Difference between revisions of "SOCR EduMaterials AnalysesCommandLineVolumeMultipleRegression"

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** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates
 
** -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
 
** -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
+
** -p [PValue_Filename]:   output the p-value volume (enter only the base of the filename)
−
** -r [RValue_Filename]:   output the effect-size/correlation volume
+
** -r [RValue_Filename]:   output the effect-size/correlation volume (enter only the base of the filename)
 
** -data_type [1,2,4]: Type=1 is for Byte, Type=2 is for Unsigned Short integer and Type=4 is for 4Byte=Float Volume Input;
 
** -data_type [1,2,4]: Type=1 is for Byte, Type=2 is for Unsigned Short integer and Type=4 is for 4Byte=Float Volume Input;
  

Revision as of 19:00, 4 February 2009

This page includes the information on how to access the Multiple Linear Regression library for the purpose of computing VOLUME/IMAGE MLR 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.

General Usage

  • Get the latest SOCR JAR files from the SOCR page (http://socr.ucla.edu/htmls/jars/).
  • The command-line interface to SOCR Analyses generally uses EXAMPLE 1 from the list of example data files for the corresponding analysis.
  • All Input files are ASCII (see examples within each of the specific analyses).
  • a -h flag at the end of the command-line indicates that the first row in all ASCII input data files is a HEADER row (so it's not interpreted as data)
  • Number of variables can be indicated at the end (after -h flag). If no number of variables is specified, 3 is set as default.

Volume Multiple Linear Regression Usage

  • Generic Setting:

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.VolumeMultipleRegression -dm DesignMatrix.txt -h -regressors [name1,name2,...name_k] -dim Zmax Ymax XMax [-p PValue_Filename] [-r RValue_Filename] -data_type [1,4]

  • Options:
    • -help: print usage
    • -dm [DesignMatrix.txt]: specify a tab-separated text file containing the design matrix
    • -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
    • -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)
    • -data_type [1,2,4]: Type=1 is for Byte, Type=2 is for Unsigned Short integer and Type=4 is for 4Byte=Float Volume Input;
  • 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 -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.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.img -r /ifs/tmp/R_Value.img -data_type 2

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.

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

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