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| NIfTI input: | |
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| Windows: prepare_fieldmap.exe --in=<scanner_saved_fieldmap> --out=<output_filename> [options] |
prepare_fieldmap.exe --out=<output_filename> [options] --in=<scanner_saved_fieldmap> }}} |
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| 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. |
Dicom input: {{{ prepare_fieldmap --out=<output_filename> [options] -d <dicom_dir 1>..<dicom_dir N> }}} 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. {{{[options]}}} is optional input defined below. {{{<dicom_dir 1>}}},..,{{{<dicom_dir N>}}} is the path to dicoms saved by scanner. These dicoms paths should contain only dicom files for fieldmap sequence. In case dicom input is not working as expected, please first convert dicom image to nifti format using some external converter and use nifti input as shown above. |
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| <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 . |
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| where, {{{<reference_volume>}}} is filename of reference volume NIfTI format (.nii or .nii.gz) which can be used to estimate or define a mask of the head. This mask is used to replace noisy fieldmap estimate outside the head by extrapolating the fieldmap. The reference volume can be the 3D/4D magnitude image used for fieldmap estimation (and as saved by the scanner) OR it can be a manually drawn mask. In the former case, {{{prepare_fieldmap}}} will estimate the head mask from the reference volume based on instensity. The Estimated mask is also saved to disk with file name as {{{<output_filename>.mask.nii.gz}}}. In case the automatic estimated mask is not accurate, please refine the mask manually in BrainSuite and re-run with refined mask as reference volume. Last Updated on: August 12, 2013 |
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| * [[http://www.mathworks.com/products/compiler/mcr/%20|Matlab MCR 2012a]] for your platform. | * [[https://www.mathworks.com/products/compiler/mcr/|Matlab MCR 2012a]] for your platform. |
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:
NIfTI input:
prepare_fieldmap.exe --out=<output_filename> [options] --in=<scanner_saved_fieldmap>
Dicom input:
prepare_fieldmap --out=<output_filename> [options] -d <dicom_dir 1>..<dicom_dir N>
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. [options] is optional input defined below. <dicom_dir 1>,..,<dicom_dir N> is the path to dicoms saved by scanner. These dicoms paths should contain only dicom files for fieldmap sequence. In case dicom input is not working as expected, please first convert dicom image to nifti format using some external converter and use nifti input as shown above.
Optional Arguments:
--ref-vol=<reference_volume>
where, <reference_volume> is filename of reference volume NIfTI format (.nii or .nii.gz) which can be used to estimate or define a mask of the head. This mask is used to replace noisy fieldmap estimate outside the head by extrapolating the fieldmap. The reference volume can be the 3D/4D magnitude image used for fieldmap estimation (and as saved by the scanner) OR it can be a manually drawn mask. In the former case, prepare_fieldmap will estimate the head mask from the reference volume based on instensity. The Estimated mask is also saved to disk with file name as <output_filename>.mask.nii.gz. In case the automatic estimated mask is not accurate, please refine the mask manually in BrainSuite and re-run with refined mask as reference volume.
Last Updated on: August 12, 2013
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