(r1.1 vs. r1.18) KristiClark < Main

Main.KristiClark (r1.1 vs. r1.18)

Diffs

<<O>> Difference Topic KristiClark (r1.18 - 24 Jul 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 80 to 80

META FILEATTACHMENT	testdata.tar.gz	attr="" comment="Test dataset 30 directions" date="1216474388" path="testdata.tar.gz" size="21647492" user="kclark" version="1.1"
META FILEATTACHMENT	dti_tools_source_code.tar	attr="" comment="Source code" date="1216475339" path="dti_tools_source_code.tar" size="2990080" user="kclark" version="1.1"
META FILEATTACHMENT	linux_binaries.tar	attr="" comment="Code compiled for linux" date="1216475815" path="linux_binaries.tar" size="25835520" user="kclark" version="1.1"

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META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="Recon data and correct slice prescription" date="1216770580" path="correct_slice_prescription.pipe" size="250470" user="kclark" version="1.1"

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META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="Reconstruct data and correct slice prescription" date="1216770580" path="correct_slice_prescription.pipe" size="250470" user="kclark" version="1.1"

META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="Correct for eddy current induced distortions & motion artifacts" date="1216770598" path="dti_eddy_motion.pipe" size="154229" user="kclark" version="1.1"

<<O>> Difference Topic KristiClark (r1.17 - 23 Jul 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 75 to 75

TWikiUsers has a list of other TWiki users.

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META FILEATTACHMENT	BasicDTIanalysis^?_howto.ppt	attr="" comment="" date="1216455537" path="BasicDTIanalysis_howto.ppt" size="6089728" user="kclark" version="1.2"
META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1216453812" path="DTI_analysis.pipe" size="328566" user="kclark" version="1.3"

>
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META FILEATTACHMENT	BasicDTIanalysis^?_howto.ppt	attr="" comment="Powerpoint tutorial" date="1216455537" path="BasicDTIanalysis_howto.ppt" size="6089728" user="kclark" version="1.2"
META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="Compute tensor, eigenvectors, eigenvalues, fiber tractography, etc." date="1216453812" path="DTI_analysis.pipe" size="328566" user="kclark" version="1.3"

META FILEATTACHMENT	testdata.tar.gz	attr="" comment="Test dataset 30 directions" date="1216474388" path="testdata.tar.gz" size="21647492" user="kclark" version="1.1"

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META FILEATTACHMENT	dti_tools_source_code.tar	attr="" comment="" date="1216475339" path="dti_tools_source_code.tar" size="2990080" user="kclark" version="1.1"
META FILEATTACHMENT	linux_binaries.tar	attr="" comment="" date="1216475815" path="linux_binaries.tar" size="25835520" user="kclark" version="1.1"
META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1216770580" path="correct_slice_prescription.pipe" size="250470" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1216770598" path="dti_eddy_motion.pipe" size="154229" user="kclark" version="1.1"

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META FILEATTACHMENT	dti_tools_source_code.tar	attr="" comment="Source code" date="1216475339" path="dti_tools_source_code.tar" size="2990080" user="kclark" version="1.1"
META FILEATTACHMENT	linux_binaries.tar	attr="" comment="Code compiled for linux" date="1216475815" path="linux_binaries.tar" size="25835520" user="kclark" version="1.1"
META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="Recon data and correct slice prescription" date="1216770580" path="correct_slice_prescription.pipe" size="250470" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="Correct for eddy current induced distortions & motion artifacts" date="1216770598" path="dti_eddy_motion.pipe" size="154229" user="kclark" version="1.1"

<<O>> Difference Topic KristiClark (r1.16 - 22 Jul 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 76 to 76

META FILEATTACHMENT	BasicDTIanalysis^?_howto.ppt	attr="" comment="" date="1216455537" path="BasicDTIanalysis_howto.ppt" size="6089728" user="kclark" version="1.2"

