【FSL/MRtrix】 NIfTIヘッダーの確認

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。

1	`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。

1	`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

MRtrixのmrinfoを用いる。

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。

1	`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。

1	`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

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