http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&feed=atom&action=historySOCR EduMaterials AnalysesCommandLineVolumeMultipleRegression - Revision history2024-03-29T11:53:47ZRevision history for this page on the wikiMediaWiki 1.15.1http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=12338&oldid=prevIvoDinov at 13:25, 12 December 20132013-12-12T13:25:16Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -help: print usage</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -help: print usage</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -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. 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.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -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. 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.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** -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 <del class="diffchange diffchange-inline">consuiderd </del>part of the mask and processed)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** -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 <ins class="diffchange diffchange-inline">considered </ins>part of the mask and processed)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -h: DesignMatrix contains a header (first row)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -h: DesignMatrix contains a header (first row)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables from the Design-Matrix should be used as regressors/covariates</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables from the Design-Matrix should be used as regressors/covariates</div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">===Errors===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">There are several types of errors (e.g., <code>Beginning the stat analyses ... VolumeMultipleRegression Error!!!!!!!!!!!!!!</code>) that can occur for various reasons related to system-memory, syntax, data format etc. Below are some examples to watch out for:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Memory Errors: Depending on the size of each subject dataset and the total number of subjects, the system may require specification of additional memory at the start of hte Java JVM (<code>java -ms200m -mx500m ...</code>).</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Incorrect Regressors: If your DM file includes a regressor listed as ''DXCUR'', however in the invocation you list the regressor as ''DX'', the call will error out (as the specified regressor is not included in the DM meta-data input file).</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Hidden/Special Characters: The DM matrix file may need to be first imported as an excel spreadsheet, and then recopied/exported back to (pure ASCII) text edit using a Linux/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 review your Design Matrix file. </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Missing values: Missing data points in the DM are indicated by "." In current implementation, 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.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Assumptions===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Assumptions===</div></td></tr>
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</table>IvoDinovhttp://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=11998&oldid=prevIvoDinov: /* Example Input data files */2013-02-02T01:15:08Z<p><span class="autocomment">Example Input data files</span></p>
<a href="http://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=11998&oldid=11614">Show changes</a>IvoDinovhttp://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=11614&oldid=prevIvoDinov at 05:33, 26 April 20122012-04-26T05:33:12Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* 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)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* 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)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Number of variables can be indicated at the end (after '''-h''' flag). If no number of variables is specified, 3 is set as default.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Number of variables can be indicated at the end (after '''-h''' flag). If no number of variables is specified, 3 is set as default.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">===Try-It-Online===</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">You can test the Multivariate Regression functionality using the [http://ucla.in/Ie80ps Pipeline PWS Web-start server].</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Volume Multiple Linear Regression Usage===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Volume Multiple Linear Regression Usage===</div></td></tr>
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</table>IvoDinovhttp://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=10845&oldid=prevIvoDinov: /* Volume Multiple Linear Regression Usage */ minor interaction term example2011-03-12T02:49:33Z<p><span class="autocomment">Volume Multiple Linear Regression Usage: </span> minor interaction term example</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: # Or</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: # Or</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><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</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><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,<ins class="diffchange diffchange-inline">CDR,AGE*</ins>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</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>2 -byteorder little &</code></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>2 -byteorder little &</code></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* Note the specification of the AGE*CDR interaction term.</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><code>date</code></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><code>date</code></div></td></tr>
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</table>IvoDinovhttp://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=10844&oldid=prevIvoDinov: /* Volume Multiple Linear Regression Usage */2011-03-12T02:34:13Z<p><span class="autocomment">Volume Multiple Linear Regression Usage</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -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)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -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)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -h: DesignMatrix contains a header (first row)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -h: DesignMatrix contains a header (first row)</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables <ins class="diffchange diffchange-inline">from the Design-Matrix </ins>should be used as regressors/covariates</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*** '''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 <del class="diffchange diffchange-inline">A</del>*<del class="diffchange diffchange-inline">B</del>*<del class="diffchange diffchange-inline">C</del>, we must (minimally) specify: <br>''-regressors <del class="diffchange diffchange-inline">A</del>,<del class="diffchange diffchange-inline">B</del>,<del class="diffchange diffchange-inline">C</del>,<del class="diffchange diffchange-inline">A</del>*<del class="diffchange diffchange-inline">B</del>,<del class="diffchange diffchange-inline">B</del>*<del class="diffchange diffchange-inline">C</del>,<del class="diffchange diffchange-inline">A</del>*<del class="diffchange diffchange-inline">C</del>,<del class="diffchange diffchange-inline">A</del>*<del class="diffchange diffchange-inline">B</del>*<del class="diffchange diffchange-inline">C</del>'' </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*** '''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 <ins class="diffchange diffchange-inline">name1</ins>*<ins class="diffchange diffchange-inline">name2</ins>*<ins class="diffchange diffchange-inline">name3</ins>, we must (minimally) specify: <br>''-regressors <ins class="diffchange diffchange-inline">name1</ins>,<ins class="diffchange diffchange-inline">name2</ins>,<ins class="diffchange diffchange-inline">name3</ins>,<ins class="diffchange diffchange-inline">name1</ins>*<ins class="diffchange diffchange-inline">name2</ins>,<ins class="diffchange diffchange-inline">name2</ins>*<ins class="diffchange diffchange-inline">name3</ins>,<ins class="diffchange diffchange-inline">name1</ins>*<ins class="diffchange diffchange-inline">name3</ins>,<ins class="diffchange diffchange-inline">name1</ins>*<ins class="diffchange diffchange-inline">name2</ins>*<ins class="diffchange diffchange-inline">name3</ins>'' </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:</div></td></tr>
