Simplifying Preprocessing Tasks with Scripts

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Simplifying Preprocessing Tasks with Scripts

• By Cinly Ooi

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Automation of preprocessing tasks

• Batch processing
• Uniform Form Design
• From WBIC (/pvCache/pvusr/nmr) to data suitable
  for BAMM and SPM entries
• Quick program development and quality assurance.

IT IS NOT A SUBSTITUTE FOR UNDERSTANDING THE
PROCESS
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The Scripts and Forms
Command perl ltscript namegt ltparameter filegt

• pvconv-batch.pl
• WBIC reconstructed data -gt 4D Bruker File
• ana4dto3d-batch.pl
• 4D Bruker File to 3D Bruker Files
• fbamm-batch.pl
• Creating the parameter files and execute fbamm
• Need modification
• imgutils-image_format_convertion-batch.pl
• Next job?
• 4D Bruker File to 3D UNC Files

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Form Design

• ltPVCONV_Programgt
  pvconv.pl,-frecofix
• ltInputSessionDirectoryPrefixgt
  /pvCache/pvuser/nmr
• ltOutputDirectoryPrefixgt /home/co224/shri-da
  ta
• ltTABLEgt
• ltDogt ltDirgt ltSeriesgt
• 1 W010208.gO1 4,5,7,8,11
• 1 W000317.gO1 5,7,8,10,11
• 1 W020523.gO1 5,6,8,9,11
• 1 W020524.gO1 4,8,9,11,14
• 1 W020560.gO1 4,5,7,8,10
• 0 W020529.gO1 4,5,7,8,10

Common section -- applies to all
separator
Individual Experiment -- exp details
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pvconv-batch.pl
ltPVCONV_Programgt
pvconv.pl,-frecofix ltInputSessionDirectoryPrefixgt
/pvCache/pvuser/nmr ltOutputDirectoryPrefixgt
/home/co224/shri-data ltTABLEgt ltDogt
ltDirgt ltSeriesgt 1
W010208.gO1 4,5,7 1 W000317.gO1
5,7,8,10,11 0 W020529.gO1 4,5,7,8,10

• First line
• mkdir /home/co224/shri-data/W010208.gO1
• cd /home/co224/shri-data/W010208.gO1
• pvconv.pl frecofix series 4 series 5 series
  7 /pvCache/pvuser/nmr/W010208.gO1
• mkdir 04 mv _04 04 copy
  W010208_04.brkhdr/hdr/img to 04
• mkdir 05 mv _05 05 copy
  W010208_05.brkhdr/hdr/img to 05
• mkdir 07 mv _07 07 copy
  W010208_07.brkhdr/hdr/img to 07

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ana4dto3d-batch.pl
ltANA4DTO3D_Programgt /app/AnalyzeTools/bi
n/ana4dto3d ltInputSessionDirectoryPrefixgt
/home/co224/shri-data ltOutputDirectoryPrefixgt
/home/co224/shri-data ltOutputDirectoryPostf
ixgt 3D ltTABLEgt ltDogt ltDirgt
ltSeriesgt 1 W010208.gO1 4,5,7 1
W000317.gO1 5,7,8,10,11 0 W020529.gO1
4,5,7,8,10
First Line (equivalent) cd /home/co224/shri-data/
W010208.gO1/04 ana4dto3d W010208_04.img 3D cd
/home/co224/shri-data/W010208.gO1/04 ana4dto3d
W010208_04.img 3D cd /home/co224/shri-data/W010208
.gO1/04 ana4dto3d W010208_04.img 3D
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Difference between the two forms
ltPVCONV_Programgt
pvconv.pl,-frecofix ltInputSessionDirectoryPrefixgt
/pvCache/pvuser/nmr ltOutputDirectoryPrefixgt
/home/co224/shri-data ltTABLEgt ltDogt
ltDirgt ltSeriesgt 1
W010208.gO1 4,5,7 1 W000317.gO1
5,7,8,10,11 0 W020529.gO1 4,5,7,8,10
ltANA4DTO3D_Programgt /app/AnalyzeTools/bi
n/ana4dto3d ltInputSessionDirectoryPrefixgt
/home/co224/shri-data ltOutputDirectoryPrefixgt
/home/co224/shri-data ltOutputDirectoryPostf
ixgt 3D ltTABLEgt ltDogt ltDirgt
ltSeriesgt 1 W010208.gO1 4,5,7 1
W000317.gO1 5,7,8,10,11 0 W020529.gO1
4,5,7,8,10
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fbamm-batch.pl
ltFBAMM_Programgt /tmp/marcel/fbamm.csh
ltTopLevelDirectorygt /tmp ltFBAMM_OutputD
irectorygt FBAMM ltFBAMM_ParamDirectorygt
/tmp/marcel/desmat ltUse_Design_Matrixgt
DESIGN_MATRIX ltRandomization_Methodgt
WAVELET ltEPPIgt 10 ltECPIgt 1
ltTRgt 3 ltTABLEgt ltDogt ltdirgt
ltDESIGN_MATRIXgt 1 autism 010042
010042.dm 1 autism 010043 010043.dm
fbamm.param
/tmp/autism/010042 /tmp/marcel/desmat/010042.dm WA
VELET 10 1 3 1 0

• First Line
• cd /tmp/autism/010042
• mkdir FBAMM
• cp .img .hdr .brkhdr FBAMM
• cd FBAMM
• /tmp/marcel/fbamm.csh lt fbamm.param gtprogress..log

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Engines

• Partially completed script ready for
  customization
• Form engine
• -batch.pl script
• Design matrix conversion engine
• dmc-.pl script
• Able to adapt engine for new task in a couple of
  hours

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THE END

• http//www.psychiatry.cam.ac.uk/BMU/SEMINARS/past.
  html