SOCR EduMaterials AnalysesCommandLineVolumeMultipleRegression - Revision history

IvoDinov: /* Example Input data files */

2013-02-02T01:15:08Z

‎Example Input data files

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IvoDinov at 05:33, 26 April 2012

2012-04-26T05:33:12Z

IvoDinov: /* Volume Multiple Linear Regression Usage */ minor interaction term example

2011-03-12T02:49:33Z

‎Volume Multiple Linear Regression Usage: minor interaction term example

IvoDinov: /* Volume Multiple Linear Regression Usage */

2011-03-12T02:34:13Z

‎Volume Multiple Linear Regression Usage

IvoDinov: /* Volume Multiple Linear Regression Usage */

2011-03-12T02:31:36Z

‎Volume Multiple Linear Regression Usage

IvoDinov: /* Volume Multiple Linear Regression Usage */ entered the info on interactions (new feature)

2011-03-12T02:30:07Z

‎Volume Multiple Linear Regression Usage: entered the info on interactions (new feature)

IvoDinov: /* Volume Multiple Linear Regression Usage */

2010-09-10T21:08:58Z

‎Volume Multiple Linear Regression Usage

IvoDinov: /* Volume Multiple Linear Regression Usage */ added the specs for -intercept interceptConstant

2010-09-10T21:08:14Z

‎Volume Multiple Linear Regression Usage: added the specs for -intercept interceptConstant

IvoDinov: /* Volume Multiple Linear Regression Usage */ linked R, b, T, p to appropriate sections in E-book

2010-08-06T16:55:59Z

‎Volume Multiple Linear Regression Usage: linked R, b, T, p to appropriate sections in E-book

IvoDinov: added assumptions section

2010-04-01T15:49:53Z

added assumptions section

@@ Line 12: / Line 12: @@
 * 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===

@@ Line 52: / Line 52: @@
 </code>
 : # Or
-<code>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
+<code>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,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
 -byteorder little &</code>
 <code>date</code>

@@ Line 22: / Line 22: @@
 ** -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
+** -regressors [name1,name2,...name_k]: specify which columns/variables from the Design-Matrix should be used as regressors/covariates
-*** '''Interactions''': Interactions are specified within the -regressors flag. For interactions, each interaction variable must be composed of individual regressor variables that must also be previously included in the regressor list. For instance, if we need a triple interaction A*B*C, we must (minimally) specify: <br>''-regressors A,B,C,A*B,B*C,A*C,A*B*C''
+*** '''Interactions''': Interactions are specified within the -regressors flag. For interactions, each interaction variable must be composed of individual regressor variables that must also be previously included in the regressor list. For instance, if we need a triple interaction name1*name2*name3, we must (minimally) specify: <br>''-regressors name1,name2,name3,name1*name2,name2*name3,name1*name3,name1*name2*name3''
 ** -dim Zmax Ymax XMax: 	specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1
 ** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:

@@ Line 23: / Line 23: @@
 ** -h: 					DesignMatrix contains a header (first row)
 ** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates
-*** '''Interactions''': Interactions are specified within the -regressors flag. For interactions, each interaction variable must be composed of individual regressor variables that must also be previously included in the regressor list. For instance, if we need a triple interaction A*B*C, we must (minimally) specify: ''-regressors A,B,C,A*B,B*C,A*C,A*B*C''.
+*** '''Interactions''': Interactions are specified within the -regressors flag. For interactions, each interaction variable must be composed of individual regressor variables that must also be previously included in the regressor list. For instance, if we need a triple interaction A*B*C, we must (minimally) specify: <br>''-regressors A,B,C,A*B,B*C,A*C,A*B*C''
 ** -dim Zmax Ymax XMax: 	specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1
 ** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:

@@ Line 23: / Line 23: @@
 ** -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
 ** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:

