NIfTI - Revision history

Jadrian Miles at 13:31, 25 June 2012

2012-06-25T13:31:23Z

← Older revision		Revision as of 13:31, 25 June 2012
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	Files ending in <tt>'''.nii'''</tt> are in the [http://nifti.nimh.nih.gov/nifti-1 NIfTI] [[Diffusion MRI\|medical image]] format~~; it~~ is becoming a standard ~~export~~ format for many different software packages, including [[FSL]]. <tt>.nii</tt> files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in <tt>'''.hdr'''</tt>/<tt>'''.img'''</tt> pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension <tt>'''.nii.gz'''</tt>. You can test for the format by using the <code>is_nifti_file()</code> function in the I/O library.		Files ending in <tt>'''.nii'''</tt> are in the [http://nifti.nimh.nih.gov/nifti-1 NIfTI] [[Diffusion MRI\|medical image]] format, which is becoming a standard format for many different medical imaging software packages, including [[FSL]]. <tt>.nii</tt> files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in <tt>'''.hdr'''</tt>/<tt>'''.img'''</tt> pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension <tt>'''.nii.gz'''</tt>. You can test for the format by using the <code>is_nifti_file()</code> function in the I/O library.

	== Paths ==		== Paths ==

Jadrian Miles: /* Coordinate System */

2010-07-19T17:31:20Z

Coordinate System

← Older revision		Revision as of 17:31, 19 July 2010
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	The NIfTI standard coordinate system has:		The NIfTI standard coordinate system has:
	* <tt>+x</tt> = Patient's Right (<tt>x</tt> increases from patient's left to patient's right)		* <tt>+x</tt> = Patient's Right (<tt>x</tt> increases from patient's left to patient's right)
	* <tt>+y</tt> = Anterior (<tt>y</tt> increases from posterior to anterior)		* <tt>+y</tt> = Anterior (<tt>y</tt> increases from posterior (back of head) to anterior (nose))
	* <tt>+z</tt> = Superior (<tt>z</tt> increases from inferior to superior)		* <tt>+z</tt> = Superior (<tt>z</tt> increases from inferior (base of head) to superior (top of head))
	Note that this is a right-handed coordinate system, and that it is ''different from the default coordinate system for [[MRIimage]]''. The <tt>nifti2mriimage</tt> program properly converts between the two coordinate systems, but if you write your own code that mixes these worlds, this is an important detail to keep in mind.		Note that this is a right-handed coordinate system, and that it is ''different from the default coordinate system for [[MRIimage]]''. The <tt>nifti2mriimage</tt> program properly converts between the two coordinate systems, but if you write your own code that mixes these worlds, this is an important detail to keep in mind.

Jadrian Miles: /* Coordinate System */

2010-07-19T17:17:47Z

Coordinate System

← Older revision		Revision as of 17:17, 19 July 2010
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	=== Coordinate System ===		=== Coordinate System ===
	NIfTI strictly defines its coordinate system, which is patient-based. The voxel indices <tt>(i,j,k)</tt> map onto an <tt>(x,y,z)</tt> coordinate system according to a transformation matrix that's stored in the header. If the matrix is the identity, then <tt>(i,j,k)</tt> of course maps directly to <tt>(x,y,z)</tt>.		NIfTI strictly defines its coordinate system, which is patient-based. The voxel indices <tt>(i,j,k)</tt> map onto a spatial <tt>(x,y,z)</tt> coordinate system according to a transformation matrix that's stored in the header. If the matrix is the identity, then <tt>(i,j,k)</tt> of course maps directly to <tt>(x,y,z)</tt>; if it is diagonal, then each spatial coordinate is a scalar multiple of each voxel index (which accounts for the voxel size).

	The NIfTI standard coordinate system has:		The NIfTI standard coordinate system has:
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	The voxel index <tt>(i,j,k)</tt> indicates a memory location <code>(i + jdim[1] + kdim[1]dim[2]) (bitpix/8)</code> into the dataset array. This means that the <tt>i</tt> index varies most rapidly, <tt>j</tt> next, and <tt>k</tt> slowest. The valid inclusive ranges for <tt>(i,j,k)</tt> are, respectively, 0 to <tt>dim[1]-1</tt>, 0 to <tt>dim[2]-1</tt>, and 0 to <tt>dim[3]-1</tt>.		The voxel index <tt>(i,j,k)</tt> indicates a memory location <code>(i + jdim[1] + kdim[1]dim[2]) (bitpix/8)</code> into the dataset array. This means that the <tt>i</tt> index varies most rapidly, <tt>j</tt> next, and <tt>k</tt> slowest. The valid inclusive ranges for <tt>(i,j,k)</tt> are, respectively, 0 to <tt>dim[1]-1</tt>, 0 to <tt>dim[2]-1</tt>, and 0 to <tt>dim[3]-1</tt>.

