1. 目的
2. FSLを用いる場合
2.1. コマンド
2.2. 使用例
3. MRtrixを用いる場合
3.1. コマンド
3.2. 使用例
1. 目的
- NIfTIヘッダーの確認
2. FSLを用いる場合
2.1. コマンド
FSLのfslhdを用いる。
fslhdのヘルプは次の通り。
Usage: fslhd [-x] <input>
-x : instead print an XML-style NIFTI header
基本的な使い方は、以下の通り。
fslhd <入力画像（NIfTI）>
2.2. 使用例
拡散MRI画像（DWI.nii.gz）のNIfTIヘッダーをみてみる。
fslhd DWI.nii.gz
以下の情報が、出力される。
Out:
filename DWI.nii.gz
sizeof_hdr 348
data_type INT16
dim0 4
dim1 130
dim2 130
dim3 82
dim4 129
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 -1.000000
pixdim1 1.769231
pixdim2 1.769231
pixdim3 1.800000
pixdim4 4.900000
pixdim5 1.000000
pixdim6 0.294996
pixdim7 73966.875000
vox_offset 352
cal_max 0.000000
cal_min 0.000000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 3
slice_name alternating_increasing_2
slice_code 5
slice_start 0
slice_end 81
slice_duration 0.000000
toffset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Scanner Anat
qform_code 1
qto_xyz:1 -1.769231 0.000000 -0.000000 119.242340
qto_xyz:2 0.000000 1.769231 -0.000000 -103.683487
qto_xyz:3 0.000000 0.000000 1.800000 -58.573616
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Scanner Anat
sform_code 1
sto_xyz:1 -1.769231 0.000000 0.000000 119.242340
sto_xyz:2 0.000000 1.769231 0.000000 -103.683487
sto_xyz:3 0.000000 0.000000 1.800000 -58.573616
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip TE=70;sec=73966.8750;phaseDir=+;dwell=0.295
aux_file
dim?は各次元でのマトリックスサイズを示しており、以下の情報から入力した拡散MRI画像（DWI.nii.gz）は、130 x 130の画像でスライス枚数が82、この画像が129ボリュームで構成される画像、であることが分かる。
dim1 130
dim2 130
dim3 82
dim4 129
pixdim?はボクセルサイズ（mm）を示しており、この場合、1.769231x 1.769231x 1.800000であることが分かる。
pixdim1 1.769231
pixdim2 1.769231
pixdim3 1.800000
また、sform_?orientは各軸（x/y/z）とMRI画像の向きの対応関係を示している。以下の場合、x軸は左右、y軸は前後、z軸は上下に対応していることが分かる。
画像の向きの詳細については、こちらを参考にするとよい。
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
3. MRtrixを用いる場合
3.1. コマンド
mrinfoのヘルプは、次の通り。
mrinfo: part of the MRtrix3 package
SYNOPSIS
Display image header information, or extract specific information from the
header
USAGE
mrinfo [ options ] image [ image ... ]
image the input image(s).
DESCRIPTION
By default, all information contained in each image header will be printed
to the console in a reader-friendly format.
Alternatively, command-line options may be used to extract specific
details from the header(s); these are printed to the console in a format
more appropriate for scripting purposes or piping to file. If multiple
options and/or images are provided, the requested header fields will be
printed in the order in which they appear in the help page, with all
requested details from each input image in sequence printed before the
next image is processed.
The command can also write the diffusion gradient table from a single
input image to file; either in the MRtrix or FSL format (bvecs/bvals file
pair; includes appropriate diffusion gradient vector reorientation)
The -dwgrad, -export_* and -shell_* options provide (information about)
the diffusion weighting gradient table after it has been processed by the
MRtrix3 back-end (vectors normalised, b-values scaled by the square of the
vector norm, depending on the -bvalue_scaling option). To see the raw
gradient table information as stored in the image header, i.e. without
MRtrix3 back-end processing, use "-property dw_scheme".
The -bvalue_scaling option controls an aspect of the import of diffusion
gradient tables. When the input diffusion-weighting direction vectors have
norms that differ substantially from unity, the b-values will be scaled by
the square of their corresponding vector norm (this is how multi-shell
acquisitions are frequently achieved on scanner platforms). However in
some rare instances, the b-values may be correct, despite the vectors not
being of unit norm (or conversely, the b-values may need to be rescaled
even though the vectors are close to unit norm). This option allows the
user to control this operation and override MRrtix3's automatic detection.
