Diffusion MRI: Difference between revisions

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| ??
| ??
| [[#Interfile|Interfile]]
| [[Interfile]]
| 1
| 1
| 83x110x64 x 36 DWIs
| 83x110x64 x 36 DWIs
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=File Formats=
=File Formats=
==DICOM==
{| {{Prettytable | width = 40%}}
 
|-
==DICOM Mosaic==
! {{Hl2}} | Format
 
! {{Hl2}} | Extension
==Analyze==
|-
 
| [[DICOM]]
==NIfTI==
| <tt>.ima</tt>; <tt>.dcm</tt>
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.  You can test for the format by using the <code>is_nifti_file()</code> function in the I/O wrapper library.
|-
 
| [[DICOM#Mosaic|DICOM Mosaic]]
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>$G/src/nifti</code> is set up to download the latest version (with <code>make download</code>), build it, and install it in <code>$G/lib/nifti</code> and <code>$G/include/nifti</code>. You might also try snooping around <code>$G/doc/nifti</code> to see what they have to say in their documentation.  <code>$G/src/nifti2mriimage/nifti2mriimage.cpp</code> demonstrates reading the header and extracting information from it, as well as reading the image data.
| <tt>.ima</tt>; <tt>.dcm</tt>
 
|-  
To use the NIfTI I/O wrapper library, simply <code>#include <nifti1_io.h></code> in your code and add the following to the library list in your makefile: <code>niftiio znz m z</code>.
| [[Analyze]]
 
| <tt>.hdr</tt> / <tt>.img</tt>
From the command line or shell scripts, the <code>nifti_tool</code> utility is pretty powerful and can read the header in a structured way.
|-
 
| [[NIfTI]]
The online documentation for NIfTI is also pretty sweet:
| <tt>.nii</tt>; <tt>.nii.gz</tt>; <tt>.hdr</tt> / <tt>.img</tt>
* [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]
| [[Interfile]]
 
| <tt>.ifh</tt> / <tt>.img</tt>
==Interfile==
|-
 
| [[MRIimage]]
==MRIimage==
| ''none''
MRIimage is our in-house format for storing MRI data.  It is manipulated by the <code>gg/mri_g++-*</code> library and its header is <code>&lt;gg/mri/image.H&gt;</code>.
|}


[[Category:Projects]]
[[Category:Projects]]

Revision as of 17:49, 19 August 2008

Collaborative Research Projects

Project Location Collaborators Dataset Date Received / Path Scanner Format # Scans Resolution (voxels) Voxel Size (mm) Orientation Status
Cognitive Aging St. Louis Rob Paul (UMSL), Tom Conturo (WUSTL)
2008-07-20
?? Interfile 1 83x110x64 x 36 DWIs 2.0x2.0x2.0 ??
Not processed
Fibers at Risk Colorado Jack Simon unknown / not transferred 1.5T ?? ?? ?? ?? ?? ??
Not downloaded
Portland, OR Jack Simon (Portland VA), Bill Rooney (phys. chemist at OHSU AIRC) not transferred 7T GE ?? ?? ?? ?? ??
Not collected

Software

File Formats

Format Extension
DICOM .ima; .dcm
DICOM Mosaic .ima; .dcm
Analyze .hdr / .img
NIfTI .nii; .nii.gz; .hdr / .img
Interfile .ifh / .img
MRIimage none
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