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Revision as of 19:09, 9 May 2009

Analyses Command-Line - False Discovery Rate (FDR) Corection

This page includes the information on how to use the SOCR Analyses library for the purpose of computing the False Discovery Rate (FDR) correction for multiple testing in volumetric ans shape-based analyses. Access is provided via shell-based command-line interface on local machines. More information about other SOCR Analyses command-line interfaces is available here.

Introduction

In addition to the graphical user interfaces, via a web-browser, all SOCR Analyses allow command-line shell execution on local systems.

FDR Usage

java -ms500m -mx1000m -cp D:\Ivo.dir\Eclipse_Projects\SOCR2.5\jars\SOCR_core.jar;D:\Ivo.dir\Eclipse_Projects\SOCR2.5\jars\SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.volume.Test_FDR -input D:\Ivo.dir\temp\SOCR_VolAnalysis_Test\RankSumTest.PValuesasText_0-0.txt -output D:\Ivo.dir\temp\SOCR_VolAnalysis_Test\RankSumTest.PValues_FDRcorrected.txt -type 0 -fdr_rate 0.05 -number 1000

  • Options:
    • -help: print usage
    • -dm [DesignMatrix.txt]: specify a tab-separated text file containing the design matrix. Note: Be careful with the construction of the design matrix ... The dm matrix file may need to be imported as an excel spreadsheet, first, and then recopied back to text edit using a PC/Windows machine. Mac and other platforms may introduce hidden characters (e.g., tab/return keys). So if you get an error like Beginning the stat analyses ... VolumeMultipleRegression Error!!!!!!!!!!!!!!, then please review your Design Matrix file. Missing values in the DM are indicated by "." Subjects with missing values in one predictor variable (see regressors) are not used in the analysis if this specific predictor is selected as a covariate.
    • -mask [Mask-volume.img]: specify a mask-volume (0 or 1 intensities) restricting the voxels, where the regression models are computed (optional), 1 Unsigned-Byte Analyze format volume of the same dimensions as the data (intensity spectrum [0:255], all intensities >0 are consuiderd part of the mask and processed)
    • -h: DesignMatrix contains a header (first row)
    • -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates
    • -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1
    • -p [PValue_Filename]: output the p-value volume (enter only the base of the filename)
    • -r [RValue_Filename]: output the effect-size/correlation volume (enter only the base of the filename)
    • -t [Tstat_Filename]: output the T-Statistics for the effect-size Beta (enter only the base of the filename)
    • -data_type [0,1,2,3,4]: Type=0 is for Unsigned Byte, Type=1 is for Signed Byte, Type=2 is for Unsigned Short Integer, Type=3 is for Signed Short Integer and Type=4 is for 4Byte=Float Volume Input;
    • -byteswap: Only enter this flag if you want the input data to be read in and byteswapped! Note that -byteswap effects : input data, mask-volume and output results!
      • A better alternative is to always swap bytes (if necessary) outside this program (e.g., %> dd conv=swab if=20088_jacobian.img of=20088_jacobian_BS.img).
    • Memory Use: Note that for some large file sizes, you may need to request more memory form the JVM. If your data is larger than 2003 then use these parameters after the initial java call (-ms1000m -mx2000m), see the example below. This requests 1-2GB or RAM memory for this process. You may need more or less memory depending on the number of volumes and dimension sizes.
  • Example: Edit a new file (VolumeMultipleRegression.csh) using any editor and paste this inside (make sure the file has executable permissions). Some operating systems/platforms may require variants of this (C-shell) script.

#!/bin/csh

date

java -ms200m -mx500m -cp /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_core.jar:/ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.volume.VolumeMultipleRegression -dm /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/DM.txt -h -regressors CDR,MMSE -dim 220 220 220 -p /ifs/tmp/P_Value -r /ifs/tmp/R_Value -t /ifs/tmp/TStat_Value -data_type 2

# Or

java -ms200m -mx500m -cp /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_core.jar:/ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.volume.VolumeMultipleRegression -dm /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/DM.txt -h -regressors AGE,CDR -dim 220 220 220 -p /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/VolumeMultipleRegressionTest/P_Value_mask_New -r /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/VolumeMultipleRegressionTest/R_Value_mask_New -mask /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/VolumeMultipleRegressionTest/UC_mask_final8bit.img -t /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/VolumeMultipleRegressionTest/T_Value_mask_New -data_type 2 -byteswap &

date

exit

Example Input data files

The design-matrix datafile must be provided as tab-separated ASCII/text file (DM.txt). The ASCII content of each of these files should follow the syntax below. Note that the first lines in these files are column headers. This requires the "-h" flag on the command line at execution so that these first lines are interpreted as column headers. The first two columns are the Subject Identifier and filenames for the corresponding imaging volumes, respectively. Columns 3 and on store the corresponding predictor variable (covariate) values. Typically there will be between 1 and 10 covariates. Note that as of March 2009, all covariates have to be numerical values - you can encode all string variables as numbers. For example, SEX can become 0(Male), 1(Female); and GROUP_ID can be 0(Normal), 1(MCI), 2(AD), as shown below.

