SOCR EduMaterials AnalysesCommandLineVolume1Sample T test - Revision history

IvoDinov: /* One-Sample T-test Usage */

2009-05-14T01:46:42Z

‎One-Sample T-test Usage

IvoDinov: added byteorder option

2009-05-14T01:45:28Z

added byteorder option

IvoDinov: /* One-Sample T-test Usage */

2009-03-26T18:25:38Z

‎One-Sample T-test Usage

IvoDinov: /* One-Sample T-test Usage */

2009-03-18T04:01:22Z

‎One-Sample T-test Usage

IvoDinov: /* Example Input data files */ changed all qualitative variables to quantitative

2009-03-17T20:44:38Z

‎Example Input data files: changed all qualitative variables to quantitative

Show changes

IvoDinov: /* One-Sample T-test Usage */

2009-03-13T00:35:10Z

‎One-Sample T-test Usage

IvoDinov: /* One-Sample T-test Usage */

2009-03-12T23:41:52Z

‎One-Sample T-test Usage

IvoDinov: /* One-Sample T-test Usage */

2009-03-12T23:32:48Z

‎One-Sample T-test Usage

IvoDinov at 22:51, 12 March 2009

2009-03-12T22:51:43Z

IvoDinov at 17:38, 12 March 2009

2009-03-12T17:38:38Z

@@ Line 28: / Line 28: @@
 ** -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;
-**  -byteorder string:		string is one of the following
+** -byteorder string: ''string'' is one of {big, little, other}.
-*** big (java.nio.ByteOrder.BIG_ENDIAN)
+*** ''big'' = BIG_ENDIAN processor
-*** little (java.nio.ByteOrder.LITTLE_ENDIAN)
+*** ''little'' = LITTLE_ENDIAN processor
-*** system (default system byteorder, java.nio.ByteOrder.nativeOrder())
+*** ''other'' = default processor (java.nio.ByteOrder.nativeOrder())
 ** -byteswap:	('''deprecated''') 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!
 ** 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 500<sup>3</sup> and you have 100's of volumes, 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.

@@ Line 15: / Line 15: @@
 ===One-Sample T-test 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.Volume_1Sample_T_test -dm DesignMatrix.txt -h -regressors [name=Label] -null value -dim Zmax Ymax XMax [-p filename] [-t filename] -data_type [0,1,2,3,4]</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.Volume_1Sample_T_test -dm DesignMatrix.txt -h -regressors [name=Label] -null value -dim Zmax Ymax XMax [-p filename] [-t filename] -data_type [0,1,2,3,4] -byteorder string</code>
 *Options:
@@ Line 28: / Line 28: @@
 ** -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!
+**  -byteorder string:		string is one of the following
 ** 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 500<sup>3</sup> and you have 100's of volumes, 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.
@@ Line 37: / Line 41: @@
 <code>java -ms500m -mx1000m -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.Volume_1Sample_T_test -dm /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/DM_1SampleTtest.txt -h -regressors GROUP=1 -dim 220 220 220 -p /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/VolumeMultipleRegressionTest/P_Value_mask_1SampleT -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/VolumeMultipleRegress
-ionTest/T_Value_mask_1SampleT -data_type 2 -null 1100</code>
+ionTest/T_Value_mask_1SampleT -data_type 2 -null 1100 -byteorder little</code>
 <code>date</code>

@@ Line 19: / Line 19: @@
 *Options:
 ** -help: print usage
-** -dm [DesignMatrix.txt]: specify a tab-separated text file containing the design matrix
+** -dm [DesignMatrix.txt]: specify a tab-separated text file containing the design matrix. <u>Note</u>: 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 <code>Beginning the stat analyses ... VolumeMultipleRegression Error!!!!!!!!!!!!!!</code>, then please review your Design Matrix file.
 ** -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)

@@ Line 29: / Line 29: @@
 ** -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!
-** 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 200<sup>3</sup> then use these parameters after the initial ''java'' call (-ms2000m -mx4000m), see the example below. This requests 2-4GB or RAM memory for this process. You may need more or less memory depending on the number of volumes and dimension sizes.
+** 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 500<sup>3</sup> and you have 100's of volumes, 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 (Volume1Sample_T_test.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.

@@ Line 37: / Line 37: @@
 <code>java -ms500m -mx1000m -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.Volume_1Sample_T_test -dm /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/DM_1SampleTtest.txt -h -regressors GROUP=1 -dim 220 220 220 -p /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/VolumeMultipleRegressionTest/P_Value_mask_1SampleT -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/VolumeMultipleRegress
-ionTest/T_Value_mask_1SampleT -data_type 2 -byteswap -null 1100</code>
+ionTest/T_Value_mask_1SampleT -data_type 2 -null 1100</code>
 <code>date</code>

@@ Line 36: / Line 36: @@
 <code>date</code>
-<code>java -ms500m -mx1000m -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.Volume_1Sample_T_test -dm /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/VolumeMultipleRegressionTest/DM1.txt -h -regressors GROUP=Normal -dim 220 220 220 -p /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/VolumeMultipleRegressionTest/P_Value_mask_1SampleT -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_1SampleT -data_type 2 -byteswap -null 1100</code>
+<code>java -ms500m -mx1000m -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.Volume_1Sample_T_test -dm /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/DM_1SampleTtest.txt -h -regressors GROUP=Normal -dim 220 220 220 -p /ifs/ccb/CCB_SW_Tools/Statistics/SOCR_Statistics/SOCR_CSV_test_Scripts_Data/VolumeMultipleRegressionTest/P_Value_mask_1SampleT -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_1SampleT -data_type 2 -byteswap -null 1100</code>
 <code>date</code>

@@ Line 13: / Line 13: @@
 * 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===
+===One-Sample T-test 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.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</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.Volume_1Sample_T_test -dm DesignMatrix.txt -h -regressors [name=Label] -null value -dim Zmax Ymax XMax [-p filename] [-t filename] -data_type [0,1,2,3,4]</code>
 *Options:
@@ 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 [name=Label]: specify which column/variable should be used and what is its value!
 ** -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)
 ** -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;
@@ Line 31: / Line 31: @@
 ** 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 200<sup>3</sup> then use these parameters after the initial ''java'' call (-ms2000m -mx4000m), see the example below. This requests 2-4GB 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.
+* Example: Edit a new file (Volume1Sample_T_test.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.
 <code>#!/bin/csh</code>