			The <tt>(x,y,z)</tt> spatial coordinate specifies the position of the ''center'' of the voxel, the central location of the physical measurement recorded in that voxel.

			For more details, please read the [http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/ NIfTI-1 Header Field Descriptions] and the [http://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h NIfTI-1 header file itself].

	== History ==		== History ==

Jadrian Miles: /* Coordinate System */

2010-07-19T17:07:43Z

Coordinate System

← Older revision		Revision as of 17:07, 19 July 2010
Line 23:		Line 23:

	=== Coordinate System ===		=== Coordinate System ===
	NIfTI strictly defines its coordinate system, which is patient-based. The voxel indices <tt>(i,j,k)</tt> map onto an <tt>(x,y,z)</tt> coordinate system according to a transformation matrix that's stored in the header. The NIfTI standard coordinate system has:		NIfTI strictly defines its coordinate system, which is patient-based. The voxel indices <tt>(i,j,k)</tt> map onto an <tt>(x,y,z)</tt> coordinate system according to a transformation matrix that's stored in the header. If the matrix is the identity, then <tt>(i,j,k)</tt> of course maps directly to <tt>(x,y,z)</tt>.

			The NIfTI standard coordinate system has:
	* <tt>+x</tt> = Patient's Right (<tt>x</tt> increases from patient's left to patient's right)		* <tt>+x</tt> = Patient's Right (<tt>x</tt> increases from patient's left to patient's right)
	* <tt>+y</tt> = Anterior (<tt>y</tt> increases from posterior to anterior)		* <tt>+y</tt> = Anterior (<tt>y</tt> increases from posterior to anterior)

Jadrian Miles: /* Documentation */

2010-07-19T17:05:42Z

Documentation

← Older revision		Revision as of 17:05, 19 July 2010
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	* [http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/ NIfTI-1 Header Field Description]		* [http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/ NIfTI-1 Header Field Description]
	* [http://nifti.nimh.nih.gov/nifti-1/documentation/faq NIfTI FAQ]		* [http://nifti.nimh.nih.gov/nifti-1/documentation/faq NIfTI FAQ]

			=== Coordinate System ===
			NIfTI strictly defines its coordinate system, which is patient-based. The voxel indices <tt>(i,j,k)</tt> map onto an <tt>(x,y,z)</tt> coordinate system according to a transformation matrix that's stored in the header. The NIfTI standard coordinate system has:
			* <tt>+x</tt> = Patient's Right (<tt>x</tt> increases from patient's left to patient's right)
			* <tt>+y</tt> = Anterior (<tt>y</tt> increases from posterior to anterior)
			* <tt>+z</tt> = Superior (<tt>z</tt> increases from inferior to superior)
			Note that this is a right-handed coordinate system, and that it is ''different from the default coordinate system for [[MRIimage]]''. The <tt>nifti2mriimage</tt> program properly converts between the two coordinate systems, but if you write your own code that mixes these worlds, this is an important detail to keep in mind.

			The voxel index <tt>(i,j,k)</tt> indicates a memory location <code>(i + jdim[1] + kdim[1]dim[2]) (bitpix/8)</code> into the dataset array. This means that the <tt>i</tt> index varies most rapidly, <tt>j</tt> next, and <tt>k</tt> slowest. The valid inclusive ranges for <tt>(i,j,k)</tt> are, respectively, 0 to <tt>dim[1]-1</tt>, 0 to <tt>dim[2]-1</tt>, and 0 to <tt>dim[3]-1</tt>.

	== History ==		== History ==

Jadrian Miles: /* Command-Line Utilities */

2009-03-02T20:44:45Z

Command-Line Utilities

← Older revision		Revision as of 20:44, 2 March 2009
Line 11:		Line 11:

	=== Command-Line Utilities ===		=== Command-Line Utilities ===
	The <code>$G/bin/nifti_tool</code> utility can read the header in a structured way and print out tons of metadata, as well as manipulating the actual data and doing a lot more. It's a good way to explore new data before deciding how to script with it.		The <code>$G/bin/nifti_tool</code> utility can read the header in a structured way and print out tons of metadata, as well as manipulating the actual data and doing a lot more. It's a good way to explore new data before deciding how to script with it. See [[nifti_tool]] for a quick guide to common operations.