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META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1216453768" path="correct_slice_prescription.pipe" size="250645" user="kclark" version="1.2"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1216453791" path="dti_eddy_motion.pipe" size="154304" user="kclark" version="1.2"

META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1216453812" path="DTI_analysis.pipe" size="328566" user="kclark" version="1.3"
META FILEATTACHMENT	testdata.tar.gz	attr="" comment="Test dataset 30 directions" date="1216474388" path="testdata.tar.gz" size="21647492" user="kclark" version="1.1"
META FILEATTACHMENT	dti_tools_source_code.tar	attr="" comment="" date="1216475339" path="dti_tools_source_code.tar" size="2990080" user="kclark" version="1.1"
META FILEATTACHMENT	linux_binaries.tar	attr="" comment="" date="1216475815" path="linux_binaries.tar" size="25835520" user="kclark" version="1.1"

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META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1216770580" path="correct_slice_prescription.pipe" size="250470" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1216770598" path="dti_eddy_motion.pipe" size="154229" user="kclark" version="1.1"

<<O>> Difference Topic KristiClark (r1.15 - 19 Jul 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 79 to 79

META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1216453768" path="correct_slice_prescription.pipe" size="250645" user="kclark" version="1.2"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1216453791" path="dti_eddy_motion.pipe" size="154304" user="kclark" version="1.2"
META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1216453812" path="DTI_analysis.pipe" size="328566" user="kclark" version="1.3"

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META FILEATTACHMENT	testdata.tar.gz	attr="" comment="Test dataset 30 directions" date="1216474388" path="testdata.tar.gz" size="21647492" user="kclark" version="1.1"
META FILEATTACHMENT	dti_tools_source_code.tar	attr="" comment="" date="1216475339" path="dti_tools_source_code.tar" size="2990080" user="kclark" version="1.1"
META FILEATTACHMENT	linux_binaries.tar	attr="" comment="" date="1216475815" path="linux_binaries.tar" size="25835520" user="kclark" version="1.1"

<<O>> Difference Topic KristiClark (r1.14 - 19 Jul 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 18 to 18

To download the flows, right click & "save link as"

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These links are for cerebro

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These links are for cranium

1. Getting started (convert data from DICOM to analyze, correct gradient table for slice prescription, generate .diff file and/or bvals/bvecs for FSL): correct_slice_prescription.pipe
2. Correct for eddy current induced distortions & motion artifacts: dti_eddy_motion.pipe
3. DTI analysis: DTI_analysis.pipe

Deleted:

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4. Combine raw DTI data: combine_raw_DTIdata.pipe

These links are for cranium
1. Getting started (convert data from DICOM to analyze, correct gradient table for slice prescription, generate .diff file and/or bvals/bvecs for FSL): correct_slice_prescription2.pipe
2. Correct for eddy current induced distortions & motion artifacts: dti_eddy_motion2.pipe
3. DTI analysis: DTI_analysis2.pipe
4. Combine raw DTI data: combine_raw_DTIdata2.pipe

DTI Tools

Line: 82 to 75

TWikiUsers has a list of other TWiki users.

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META FILEATTACHMENT	BasicDTIanalysis^?_howto.ppt	attr="" comment="" date="1203547611" path="BasicDTIanalysis_howto.ppt" size="5044736" user="kclark" version="1.1"
META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1204098232" path="correct_slice_prescription.pipe" size="22744" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1204098244" path="dti_eddy_motion.pipe" size="110661" user="kclark" version="1.1"
META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1205170710" path="DTI_analysis.pipe" size="58305" user="kclark" version="1.2"
META FILEATTACHMENT	combine_raw_DTIdata.pipe	attr="" comment="" date="1204098270" path="combine_raw_DTIdata.pipe" size="17430" user="kclark" version="1.1"
META FILEATTACHMENT	correct_slice_prescription2.pipe	attr="" comment="" date="1204098599" path="correct_slice_prescription2.pipe" size="22580" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion2.pipe	attr="" comment="" date="1204098612" path="dti_eddy_motion2.pipe" size="110699" user="kclark" version="1.1"
META FILEATTACHMENT	DTI_analysis2.pipe	attr="" comment="" date="1205170732" path="DTI_analysis2.pipe" size="58305" user="kclark" version="1.2"
META FILEATTACHMENT	combine_raw_DTIdata2.pipe	attr="" comment="" date="1204098644" path="combine_raw_DTIdata2.pipe" size="17430" user="kclark" version="1.1"

