Conversion of Dicom files into a analyze.img

Dicom to Analyze

Written by Owen Phillips . Email if you have any questions.

There are a couple of options for converting dicom data into a useable image format. For the Depression ECT project, use /ifs/woods/AIR/dicom2analyze and the script */narr/schizo/DEPRESSION/SCRIPTS/Processor.csh. For the Processor.csh script, you just need to change the subject ID within the foreach loop.

• Siemens to analyze = Converts all your Dicom Folders into Analyze (.img/.hdr) formate. It's easy to use and converts multiple folders but it does not preserve left right orientation.
• Dicom2analyze = An AIR tool which will convert a specific dicom folder into analyze format. It's useful because you can output a .air file with the convertion.
• PipelineTranslations_05Dec2008.jar = It's useful because it will convert to NIFTI format, which will preserve left and right orientation. This is helpful down the line since new versions of FSL & Freesurfer prefer this format. Otherwise, these programs may flip left and right and it becomes a struggle.

Siemenstoanalyze.jar file.

1. Download Siemens to analyze.jar.
2. You can run SiemensToAnalyze.jar locally or on qsub.loni.ucla.edu or cerebro-dev-0.loni.ucla.edu.
3. First ssh -X username@qsub.loni.ucla.edu
4. /usr/java2v14/bin/java -Xmx400000000 -jar SiemensToAnalyze.jar -recursive -target analyze_source -input [directory]
5. Note, if you are part of the Narr group, you don't have to download the .jar file. Instead use, ~narr/SiemensToAnalyze.jar

Dicom2analyze

• Run on qsub.loni.ucla.edu or cerebro-dev-0.loni.ucla.edu.
• First ssh -X username@qsub.loni.ucla.edu
• Below is an example where the T1data has 128 files and we are outputting an .air file.
• /ifs/woods/AIR/dicom2analyze ${dir}/${x}/A*/*/*/TFL_MGH_ME_VNAV_RMS*/ null ${dir}/${x}/${x}_native 1 128 -f ${dir}/${x}/${x}_native.air -o
  

PipelineTranslations.jar

• You can run this by accessing /ifs/faculty/narr/schizo/family_study/Owen/SCRIPTS/pipelineTranslations_05Dec2008.jar, or by downloading the file here: Downloads.
• Run on qsub.loni.ucla.edu or cerebro-dev-0.loni.ucla.edu.
• First ssh -X username@qsub.loni.ucla.edu
• java -Xmx900M -jar pipelineTranslations_05Dec2008.jar -input <dicom directory> -args <output name> -target nifti
  
  

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