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</table>IvoDinovhttp://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=10843&oldid=prevIvoDinov: /* Volume Multiple Linear Regression Usage */2011-03-12T02:31:36Z<p><span class="autocomment">Volume Multiple Linear Regression Usage</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -h: DesignMatrix contains a header (first row)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -h: DesignMatrix contains a header (first row)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*** '''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''<del class="diffchange diffchange-inline">. </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*** '''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: <ins class="diffchange diffchange-inline"><br></ins>''-regressors A,B,C,A*B,B*C,A*C,A*B*C'' </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:</div></td></tr>
<!-- diff generator: internal 2024-03-29 11:53:48 -->
</table>IvoDinovhttp://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=10842&oldid=prevIvoDinov: /* Volume Multiple Linear Regression Usage */ entered the info on interactions (new feature)2011-03-12T02:30:07Z<p><span class="autocomment">Volume Multiple Linear Regression Usage: </span> entered the info on interactions (new feature)</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -h: DesignMatrix contains a header (first row)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -h: DesignMatrix contains a header (first row)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*** '''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''. </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:</div></td></tr>
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</table>IvoDinovhttp://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=10571&oldid=prevIvoDinov: /* Volume Multiple Linear Regression Usage */2010-09-10T21:08:58Z<p><span class="autocomment">Volume Multiple Linear Regression Usage</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><code>date</code></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><code>date</code></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><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</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><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 <ins class="diffchange diffchange-inline">-intercept interceptConstant </ins>-p /ifs/tmp/P_Value -r /ifs/tmp/R_Value -t /ifs/tmp/TStat_Value -data_type 2</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></code></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></code></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: # Or</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>: # Or</div></td></tr>
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</table>IvoDinovhttp://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=10570&oldid=prevIvoDinov: /* Volume Multiple Linear Regression Usage */ added the specs for -intercept interceptConstant2010-09-10T21:08:14Z<p><span class="autocomment">Volume Multiple Linear Regression Usage: </span> added the specs for -intercept interceptConstant</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Volume Multiple Linear Regression Usage===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Volume Multiple Linear Regression Usage===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Generic Setting:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Generic Setting:</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><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></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><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 <ins class="diffchange diffchange-inline">[-intercept interceptConstant] </ins>[-p PValue_Filename] [-r RValue_Filename] [-t TStat_Filename] -data_type [0,1,2,3,4] -mask /ifs/tmp/myMaskVolume.img [-byteorder string]</code></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Options:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Options:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">** -intercept [Base_Filename]: Base Filename for the 4 Intercept Estimates. This base filename will be appended with:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*** _Intercept_Pvalue.img</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*** _Intercept_Beta.img</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*** _Intercept_RPartCorr.img</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">*** _Intercept_TStat.img</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">** -i [Base_Filename]: Identical to -intercept [Base_Filename]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -p [PValue_Filename]: output the [[AP_Statistics_Curriculum_2007_GLM_Regress#Regression_Coefficients_Inference | p-value]] volume (enter only the base of the filename)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -p [PValue_Filename]: output the [[AP_Statistics_Curriculum_2007_GLM_Regress#Regression_Coefficients_Inference | p-value]] volume (enter only the base of the filename)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -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)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -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)</div></td></tr>
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</table>IvoDinovhttp://wiki.stat.ucla.edu/socr/index.php?title=SOCR_EduMaterials_AnalysesCommandLineVolumeMultipleRegression&diff=10491&oldid=prevIvoDinov: /* Volume Multiple Linear Regression Usage */ linked R, b, T, p to appropriate sections in E-book2010-08-06T16:55:59Z<p><span class="autocomment">Volume Multiple Linear Regression Usage: </span> linked R, b, T, p to appropriate sections in E-book</p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -regressors [name1,name2,...name_k]: specify which columns/variables should be used as regressors/covariates</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -dim Zmax Ymax XMax: specify the dimension-sizes (for 2D images use ZMax=1, for 1D, Zmax=Y_Max=1</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** -p [PValue_Filename]: output the p-value volume (enter only the base of the filename)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** -p [PValue_Filename]: output the <ins class="diffchange diffchange-inline">[[AP_Statistics_Curriculum_2007_GLM_Regress#Regression_Coefficients_Inference | </ins>p-value<ins class="diffchange diffchange-inline">]] </ins>volume (enter only the base of the filename)</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** -b [Beta_Filename]: output the Beta effect-size coefficient volume (enter only the base of the filename)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** -b [Beta_Filename]: output the <ins class="diffchange diffchange-inline">[AP_Statistics_Curriculum_2007_GLM_Regress#Estimating_the_Best_Linear_Fit | </ins>Beta effect-size coefficient<ins class="diffchange diffchange-inline">]] </ins>volume (enter only the base of the filename)</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** -r [RValue_Filename]: output the partial-correlation volume (enter only the base of the filename)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** -r [RValue_Filename]: output the <ins class="diffchange diffchange-inline">[[AP_Statistics_Curriculum_2007_GLM_Regress#Estimating_the_Best_Linear_Fit | </ins>partial-correlation<ins class="diffchange diffchange-inline">]] </ins>volume (enter only the base of the filename)</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>** -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)]].</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>** -t [Tstat_Filename]: output the <ins class="diffchange diffchange-inline">[[AP_Statistics_Curriculum_2007_GLM_Regress#Regression_Coefficients_Inference | </ins>T-Statistics for the effect-size Beta<ins class="diffchange diffchange-inline">]] </ins>(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)]].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -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;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -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;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -byteorder string: ''string'' is one of {big, little, other}.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** -byteorder string: ''string'' is one of {big, little, other}.</div></td></tr>
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</table>IvoDinov