/fod_input/1.mif"
************************************************
Dimensions: 197 x 197 x 115 x 45
Voxel size: 1.3 x 1.3 x 1.3 x ?
Data strides: [ -2 -3 4 1 ]
Format: MRtrix
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 -0 0 -120.4
-0 1 0 -111.1
-0 -0 1 -83.46
EchoTime: 0.0744
FlipAngle: 90
RepetitionTime: 10
command_history: dwidenoise "sharefolder/study/001_control" "sharefolder/study/001_control/den.mif" (version=3.0_RC3_latest-5-g81036fcc)
[8 entries] mrdegibbs "sharefolder/study/001_control/den.mif" "sharefolder/study/001_control/unring.mif" "-axes" "0,1" (version=3.0_RC3_latest-5-g81036fcc)
...
dwi2fod "msmt_csd" "sharefolder/study/001_control/upsamped.mif" "sharefolder/study/001_control/ga-wm.txt" "sharefolder/study/001_control/wmfod.mif" "-mask" "sharefolder/study/001_control/mask.mif" (version=3.0_RC3_latest-5-g81036fcc)
mtnormalise "sharefolder/study/001_control/wmfod.mif" "sharefolder/study/001_control/wmfod_norm.mif" "-mask" "sharefolder/study/001_control/mask.mif" (version=3.0_RC3_latest-5-g81036fcc)
comments: lin yuan chang (geservice) [MR] Ax DTI 64 Directions
study: D02 [ ORIGINAL PRIMARY OTHER ]
DOS: 02/11/2017 22:19:36
lognorm_scale: 1.03289974
mrtrix_version: 3.0_RC3_latest-5-g81036fcc
prior_dw_scheme: 0,0,0,0
[69 entries] 0,0,0,0
...
-0.7210977154,-0.6080824007,-0.3320449951,999.729
-0.2669847823,-0.9599452847,0.08499515541,1000.114
************************************************
Image: "average_header.mif"
************************************************
Dimensions: 121 x 172 x 163 x 45
Voxel size: 1.3 x 1.3 x 1.3 x ?
Data strides: [ 1 2 3 4 ]
Format: MRtrix
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 0 0 -66.75
0 1 0 -108.8
0 0 1 -96.35
command_history: /home/siying/mrtrix3/bin/mraverageheader "-fill" "/home/siying/sharefolder/study/template/fod_input/1.mif" "/home/siying/sharefolder/study/template/fod_input/2.mif" "/home/siying/sharefolder/study/template/fod_input/3.mif" "/home/siying/sharefolder/study/template/fod_input/4.mif" "-" (version=3.0_RC3_latest-5-g81036fcc)
/home/siying/mrtrix3/bin/mrresize "-" "-voxel" "1.3,1.3,1.3" "average_header.mif" (version=3.0_RC3_latest-5-g81036fcc)
/home/siying/mrtrix3/bin/mrcrop "average_header.mif" "-mask" "mask_initial.mif" "average_header_cropped.mif" (version=3.0_RC3_latest-5-g81036fcc)
mrtrix_version: 3.0_RC3_latest-5-g81036fcc
siying@siying-vbox:~/population_template-tmp-WZ4837$ mrstats average_header.mif
volume mean median stdev min max count
[ 0 ] 1 1 0 1 1 3392356
[ 1 ] 0 0 0 0 0 3392356
[ 2 ] 0 0 0 0 0 3392356
[ 3 ] 0 0 0 0 0 3392356
[ 4 ] 0 0 0 0 0 3392356
[ 5 ] 0 0 0 0 0 3392356
[ 6 ] 0 0 0 0 0 3392356
[ 7 ] 0 0 0 0 0 3392356
[ 8 ] 0 0 0 0 0 3392356
[ 9 ] 0 0 0 0 0 3392356
[ 10 ] 0 0 0 0 0 3392356
[ 11 ] 0 0 0 0 0 3392356
[ 12 ] 0 0 0 0 0 3392356
[ 13 ] 0 0 0 0 0 3392356
[ 14 ] 0 0 0 0 0 3392356
[ 15 ] 0 0 0 0 0 3392356
[ 16 ] 0 0 0 0 0 3392356
[ 17 ] 0 0 0 0 0 3392356
[ 18 ] 0 0 0 0 0 3392356
[ 19 ] 0 0 0 0 0 3392356
[ 20 ] 0 0 0 0 0 3392356
[ 21 ] 0 0 0 0 0 3392356
[ 22 ] 0 0 0 0 0 3392356
[ 23 ] 0 0 0 0 0 3392356
[ 24 ] 0 0 0 0 0 3392356
[ 25 ] 0 0 0 0 0 3392356
[ 26 ] 0 0 0 0 0 3392356
[ 27 ] 0 0 0 0 0 3392356
[ 28 ] 0 0 0 0 0 3392356
