AMARES batch processing

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This topic contains 3 replies, has 3 voices, and was last updated by  Ronald Ouwerkerk 1 month ago.

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    Travis Carrell


    I am trying to batch process some 31P data with the AMARES quantification. I have saved,, and overall_phasing.op files, which I would like to use with the batch function. Whenever I run the batch process, the apodize properly works, but the AMARES processing shows that it fails, despite showing the saved files for processing. I even tried running the saved actions on the original file which with I created the process. It still failed. Are there any additional steps needed for batch processing?




    How do you run the batch process? From the jMRUI GUI or from the command line?


    Travis Carrell

    I tried running it through the jMRUI GUI. Will that process only work through the command line?


    Ronald Ouwerkerk

    I have given up on batch processing a long time ago. I do however process my data in batches. Similar spectra are just grouped in directories. If I varied a parameter in this series (e.g. TE) I have this information in the filename. It would make more sense to have it in the metadata or header, but as far as I know, that information is not available in any of the data export formats formats of jMUI.
    I read the whole set and then phase correct all or individual (as needed), correct frequency offsets etc..
    I found that batch processing does not work for this step because the same parameters are used for each step.
    After I save the corrected spectra (Save in separated files) I do an AMARES fit.
    I save the results in HTML (publish-all results) format because the HTML file has the individual filenames of the spectra. The text export does not (I wish the MRUI format header data: patient name, date, the frequency correction and the reference PPM and Hz were also part of the output).
    I then use a Matlab script to read the html code and collect the data. Data are then saved in a comma separated value file with one spectrum per row and columns for amplitude frequency etc for each resonance fitted and a column for noise estimate. I wish there was a more direct way to obtain this output format because especially in v6.0beta the HTML produces an absurd amount of graphics files.
    For batch processing to really work one would have to be able to do the phase correction/frequency shift automatically in a reliable fashion. Even though AMARES allows some shifts in frequency and fits the phase I find that results are better when all spectra are properly aligned and frequency shifts are only reliable on properly phased spectra.

    Ronald Ouwerkerk
    National Institutes of Health (NIH)

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