Difference between revisions of "Automatic DBS lead topology correction"

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(Created page with "=== Citation === Guérin B, Gebhardt M, Cauley S, Adalsteinsson E, Wald LL (2014). "[http://onlinelibrary.wiley.com/doi/10.1002/mrm.24800/pdf Local specific absorption rate (S...")
 
(Replaced content with "=== Citation === === What this code does === === Download files === === Instructions ===")
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=== Citation ===
 
=== Citation ===
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Guérin B, Gebhardt M, Cauley S, Adalsteinsson E, Wald LL (2014). "[http://onlinelibrary.wiley.com/doi/10.1002/mrm.24800/pdf Local specific absorption rate (SAR), global SAR, transmitter power, and excitation accuracy trade‐offs in low flip‐angle parallel transmit pulse design.]" Magnetic Resonance in Medicine 71(4): 1446-1457.
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=== What this code does ===
 
=== What this code does ===
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This Matlab code (no MEX, no GPU code) computes least-squares and magnitude least-squares pTx spoke pulses. The MLS problem can be solved using the phase adoption approach of Setsompop et al. or a full optimization strategy (see the file spokes_3/run_spokes.m and options therein). Spokes can be optimized for several frequencies (spatio-spectral design) in order to build in robustness to off-resonance effects.
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=== Download files ===
 
=== Download files ===
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The code can be downloaded [https://ptx.martinos.org/images/f/f2/SpokesMinExcErrLocGlobSARPuPow_fmincon_v12.zip here]. A test dataset can be downloaded [https://ptx.martinos.org/images/e/e2/Spokes_3.zip here]. If you wonder how I obtained the field maps, ROI and SODA (=slice information) files, download [https://ptx.martinos.org/images/c/c0/Prescan_data.zip this file].
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=== Instructions ===
 
=== Instructions ===
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==== Pre-scan data format ====
 
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The format of the pre-scan data (e.g., B0 map, B1+ maps, slice information in the SODA file) matches the Siemens pTx "Step 2" data format. To take a closer look at this, download the prescan_data.zip file,
 
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* An ROI file in NIFTI format.
 
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* A B0 map in NIFTI format.
 
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* An FLD file containing the B1+ maps for the slice considered as obtained by pushing "save dataset" in the B1 mapping tab of the Siemens pTx "Step 2" interface.
 
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To get the ROI and B0 maps, I use the Siemens product gre_fieldmapping sequence (make sure to chose "save magnitude/phase" in order to get both the B0 and ROI maps in the same scan). The B0, B1 and ROI datasets must have the same number of pixels and same dimensions.
 
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==== Spokes optimization ====
 
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Unzip the code folder and add it to your path. Unzip the data folder and run the script run_spokes.m. There are several options in it that are straightforward to understand (e.g., LS/MLS, spatio-spectral design). The frequencies of the spatio-spectral design are expressed in Hz and are offset with respect to the Larmor frequency (i..e, +50 means Larmor frequency+50 Hz). Most of the spoke options (such as slice-thickness, slice-selection gradient, time-bandwidth product etc...) are specified in the text file spokes_def.txt and can be changed there.
 

Revision as of 14:16, 15 April 2016

Citation

What this code does

Download files

Instructions

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