[ 29 ] 0 0 0 0 0 3392356
[ 30 ] 0 0 0 0 0 3392356
[ 31 ] 0 0 0 0 0 3392356
[ 32 ] 0 0 0 0 0 3392356
[ 33 ] 0 0 0 0 0 3392356
[ 34 ] 0 0 0 0 0 3392356
[ 35 ] 0 0 0 0 0 3392356
[ 36 ] 0 0 0 0 0 3392356
[ 37 ] 0 0 0 0 0 3392356
[ 38 ] 0 0 0 0 0 3392356
[ 39 ] 0 0 0 0 0 3392356
[ 40 ] 0 0 0 0 0 3392356
[ 41 ] 0 0 0 0 0 3392356
[ 42 ] 0 0 0 0 0 3392356
[ 43 ] 0 0 0 0 0 3392356
[ 44 ] 0 0 0 0 0 3392356
siying@siying-vbox:~/population_template-tmp-WZ4837$ mrstats /home/siying/sharefolder/study/template/mask_input/1.mif
volume mean median stdev min max count
[ 0 ] 0.154272 0 0.361209 0 1 4463035
siying@siying-vbox:~/population_template-tmp-WZ4837$ mrstats /home/siying/sharefolder/study/template/fod_input/1.mif
volume mean median stdev min max count
[ 0 ] 0.0434862 0 0.105995 0 2.56645 4463035
[ 1 ] 8.81935e-05 0 0.0281385 -1.28843 0.660419 4463035
[ 2 ] 0.000182661 0 0.0281531 -0.547882 0.721938 4463035
[ 3 ] -0.00164242 0 0.0316931 -1.05066 0.566322 4463035
[ 4 ] 0.000643814 0 0.0286158 -0.580784 0.824323 4463035
[ 5 ] -0.00152697 0 0.0298275 -0.791108 0.868038 4463035
[ 6 ] -0.00597829 0 0.0472077 -2.13826 1.35961 4463035
[ 7 ] 0.00049116 0 0.0307039 -1.28812 1.20331 4463035
[ 8 ] -0.00254696 0 0.0306594 -0.830143 0.664666 4463035
[ 9 ] 0.00161189 0 0.0304129 -1.13738 0.887283 4463035
[ 10 ] 0.00145269 0 0.0283685 -0.618416 1.50642 4463035
[ 11 ] -0.00288342 0 0.0375411 -1.57604 1.05164 4463035
[ 12 ] 0.00276685 0 0.0334135 -0.667346 0.798248 4463035
[ 13 ] -0.000201019 0 0.0319238 -0.941905 0.955526 4463035
[ 14 ] 0.00336465 0 0.0303689 -0.96729 0.957301 4463035
[ 15 ] 0.00148196 0 0.0184386 -0.52444 0.782449 4463035
[ 16 ] -0.00175365 0 0.0199365 -0.682199 0.701526 4463035
[ 17 ] -0.000686545 0 0.0177621 -0.510572 0.686549 4463035
[ 18 ] 0.00214737 0 0.0196325 -0.861786 0.758995 4463035
[ 19 ] 0.00142313 0 0.0187015 -0.536706 0.555548 4463035
[ 20 ] -0.000549965 0 0.0180521 -0.590082 0.719643 4463035
[ 21 ] -8.85688e-05 0 0.0174927 -0.592256 0.957868 4463035
[ 22 ] 0.00108068 0 0.0189456 -0.891356 0.606004 4463035
[ 23 ] -0.000447615 0 0.0190823 -0.501529 0.657462 4463035
[ 24 ] -0.00123491 0 0.0184513 -0.620752 0.590906 4463035
[ 25 ] 0.000570479 0 0.0173091 -0.580179 0.392825 4463035
[ 26 ] -0.000206837 0 0.0177055 -0.579236 0.917155 4463035
[ 27 ] -0.000500276 0 0.0187025 -0.547967 0.622003 4463035
[ 28 ] -0.000367727 0 0.0103515 -0.564327 0.489931 4463035
[ 29 ] -0.000636858 0 0.0100267 -0.326211 0.273907 4463035
[ 30 ] -0.0010157 0 0.0101194 -0.26245 0.264706 4463035
[ 31 ] 0.00036333 0 0.00940278 -0.269023 0.252457 4463035
[ 32 ] -0.000427559 0 0.00933055 -0.255775 0.227472 4463035
[ 33 ] 0.000756488 0 0.00962527 -0.359634 0.371638 4463035
[ 34 ] -0.000401412 0 0.00910601 -0.478204 0.239961 4463035
[ 35 ] 3.74683e-05 0 0.00862521 -0.447015 0.442416 4463035
[ 36 ] -0.000397719 0 0.00888562 -0.295855 0.40002 4463035
[ 37 ] 0.000315914 0 0.00897516 -0.529644 0.298329 4463035
[ 38 ] 0.000523777 0 0.0097987 -0.380983 0.36001 4463035
[ 39 ] -0.000134201 0 0.00860429 -0.312581 0.244755 4463035
[ 40 ] 7.23396e-05 0 0.00865034 -0.237124 0.258639 4463035
[ 41 ] 0.000331303 0 0.00915974 -0.292847 0.321768 4463035
[ 42 ] -0.000859654 0 0.0096552 -0.319278 0.291635 4463035