@@ Line 48: / Line 48: @@
 <code>date</code>
-<code>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
+<code>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 -intercept interceptConstant -p /ifs/tmp/P_Value -r /ifs/tmp/R_Value -t /ifs/tmp/TStat_Value -data_type 2
 </code>
 : # Or

@@ Line 15: / Line 15: @@
 ===Volume Multiple Linear Regression Usage===
 * Generic Setting:
-<code> 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.volume.VolumeMultipleRegression -dm DesignMatrix.txt -h -regressors [name1,name2,...,name_k] -dim Zmax Ymax XMax [-p PValue_Filename] [-r RValue_Filename] [-t TStat_Filename] -data_type [0,1,2,3,4] -mask /ifs/tmp/myMaskVolume.img [-byteorder string]</code>
+<code> 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.volume.VolumeMultipleRegression -dm DesignMatrix.txt -h -regressors [name1,name2,...,name_k] -dim Zmax Ymax XMax [-intercept interceptConstant] [-p PValue_Filename] [-r RValue_Filename] [-t TStat_Filename] -data_type [0,1,2,3,4] -mask /ifs/tmp/myMaskVolume.img [-byteorder string]</code>
 *Options:
@@ Line 24: / Line 24: @@
 ** -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 [[AP_Statistics_Curriculum_2007_GLM_Regress#Regression_Coefficients_Inference | p-value]] volume (enter only the base of the filename)
 ** -b [Beta_Filename]: output the [AP_Statistics_Curriculum_2007_GLM_Regress#Estimating_the_Best_Linear_Fit | Beta effect-size coefficient]] volume (enter only the base of the filename)

@@ Line 24: / Line 24: @@
 ** -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)
+** -p [PValue_Filename]: output the [[AP_Statistics_Curriculum_2007_GLM_Regress#Regression_Coefficients_Inference | p-value]] volume (enter only the base of the filename)
-** -b [Beta_Filename]: output the Beta effect-size coefficient volume (enter only the base of the filename)
+** -b [Beta_Filename]: output the [AP_Statistics_Curriculum_2007_GLM_Regress#Estimating_the_Best_Linear_Fit | Beta effect-size coefficient]] volume (enter only the base of the filename)
-** -r [RValue_Filename]: output the partial-correlation volume (enter only the base of the filename)
+** -r [RValue_Filename]: output the [[AP_Statistics_Curriculum_2007_GLM_Regress#Estimating_the_Best_Linear_Fit | partial-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). Note that if you have one-factor (like CDR scores), this factor may have different levels (e.g., CDR score in {0.0, 0.5, 1.0, 1.5, etc.}). When the number of levels > 2, the results stored in the files specified by the –t flag contain the [[AP_Statistics_Curriculum_2007_ANOVA_1Way |F-statistics (F-maps)]] for the effect of this one-factor (CDR). In the special case of the CDR factor having only 2 levels, then the F-map is actually identical to the [[AP_Statistics_Curriculum_2007_Infer_2Means_Dep |T-statistics (T-Map)]].
+** -t [Tstat_Filename]:	output the [[AP_Statistics_Curriculum_2007_GLM_Regress#Regression_Coefficients_Inference | T-Statistics for the effect-size Beta]] (enter only the base of the filename). Note that if you have one-factor (like CDR scores), this factor may have different levels (e.g., CDR score in {0.0, 0.5, 1.0, 1.5, etc.}). When the number of levels > 2, the results stored in the files specified by the –t flag contain the [[AP_Statistics_Curriculum_2007_ANOVA_1Way |F-statistics (F-maps)]] for the effect of this one-factor (CDR). In the special case of the CDR factor having only 2 levels, then the F-map is actually identical to the [[AP_Statistics_Curriculum_2007_Infer_2Means_Dep |T-statistics (T-Map)]].
 ** -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;
 ** -byteorder string: ''string'' is one of {big, little, other}.

@@ Line 161: / Line 161: @@
 |}
 </center>
 ===Supplementary information===