SUBJECT_ID FILENAME SEX GROUP_ID AGE CDR MMSE
002_S_0413 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_002_S_0413.img 1 0 76.38 0 29
002_S_0559 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_002_S_0559.img 0 0 79.37 0 30
002_S_0729 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_002_S_0729.img 1 1 65.22 0.5 27
002_S_0954 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_002_S_0954.img 1 1 69.42 0.5 25
002_S_1018 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_002_S_1018.img 1 2 70.75 0.5 26
002_S_1070 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_002_S_1070.img 0 1 73.73 0.5 25
002_S_1261 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_002_S_1261.img 1 0 71.2 0 30
002_S_1268 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_002_S_1268.img 0 1 82.78 0.5 28
002_S_1280 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_002_S_1280.img 1 0 70.8 0 30
005_S_0324 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_005_S_0324.img 1 1 75.35 0.5 24
005_S_0448 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_005_S_0448.img 0 1 85.65 0.5 26
005_S_0553 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_005_S_0553.img 0 0 84.76 0 30
005_S_0572 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_005_S_0572.img 0 1 78.87 0.5 26
005_S_0602 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_005_S_0602.img 0 0 70.87 0 29
005_S_0814 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_005_S_0814.img 1 2 71.12 0.5 21
007_S_1206 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_007_S_1206.img 0 0 72.98 0 29
007_S_1222 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_007_S_1222.img 1 0 73.44 0 30
007_S_1304 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_007_S_1304.img 1 2 74.76 1 25
012_S_0689 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_012_S_0689.img 0 2 63.65 0.5 22
012_S_1009 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_012_S_1009.img 0 0 75.91 0 28
012_S_1212 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_012_S_1212.img 1 0 75.4 0 27
012_S_1292 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_012_S_1292.img 0 1 76.31 0.5 26
012_S_1321 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_012_S_1321.img 0 1 83.24 0.5 28
013_S_0996 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_013_S_0996.img 1 2 90.99 0.5 26
013_S_1035 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_013_S_1035.img 0 0 87.33 0 30
013_S_1276 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_013_S_1276.img 1 0 71.94 0 30
016_S_1117 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_016_S_1117.img 1 1 68.98 0.5 26
016_S_1121 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_016_S_1121.img 1 1 56.25 0.5 24
016_S_1138 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_016_S_1138.img 0 1 67.49 0.5 27
016_S_1149 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_016_S_1149.img 0 1 84.44 0.5 29
016_S_1326 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_016_S_1326.img 0 1 66.37 0.5 28
018_S_0335 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_018_S_0335.img 1 2 83.66 1 20
018_S_0369 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_018_S_0369.img 0 0 76.11 0 30
018_S_0406 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_018_S_0406.img 0 1 77.87 0.5 29
018_S_0450 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_018_S_0450.img 0 1 68.54 0.5 30
018_S_0633 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_018_S_0633.img 0 2 83.37 1 20
020_S_1288 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_020_S_1288.img 0 0 59.98 0 30
021_S_0332 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_021_S_0332.img 0 1 70.03 0.5 25
021_S_0753 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_021_S_0753.img 0 2 65.56 1 24
023_S_0030 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0030.img 1 1 80.04 0.5 29
023_S_0031 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0031.img 1 0 77.81 0 30
023_S_0058 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0058.img 0 0 70.2 0 30
023_S_0061 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0061.img 1 0 77.14 0 29
023_S_0078 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0078.img 1 1 76.07 0.5 24
023_S_0139 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0139.img 1 2 65.94 0.5 25
023_S_0331 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0331.img 1 1 64.66 0.5 27
023_S_0376 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0376.img 0 1 70.55 0.5 28
023_S_0388 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0388.img 0 1 71.3 0.5 25
023_S_0604 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0604.img 0 1 86.59 0.5 25
023_S_0613 /ifs/adni/3T/PERMS/IVO/JACOBIANS/3T_bl_023_S_0613.img 1 1 84.09 0.5 24

Supplementary information

Auxiliary tools

Masking statistical volumes

This tool provides the functionality to construct Masks of Stat Analysis results (e.g., P, R or T-stat maps outputted by VolumeMultipleRegression) given a user-specified threshold value. The output masks are 0 and 1 Byte volumes (determined by the threshold value).

  • Example call:

java -cp /ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_core.jar:/ifs/ccb/CCB_SW_Tools/others/Statistics/SOCR_Statistics/bin/SOCR_plugin.jar edu.ucla.stat.SOCR.analyses.command.SplitMaskPositiveNegativeAnalysisResults -dim Zmax Ymax XMax -input filename -mask mask_filename -threshold Value [-below filename] [-above filename] -data_type [0,1,2,3,4]

  • Options:
    • -help: print usage
    • -mask [Mask-volume.img]: specify a mask-volume (0 or 1 intensities) restricting the voxels where the regression models are computed (optional), 1Byte Analyze format volume of the same dimensions as the data
    • -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1
    • -below [Filename]: output mask of the intensities, where input <= threshold (1-Byte)
    • -above [Filename]: output mask of the intensities, where input < threshold (1-Byte)
    • -threshold [threshold_value]: threshold value separating the below/above intensities of the input file
    • -input [Filename]: input file-name
    • -data_type [0,1,2,3,4]:
      • Type=0 is for Unsigned Byte input volumes;
      • Type=1 is for Signed Byte input volumes;
      • Type=2 is for Unsigned-short integers
      • Type=3 is for Signed-short integers
      • Type=4 is for 4Byte=Float Volumes
    • -byteswap:Only enter this flag if you want the input data to be read in and byteswapped! Note that -byteswap effects: input data, mask-volume and output results!

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