[ 43 ] -0.00012253 0 0.0101246 -0.490538 0.292563 4463035
[ 44 ] -0.00119899 0 0.0112418 -0.650806 0.296837 4463035
siying@siying-vbox:~/population_template-tmp-WZ4837$ mrregister /home/siying/sharefolder/study/template/fod_input/1.mif average_header.mif -mask1 /home/siying/sharefolder/study/template/mask_input/1.mif -rigid_scale 1 -rigid_niter 0 -type rigid -noreorientation -rigid_init_translation mass -datatype float32 -rigid linear_transforms_initial/1.txt -debug
mrregister: [DEBUG] No config file found at "/etc/mrtrix.conf"
mrregister: [DEBUG] No config file found at "/home/siying/.mrtrix.conf"
mrregister: [INFO] opening image "/home/siying/sharefolder/study/template/fod_input/1.mif"...
mrregister: [DEBUG] reading key/value file "/home/siying/sharefolder/study/template/fod_input/1.mif"...
mrregister: [DEBUG] sanitising image information...
mrregister: [INFO] image "/home/siying/sharefolder/study/template/fod_input/1.mif" opened with dimensions 197x197x115x45, voxel spacing 1.3x1.3x1.3xnan, datatype Float32LE
mrregister: [DEBUG] memory-mapping file "/home/siying/sharefolder/study/template/fod_input/1.mif"...
mrregister: [DEBUG] file "/home/siying/sharefolder/study/template/fod_input/1.mif" mapped at 0x7f4cde4d4000, size 803346300 (read-only)
mrregister: [DEBUG] image "/home/siying/sharefolder/study/template/fod_input/1.mif" loaded
mrregister: [DEBUG] image "/home/siying/sharefolder/study/template/fod_input/1.mif" initialised with strides = [ -45 -8865 1746405 1 ], start = 1746360, using indirect IO
mrregister: [DEBUG] initialising threads...
mrregister: [DEBUG] launching 2 threads "loop threads"...
mrregister: [DEBUG] waiting for completion of threads "loop threads"...
mrregister: [ 0%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 1%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 2%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 3%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 4%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 5%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 6%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 7%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 8%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 9%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 10%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 11%] preloading data for "/home/siying/sharefolder/study/template/mrregister: [ 12%] preloading data for 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mrregister: [DEBUG] threads "loop threads" completed OK
mrregister: [100%] preloading data for "/home/siying/sharefolder/study/template/fod_input/1.mif"
mrregister: [DEBUG] image "/home/siying/sharefolder/study/template/fod_input/1.mif" initialised with strides = [ -45 -8865 1746405 1 ], start = 1746360, using direct IO
mrregister: [INFO] opening image "average_header.mif"...
mrregister: [DEBUG] reading key/value file "average_header.mif"...
mrregister: [DEBUG] sanitising image information...
mrregister: [INFO] image "average_header.mif" opened with dimensions 121x172x163x45, voxel spacing 1.3x1.3x1.3xnan, datatype Float32LE
mrregister: [DEBUG] memory-mapping file "average_header.mif"...