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META FILEATTACHMENT	BasicDTIanalysis^?_howto.ppt	attr="" comment="" date="1216455537" path="BasicDTIanalysis_howto.ppt" size="6089728" user="kclark" version="1.2"
META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1216453768" path="correct_slice_prescription.pipe" size="250645" user="kclark" version="1.2"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1216453791" path="dti_eddy_motion.pipe" size="154304" user="kclark" version="1.2"
META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1216453812" path="DTI_analysis.pipe" size="328566" user="kclark" version="1.3"

<<O>> Difference Topic KristiClark (r1.13 - 15 Jul 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 14 to 14

Work Flows

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NOTE: the previous version of DTI_analysis.pipe & DTI_analysis2.pipe were incorrect in the Streamline FT module. Also the Streamline FT module that is now available in the pull-down menu in pipeline is also incorrect. Correction: if you open the Streamline FT module, the option for "tractography method" should be -m not -t. Updated this website 3/10/08 at 1:30pm EST.

To download the flows, right click & "save link as"

<<O>> Difference Topic KristiClark (r1.12 - 10 Mar 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 14 to 14

Work Flows

Added:

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NOTE: the previous version of DTI_analysis.pipe & DTI_analysis2.pipe were incorrect in the Streamline FT module. Also the Streamline FT module that is now available in the pull-down menu in pipeline is also incorrect. Correction: if you open the Streamline FT module, the option for "tractography method" should be -m not -t. Updated this website 3/10/08 at 1:30pm EST.

To download the flows, right click & "save link as"
These links are for cerebro

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Line: 83 to 86

META FILEATTACHMENT	BasicDTIanalysis^?_howto.ppt	attr="" comment="" date="1203547611" path="BasicDTIanalysis_howto.ppt" size="5044736" user="kclark" version="1.1"
META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1204098232" path="correct_slice_prescription.pipe" size="22744" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1204098244" path="dti_eddy_motion.pipe" size="110661" user="kclark" version="1.1"

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META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1204098258" path="DTI_analysis.pipe" size="58470" user="kclark" version="1.1"

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META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1205170710" path="DTI_analysis.pipe" size="58305" user="kclark" version="1.2"

META FILEATTACHMENT	combine_raw_DTIdata.pipe	attr="" comment="" date="1204098270" path="combine_raw_DTIdata.pipe" size="17430" user="kclark" version="1.1"
META FILEATTACHMENT	correct_slice_prescription2.pipe	attr="" comment="" date="1204098599" path="correct_slice_prescription2.pipe" size="22580" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion2.pipe	attr="" comment="" date="1204098612" path="dti_eddy_motion2.pipe" size="110699" user="kclark" version="1.1"

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META FILEATTACHMENT	DTI_analysis2.pipe	attr="" comment="" date="1204098623" path="DTI_analysis2.pipe" size="58470" user="kclark" version="1.1"

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META FILEATTACHMENT	DTI_analysis2.pipe	attr="" comment="" date="1205170732" path="DTI_analysis2.pipe" size="58305" user="kclark" version="1.2"

META FILEATTACHMENT	combine_raw_DTIdata2.pipe	attr="" comment="" date="1204098644" path="combine_raw_DTIdata2.pipe" size="17430" user="kclark" version="1.1"

<<O>> Difference Topic KristiClark (r1.11 - 05 Mar 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 17 to 17

To download the flows, right click & "save link as"

Deleted:

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Note: these flows are not quite in working order yet, pending some distribution of perl scripts.