OPTIONS
-all
print all properties, rather than the first and last 2 of each.
-name
print the file system path of the image
-format
image file format
-ndim
number of image dimensions
-size
image size along each axis
-spacing
voxel spacing along each image dimension
-datatype
data type used for image data storage
-strides
data strides i.e. order and direction of axes data layout
-offset
image intensity offset
-multiplier
image intensity multiplier
-transform
the transformation from image coordinates [mm] to scanner / real world
coordinates [mm]
Options for exporting image header fields
-property key (multiple uses permitted)
any text properties embedded in the image header under the specified key
(use 'all' to list all keys found)
-json_keyval file
export header key/value entries to a JSON file
-json_all file
export all header contents to a JSON file
DW gradient table import options
-grad file
Provide the diffusion-weighted gradient scheme used in the acquisition in
a text file. This should be supplied as a 4xN text file with each line is
in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the
applied gradient, and b gives the b-value in units of s/mm^2. If a
diffusion gradient scheme is present in the input image header, the data
provided with this option will be instead used.
-fslgrad bvecs bvals
Provide the diffusion-weighted gradient scheme used in the acquisition in
FSL bvecs/bvals format files. If a diffusion gradient scheme is present in
the input image header, the data provided with this option will be instead
used.
-bvalue_scaling mode
enable or disable scaling of diffusion b-values by the square of the
corresponding DW gradient norm (see Desciption). Valid choices are yes/no,
true/false, 0/1 (default: automatic).
DW gradient table export options
-export_grad_mrtrix path
export the diffusion-weighted gradient table to file in MRtrix format
-export_grad_fsl bvecs_path bvals_path
export the diffusion-weighted gradient table to files in FSL (bvecs /
bvals) format
-dwgrad
the diffusion-weighting gradient table, as interpreted by MRtrix3
-shell_bvalues
list the average b-value of each shell
-shell_sizes
list the number of volumes in each shell
-shell_indices
list the image volumes attributed to each b-value shell
Options for exporting phase-encode tables
-export_pe_table file
export phase-encoding table to file
-export_pe_eddy config indices
export phase-encoding information to an EDDY-style config / index file
pair
-petable
print the phase encoding table
Standard options
-info
display information messages.
-quiet
do not display information messages or progress status; alternatively,
this can be achieved by setting the MRTRIX_QUIET environment variable to a
non-empty string.
-debug
display debugging messages.
-force
force overwrite of output files (caution: using the same file as input and
output might cause unexpected behaviour).
-nthreads number
use this number of threads in multi-threaded applications (set to 0 to
disable multi-threading).
-config key value (multiple uses permitted)
temporarily set the value of an MRtrix config file entry.
-help
display this information page and exit.
-version
display version information and exit.
基本的な使い方は、次の通り。
mrinfo <入力画像（NIfTI）>
3.2. 使用例
拡散MRI画像（DWI.nii.gz）のNIfTIヘッダーをみてみる。
mrinfo DWI.nii.gz
以下の情報が出力される。
Out:
************************************************
Image name: "DWI.nii.gz"
************************************************
Dimensions: 130 x 130 x 82 x 129
Voxel size: 1.76923 x 1.76923 x 1.8 x 4.9
Data strides: [ -1 2 3 4 ]
Format: NIfTI-1.1 (GZip compressed)
Data type: signed 16 bit integer (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 1 0 0 -109
-0 1 0 -103.7
-0 0 1 -58.57
comments: TE=70;sec=73966.8750;phaseDir=+;dwell=0.295
以上の情報から、次のことが分かる。
- マトリックスサイズ (タグ：Dimensions)：130 x 130
- スライス枚数 (タグ：Dimensions)：82
- ボリューム数 (タグ：Dimensions)：129
- ボクセルサイズ (タグ：Voxel size)：1.76923 x 1.76923 x 1.8
著者情報： 斎藤 勇哉
順天堂大学医学部 大学院医学研究科 放射線診断学講座所属脳MRI 画像解析が専門であり、テーマは①神経変性疾患の機序解明、②医用人工知能の開発、③多施設データのハーモナイゼーション、④速読が脳に与える影響や学習効果、⑤SNS解析を用いたマーケティング戦略の改善。
医療分野に関わらず、自然言語処理・スクレイピング・データ分析・Web アプリ開発を得意とし、企業や他大学の研究を支援。
主な使用言語は、Python、Shell Script、MATLAB、HTML、CSS
ピングバック： 【FSL/MRtrix】4D画像から3D画像を抽出