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DatastatsContent-type: text/html datastatsSection: User Commands (1)Index Return to Main Contents NAMEdatastats - Computes simple statistics of each diffusion weighted measurement within a region of interest. Useful for estimating the noise level.SYNOPSISdatastats [-schemefile <filename> -bgmask <filename>]DESCRIPTIONReads a data file from the acquisition scheme specified in the schemefile. The ROI can be specified in a mask file or by thresholding the b=0 image using -bgthresh. The program computes the mean, mean squared, variance and standard deviation of each image in the foreground region specified by the mask file.EXAMPLESCreate a mask for data file SubjectA.Bfloat: mask -inputfile SubjectA.Bfloat -schemefile A.scheme -bgthresh 200 -outputdatatype short > SubjectA_M200.Bshort Compute the statistics: datastats -inputfile SubjectA.Bfloat -schemefile A.scheme -bgmask SubjectA_M200.Bshort Foreground voxel count: 3248 Component E(S) E(S^2) Var(S) Std(S)
Useful for estimating the noise level (as required for restore or mbalign) or signal to noise. An estimate of the noise level sigma (standard deviation of each component of the complex noise on the signal) is sqrt(E(S^2)/2) from an ROI entirely in background. Eg, draw an ROI in background on the FA image from the data set using MRIcro. (The mask volume should be the same size as one component of the full DWI data set.) Save the mask as an analyze image ROI->Export ROI as Analyze Image; Save [Sun]. MRIcro saves the mask as type char, so to measure the statistics in the region run: datastats -inputfile SubjectA.Bfloat -schemefile A.scheme -bgmask A_BG.img -maskdatatype char If the ROI is truly in background, you should see little variation among the different diffusion weighted images, so can choose any to compute sigma. OPTIONS
AUTHORSDaniel Alexander <camino@cs.ucl.ac.uk>SEE ALSOmask(1), restore(1), mbalign(1), modelfit(1).BUGSNo known bugs.
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