These links are for cerebro
1. Getting started (convert data from DICOM to analyze, correct gradient table for slice prescription, generate .diff file and/or bvals/bvecs for FSL): correct_slice_prescription.pipe
2. Correct for eddy current induced distortions & motion artifacts: dti_eddy_motion.pipe

<<O>> Difference Topic KristiClark (r1.10 - 27 Feb 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 17 to 17

To download the flows, right click & "save link as"

Added:

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Note: these flows are not quite in working order yet, pending some distribution of perl scripts.

<<O>> Difference Topic KristiClark (r1.9 - 27 Feb 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 40 to 40

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ResliceDiff

<<O>> Difference Topic KristiClark (r1.8 - 27 Feb 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 14 to 14

Work Flows

Changed:

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1. Getting started (convert data from DICOM to analyze, correct gradient table for slice prescription, generate .diff file and/or bvals/bvecs for FSL): correct_slice_prescription.pipe

>
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To download the flows, right click & "save link as"
These links are for cerebro
1. Getting started (convert data from DICOM to analyze, correct gradient table for slice prescription, generate .diff file and/or bvals/bvecs for FSL): correct_slice_prescription.pipe

2. Correct for eddy current induced distortions & motion artifacts: dti_eddy_motion.pipe
3. DTI analysis: DTI_analysis.pipe

Added:

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DTI Tools

Line: 69 to 80

META FILEATTACHMENT	BasicDTIanalysis^?_howto.ppt	attr="" comment="" date="1203547611" path="BasicDTIanalysis_howto.ppt" size="5044736" user="kclark" version="1.1"

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META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1204098232" path="correct_slice_prescription.pipe" size="22744" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1204098244" path="dti_eddy_motion.pipe" size="110661" user="kclark" version="1.1"
META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1204098258" path="DTI_analysis.pipe" size="58470" user="kclark" version="1.1"
META FILEATTACHMENT	combine_raw_DTIdata.pipe	attr="" comment="" date="1204098270" path="combine_raw_DTIdata.pipe" size="17430" user="kclark" version="1.1"
META FILEATTACHMENT	correct_slice_prescription2.pipe	attr="" comment="" date="1204098599" path="correct_slice_prescription2.pipe" size="22580" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion2.pipe	attr="" comment="" date="1204098612" path="dti_eddy_motion2.pipe" size="110699" user="kclark" version="1.1"
META FILEATTACHMENT	DTI_analysis2.pipe	attr="" comment="" date="1204098623" path="DTI_analysis2.pipe" size="58470" user="kclark" version="1.1"
META FILEATTACHMENT	combine_raw_DTIdata2.pipe	attr="" comment="" date="1204098644" path="combine_raw_DTIdata2.pipe" size="17430" user="kclark" version="1.1"

<<O>> Difference Topic KristiClark (r1.7 - 21 Feb 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark
Email: kaclark@ucla.edu
Department: Neurology

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Location: (Please specify office location)

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Location: Brain Mapping Center 237

Comment:

DTI Documents

Line: 14 to 14

Work Flows

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1. Getting started (convert data from DICOM to analyze, correct gradient table for slice prescription, generate .diff file and/or bvals/bvecs for FSL): correct_slice_prescription.pipe

>
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1. Getting started (convert data from DICOM to analyze, correct gradient table for slice prescription, generate .diff file and/or bvals/bvecs for FSL): correct_slice_prescription.pipe

2. Correct for eddy current induced distortions & motion artifacts: dti_eddy_motion.pipe
3. DTI analysis: DTI_analysis.pipe

<<O>> Difference Topic KristiClark (r1.6 - 21 Feb 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 69 to 69

META FILEATTACHMENT	BasicDTIanalysis^?_howto.ppt	attr="" comment="" date="1203547611" path="BasicDTIanalysis_howto.ppt" size="5044736" user="kclark" version="1.1"