	=== Format Conversion ===		=== Format Conversion ===

Jadrian Miles at 21:58, 17 November 2008

2008-11-17T21:58:47Z

← Older revision		Revision as of 21:58, 17 November 2008
Line 1:		Line 1:
	Files ending in <tt>'''.nii'''</tt> are in the [http://nifti.nimh.nih.gov/nifti-1 NIfTI] [[Diffusion MRI\|medical image]] format; it is becoming a standard export format for many different software packages, including [~~http://www.fmrib.ox.ac.uk/fsl/~~ FSL]. <tt>.nii</tt> files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in <tt>'''.hdr'''</tt>/<tt>'''.img'''</tt> pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension <tt>'''.nii.gz'''</tt>. You can test for the format by using the <code>is_nifti_file()</code> function in the I/O library.		Files ending in <tt>'''.nii'''</tt> are in the [http://nifti.nimh.nih.gov/nifti-1 NIfTI] [[Diffusion MRI\|medical image]] format; it is becoming a standard export format for many different software packages, including [[FSL]]. <tt>.nii</tt> files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in <tt>'''.hdr'''</tt>/<tt>'''.img'''</tt> pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension <tt>'''.nii.gz'''</tt>. You can test for the format by using the <code>is_nifti_file()</code> function in the I/O library.

	== Paths ==		== Paths ==

Jadrian Miles at 21:11, 21 August 2008

2008-08-21T21:11:52Z

← Older revision		Revision as of 21:11, 21 August 2008
Line 1:		Line 1:
	Files ending in <tt>'''.nii'''</tt> are in the [http://nifti.nimh.nih.gov/nifti-1 NIfTI medical image format]; it is becoming a standard export format for many different software packages, including [http://www.fmrib.ox.ac.uk/fsl/ FSL]. <tt>.nii</tt> files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in <tt>'''.hdr'''</tt>/<tt>'''.img'''</tt> pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension <tt>'''.nii.gz'''</tt>. You can test for the format by using the <code>is_nifti_file()</code> function in the I/O library.		Files ending in <tt>'''.nii'''</tt> are in the [http://nifti.nimh.nih.gov/nifti-1 NIfTI] [[Diffusion MRI\|medical image]] format; it is becoming a standard export format for many different software packages, including [http://www.fmrib.ox.ac.uk/fsl/ FSL]. <tt>.nii</tt> files combine the metadata header and image data into a single file, but NIfTI-1 is a modified form of Analyze 7.5, so it sometimes comes in <tt>'''.hdr'''</tt>/<tt>'''.img'''</tt> pairs. The NIfTI I/O library and command line tools also directly handle compressed NIfTI, with the extension <tt>'''.nii.gz'''</tt>. You can test for the format by using the <code>is_nifti_file()</code> function in the I/O library.

	== Paths ==		== Paths ==

Jadrian Miles at 21:03, 21 August 2008

2008-08-21T21:03:44Z

← Older revision		Revision as of 21:03, 21 August 2008
Line 24:		Line 24:
	== History ==		== History ==
	The format was created by the [http://nifti.nimh.nih.gov Neuroimaging Informatics Technology Initiative] at NIH. It is a superset of Analyze 7.5, re-purposing empty fields in the Analyze format to support more features. Fortunately for us, the NIfTI reference library is available in the public domain, and <code>$G/src/nifti</code> is set up to download the latest version (with <code>make download</code>), build it, and install it. NIfTI is an actively developed format, but the NIfTI-1 specification is fixed; NIfTI-2 will be formulated and released at some point in the future.		The format was created by the [http://nifti.nimh.nih.gov Neuroimaging Informatics Technology Initiative] at NIH. It is a superset of Analyze 7.5, re-purposing empty fields in the Analyze format to support more features. Fortunately for us, the NIfTI reference library is available in the public domain, and <code>$G/src/nifti</code> is set up to download the latest version (with <code>make download</code>), build it, and install it. NIfTI is an actively developed format, but the NIfTI-1 specification is fixed; NIfTI-2 will be formulated and released at some point in the future.

			[[Category:Diffusion MRI]][[Category:File Formats]]

Jadrian Miles: /* Command-Line Utilities */

2008-08-21T20:57:00Z

Command-Line Utilities

← Older revision		Revision as of 20:57, 21 August 2008
Line 11:		Line 11:

	=== Command-Line Utilities ===		=== Command-Line Utilities ===
	The <code>nifti_tool</code> utility can read the header in a structured way and print out tons of metadata, as well as manipulating the actual data and doing a lot more. It's a good way to explore new data before deciding how to script with it.		The <code>$G/bin/nifti_tool</code> utility can read the header in a structured way and print out tons of metadata, as well as manipulating the actual data and doing a lot more. It's a good way to explore new data before deciding how to script with it.

	=== Format Conversion ===		=== Format Conversion ===