mrregister: [DEBUG] file "average_header.mif" mapped at 0x7f4c4b9a9000, size 610624080 (read-only)
mrregister: [DEBUG] image "average_header.mif" loaded
mrregister: [DEBUG] image "average_header.mif" initialised with strides = [ 1 121 20812 3392356 ], start = 0, using indirect IO
mrregister: [DEBUG] initialising threads...
mrregister: [DEBUG] launching 2 threads "loop threads"...
mrregister: [DEBUG] waiting for completion of threads "loop threads"...
mrregister: [100%] preloading data for "average_header.mif"...
mrregister: [DEBUG] threads "loop threads" completed OK
mrregister: [100%] preloading data for "average_header.mif"
mrregister: [DEBUG] image "average_header.mif" initialised with strides = [ 45 5445 936540 1 ], start = 0, using direct IO
mrregister: [INFO] opening image "/home/siying/sharefolder/study/template/mask_input/1.mif"...
mrregister: [DEBUG] reading key/value file "/home/siying/sharefolder/study/template/mask_input/1.mif"...
mrregister: [DEBUG] sanitising image information...
mrregister: [INFO] image "/home/siying/sharefolder/study/template/mask_input/1.mif" opened with dimensions 197x197x115, voxel spacing 1.3x1.3x1.3, datatype Bit
mrregister: [DEBUG] memory-mapping file "/home/siying/sharefolder/study/template/mask_input/1.mif"...
mrregister: [DEBUG] file "/home/siying/sharefolder/study/template/mask_input/1.mif" mapped at 0x7f4d104af000, size 557880 (read-only)
mrregister: [DEBUG] image "/home/siying/sharefolder/study/template/mask_input/1.mif" loaded
mrregister: [DEBUG] image "/home/siying/sharefolder/study/template/mask_input/1.mif" initialised with strides = [ -1 -197 38809 ], start = 38808, using indirect IO
mrregister: running rigid registration
mrregister: initialising translation and centre of rotation using centre of mass
mrregister: [DEBUG] centre of mass of /home/siying/sharefolder/study/template/fod_input/1.mif: 5.6452739972990846 8.6928643736261897 -4.2816489071712409
mrregister: [DEBUG] centre of mass of average_header.mif: 11.252000000074563 2.3473999999859569 8.9453999997569902
mrregister: [DEBUG] centre: 8.4486369986868244 5.5201321868060731 2.3318755462928746
mrregister: [INFO] Transformation before registration:
mrregister: [INFO] transformation:
1, 0, 0, -5.606726002775479
0, 1, 0, 6.345464373640233
0, 0, 1, -13.22704890692823
mrregister: [INFO] transformation_half:
1, 0, 0, -2.803363001387739
0, 1, 0, 3.172732186820117
0, 0, 1, -6.613524453464116
mrregister: [INFO] transformation_half_inverse:
1, 0, 0, 2.803363001387739
0, 1, 0, -3.172732186820117
0, 0, 1, 6.613524453464116
mrregister: [INFO] centre: 8.44863699869 5.52013218681 2.33187554629
mrregister: [INFO] Linear registration stage parameters:
mrregister: [INFO] scale factor 1, lmax 0, GD max_iter 0, optimiser: BBGD
mrregister: [DEBUG] compute_average_voxel2scanner num_images:2
mrregister: [DEBUG] compute_minimum_average_header header_out.spacing: 1.3, 1.3, 1.3
mrregister: [DEBUG] compute_minimum_average_header header_out.size: 199, 199, 165
mrregister: linear stage 1/1, scale factor 1, GD max_iter 0, optimiser: BBGD
mrregister: [INFO] smoothing image 1
mrregister: [DEBUG] creating scratch image for smoothing input image...
mrregister: [DEBUG] sanitising image information...
mrregister: [DEBUG] allocating scratch buffer for image "scratch image"...
mrregister: [DEBUG] unmapping file "/home/siying/sharefolder/study/template/mask_input/1.mif"
mrregister: [DEBUG] image "/home/siying/sharefolder/study/template/mask_input/1.mif" unloaded
mrregister: [DEBUG] unmapping file "average_header.mif"
mrregister: [DEBUG] image "average_header.mif" unloaded
mrregister: [DEBUG] unmapping file "/home/siying/sharefolder/study/template/fod_input/1.mif"
mrregister: [DEBUG] image "/home/siying/sharefolder/study/template/fod_input/1.mif" unloaded
mrregister: **[ERROR] Error allocating memory for scratch buffer**
- I really hope to learn this software, please give me more advice ! Thanks !