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META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1203547805" path="correct_slice_prescription.pipe" size="22603" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1203547820" path="dti_eddy_motion.pipe" size="110638" user="kclark" version="1.1"
META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1203547833" path="DTI_analysis.pipe" size="58365" user="kclark" version="1.1"

<<O>> Difference Topic KristiClark (r1.5 - 20 Feb 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 9 to 9

DTI Documents

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Getting started/Overview powerpoint:

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Getting started/Overview powerpoint: BasicDTIanalysis_howto.ppt

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Work Flows

DTI Tools

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DTI processing

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WebPreferences has preferences of the TWiki.Main web.
TWikiUsers has a list of other TWiki users.

Added:

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META FILEATTACHMENT	BasicDTIanalysis^?_howto.ppt	attr="" comment="" date="1203547611" path="BasicDTIanalysis_howto.ppt" size="5044736" user="kclark" version="1.1"
META FILEATTACHMENT	correct_slice_prescription.pipe	attr="" comment="" date="1203547805" path="correct_slice_prescription.pipe" size="22603" user="kclark" version="1.1"
META FILEATTACHMENT	dti_eddy_motion.pipe	attr="" comment="" date="1203547820" path="dti_eddy_motion.pipe" size="110638" user="kclark" version="1.1"
META FILEATTACHMENT	DTI_analysis.pipe	attr="" comment="" date="1203547833" path="DTI_analysis.pipe" size="58365" user="kclark" version="1.1"

<<O>> Difference Topic KristiClark (r1.4 - 20 Feb 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Name: Kristi Clark
Login Name: kclark

Line: 6 to 6

Department: Neurology
Location: (Please specify office location)
Comment:

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DTI Documents

Getting started/Overview powerpoint:

DTI Tools

Click each filename for a description & help file

Creation and manipulation of .diff files

DTI processing

My Links

WelcomeGuest to learn TWiki

<<O>> Difference Topic KristiClark (r1.3 - 26 Jan 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

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Name: kclark

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Name: Kristi Clark

Login Name: kclark
Email: kaclark@ucla.edu
Department: Neurology

<<O>> Difference Topic KristiClark (r1.2 - 24 Jan 2008 - KristiClark)

META TOPICPARENT	TWikiUsers

Deleted:

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Name: kclark
Login Name: kclark
Email: kaclark@ucla.edu

Line: 4 to 3

Name: kclark
Login Name: kclark
Email: kaclark@ucla.edu

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Department:

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Department: Neurology

Location: (Please specify office location)
Comment:

<<O>> Difference Topic KristiClark (r1.1 - 22 Jan 2008 - KristiClark)

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META TOPICPARENT	TWikiUsers

Name: kclark
Login Name: kclark
Email: kaclark@ucla.edu
Department:
Location: (Please specify office location)
Comment:

My Links

WelcomeGuest to learn TWiki
Sandbox web to try out TWiki
KristiClarkSandbox^? just for me

Personal Preferences (details in TWikiVariables)

Show tool-tip topic info on mouse-over of WikiWord links, on or off: (see details in TWikiPreferences)
- Set LINKTOOLTIPINFO = off
Horizontal size of text edit box:
- Set EDITBOXWIDTH = 70
Vertical size of text edit box:
- Set EDITBOXHEIGHT = 22
Style of text edit box. width: 99% for full window width (default), width: auto to disable.
- Set EDITBOXSTYLE = width: 99%
Optionally write protect your home page: (set it to your WikiName)
- Set ALLOWTOPICCHANGE = KristiClark

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Topic: KristiClark . { View | Diffs | r1.18 | > | r1.17 | > | r1.16 | More }

Revision r1.1 - 22 Jan 2008 - 22:02 - KristiClark
Revision r1.18 - 24 Jul 2008 - 15:44 - KristiClark