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Streaming Scans for Offline Processing

Exvivo data collected with the 32 channel coils on the 7T scanner (Bay 5) is too big for the MRIR to reconstruct because the data overwrites itself on the RAID before the scan finishes, so the raw data must be streamed off of the RAID during scanning. To get images, the raw data must then be reconstructed offline (i.e. not on the scanner but on another machine). This wiki details the steps to reconstruct this raw data (assuming all necessary files were already collected) .

Scanning Instructions

Instructions for setting up streaming on the scanner and running a streamed scan can be found at the path below. Make sure you copy all relevant header and dat files from twix as listed in the instructions:

/autofs/cluster/exvivo/rock/4/users/hires/exvivo_data_collection/scanning_instructions/Streaming_instructions_oribi.doc

Approximate size of raw data

Be sure you have enough empty space on the RAID the data is being streamed to!

Directory Structure

The directory structure should consist of a parent directory (<subject name> for Fischl scan, <subject name>/7T for Edlow scans), which contains NOTES and protocol.pdf files, as well as directories called headers, raw, mri, scripts and snapshots. After raw data has been deleted, there should be a file in the raw directory called deleted_files containing a list of the segment names, who deleted them, and the date they were deleted. The mri directory should contain a subdirectory for each flip angle collected and for parameter_maps. An example directory structure is below:

<SUBJECT>
    headers
        meas_*_<scan name>.dat
        meas_*_<scan name>.hdr
        meas_*CoilCovariance.dat
        <other files>.dat
    mri
        FA??
            <offline recon output files>
        FA??
            <offline recon output files>
        <other FAs>
        parameter_maps
            <mri_msfitparms output files>
    NOTES
    protocol.pdf
    raw
        <streamed *.dat files> OR deleted_files
    scripts
        <scripts used for processing>
    snapshots
        <snapshots of parameter maps or scans of interest>

Documentation of files

Make a note file called NOTES which includes the following:

Be sure to delete all the .hybrid files after they have been used to create satisfactory .mgh files! These take up a lot of space. After all processing is complete (or at a safe point in the processing ,if space is desperately needed), the raw data can be removed from the cluster. A note called deleted_files should be left in the raw directory including the file names, date and user who deleted the files. For special cases, the raw data may be stored off the cluster on a hard drive instead of being deleted.

Current Offline Recon Method

Below is what is currently being used to process an offline recon. There are several different methods: OfflineReconDylan, OfflineReconTwitzel, as well as Jon Polimeni's personal scripts which are not documented here. Also, if using an external RAID instead of oribi, follow the instructions on the OfflineReconSshfs wiki to process the images without needing to transfer data to the cluster space first.

If you also acquired non-streaming data during the scan session (i.e. data that was reconstructed "online", on the scanner, and saved as dicoms in the patient browser), don't forget to process that data as well. Instructions for processing those are here: ExvivoRecons

OfflineRecon (last edited 2021-04-21 14:18:53 by DevaniCordero)