⇤ ← Revision 1 as of 2013-05-03 06:42:35
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where, <scanner_saved_fieldmap> is the input filename of scanner saved | where, <scanner_saved_fieldmap> is the input filename of scanner saved |
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realistic values estimated based on smoothness of fieldmap. No values inside the mask is modified. |
realistic values estimated based on smoothness of fieldmap. Estimated mask is also saved to disk with file name as <output_filename>.mask.nii.gz . |
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Prepare Fieldmap
prepare_fieldmap is a command line tool for converting scanner saved fieldmap to units of radians/sec. As of now it only works with fieldmap saved with Siemens sequence 'gre_field_mapping'. prepare_fieldmap can be run from command line using following syntax:
Windows: prepare_fieldmap.exe --in=<scanner_saved_fieldmap> --out=<output_filename> [options] Linux and Mac: prepare_fieldmap.sh --in=<scanner_saved_fieldmap> --out=<output_filename> [options] where, <scanner_saved_fieldmap> is the input filename of scanner saved fieldmap in NIfTI format (.nii or .nii.gz), <output_filename> is the output filename. Optional Arguments: --ref-vol=<reference_volume> <reference_volume> is filename of reference volume which can be used to estimate a mask of head to extrapolate fieldmap outside the mask. This can be the 3D/4D magnitude image used for fieldmap estimation and saved by the scanner OR it can be a manually drawn mask. It is used to replace inaccurate fieldmap estimation by realistic values estimated based on smoothness of fieldmap. Estimated mask is also saved to disk with file name as <output_filename>.mask.nii.gz .
Download Links
Required runtime packages
Matlab MCR 2012a for your platform.
Only for Windows: Visual C++ runtime package
Prepare Fieldmap Tool
- Linux 64 bit
- Mac 64 bit
Authors: Chitresh Bhushan