Difference between revisions of "SOCR EduMaterials AnalysesCommandLineVolumeMultipleRegression"

Revision as of 23:37, 7 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] -mask /ifs/tmp/myMaskVolume.img

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

Translate this page:

(default)	Deutsch	Español	Français	Italiano	Português	日本語	България	الامارات العربية المتحدة	Suomi	इस भाषा में	Norge
한국어	中文	繁体中文	Русский	Nederlands	Ελληνικά	Hrvatska	Česká republika	Danmark	Polska	România	Sverige

@@ Line 13: / Line 13: @@
 ==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.VolumeMultipleRegression -dm DesignMatrix.txt -h -regressors [name1,name2,...name_k] -dim Zmax Ymax XMax [-p PValue_Filename] [-r RValue_Filename] -data_type [1,4]</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.VolumeMultipleRegression -dm DesignMatrix.txt -h -regressors [name1,name2,...name_k] -dim Zmax Ymax XMax [-p PValue_Filename] [-r RValue_Filename] -data_type [1,4] -mask /ifs/tmp/myMaskVolume.img</code>
 *Options:
@@ Line 24: / Line 24: @@
 ** -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;
+** -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.

Difference between revisions of "SOCR EduMaterials AnalysesCommandLineVolumeMultipleRegression"

Revision as of 23:37, 7 February 2009

Contents

Introduction

General Usage

Volume Multiple Linear Regression Usage

Example Input data files

Navigation menu

Personal tools

Namespaces

Variants

Views

More

Search

Navigation

Tools