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stowler/fmriQC-intro-exampleScript-20130930.sh

Created September 30, 2013 21:18
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  1. stowler created this gist Sep 30, 2013.
    182 changes: 182 additions & 0 deletions fmriQC-intro-exampleScript-20130930.sh
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    #!/bin/bash
    #
    # created: 20130724 by [email protected]
    # edited: 20130724 by [email protected]
    #
    # This is a short script to illustrate quality control (qc) and conversion of
    # Hackney PIT DICOM data.
    # - It is currently designed for FMRI runs from a single session of scanning
    # (i.e., one trip to the scanner, or one "study").
    # - It is not written to accept commandline arguments. Instead, make a copy of
    # the script and edit the information specific to your particpant, session, and
    # sequences.

    clear

    #############################################################################
    # STEP 0: Assign values to variables that will be used in output file names:
    # e.g.,
    # participant=CDA100
    # session=pre
    # sequences=fmriCategoryMemberGen
    #
    projectName=PIT
    participant=PIT005
    session=1scr
    sequences=FmriFingerTapping


    #############################################################################
    # STEP 1: Create the variable ${tempDir} , and assign to it the full path of a
    # temporary output directory in which we'll inspect output
    #
    # Details: We'll start by deleting any existing version of this directory, and
    # the recreating it. That avoids accidentally mixing old aborted data with your
    # current QC data.
    #
    # e.g., tempDir=/tmp/qc-nocera-CDA100-pre-namingruns
    #
    tempDir=/tmp/qcPIT-${participant}-${session}-${sequences}
    rm -fr ${tempDir}
    mkdir ${tempDir}


    #############################################################################
    # STEP 2: Create the variable ${dicomParentDir}
    #
    # Details: Create the variable ${dicomParentDir} and assign to it the full path
    # of the parent folder that contains DICOM folders for each of the series in
    # this session:
    #
    # e.g., dicomParentDir=/data/birc/Atlanta/DICOMreceivers/DICOMSTORE_viaRamaOnly/CDA100/MR/20130624/084914.000000/1
    #
    dicomParentDir=/data/birc/Atlanta/PIT/origUnzipped/PIT_05_20110803


    #############################################################################
    # STEP 3: Create the variable ${fmriSeriesList}, and assign its value: a
    # space-separated list of the FMRI series you are about to QC.
    #
    # Details: Per the configuration of our dicom store, DICOMs for individual
    # series are stored in folders named according to series number.
    # For example, the DICOM files of a hypothetical series number 3 (the third
    # series eported from the MRI console), are contained in a folder named "3",
    # which is a child of ${dicomParentDir}, which you defined in the previous
    # step.
    #
    # Note: The scanner console creates this numbering when it exports the data, so
    # this is different numbering than, for example, the list "1 2 3 4 5 6" which
    # codes what you will later call run1-run6.
    #
    # e.g., fmriSeriesList="4 5 6 7 8 9"
    #
    fmriSeriesList="fMRI_1_6 fMRI_2_7"


    #############################################################################
    # STEP 4: For each FMRI series, do four things:
    #
    # 1) count the number of DICOM files for your manual verification (command: ls -1 | wc -l)
    # 2) create a .bxh file containing the series' metadata (command: dicom2bxh)
    # 3) create a 4D nifti file (command: bxh2analyze --nii)
    # 4) reorient that 4D nifti file into gross alignment with the MNI 152 template (command: fslreorient2std)
    #

    echo ""
    echo ""
    echo "For each FMRI series: "
    echo " 1) counting the number of DICOMs"
    echo " 2) converting the series into a 4D nifti file:"
    echo ""
    for seriesNumber in ${fmriSeriesList}; do
    echo ""
    echo "############### DICOMs from series ${seriesNumber} : ###############"
    echo "LOCATION : ${dicomParentDir}/${seriesNumber}"
    echo -n "FILE COUNT: "
    ls -1 ${dicomParentDir}/${seriesNumber} | wc -l
    echo "If that's the expected DICOM count for the series, hit "
    echo -n "Enter to continue. (or CTRL-C to quit)"
    read
    echo "Creating .bxh metafile for series ${seriesNumber}..."
    echo ""
    dicom2bxh ${dicomParentDir}/${seriesNumber}/* ${tempDir}/fmriSeries${seriesNumber}.bxh
    echo ""
    echo "...done."
    echo ""
    echo "Creating nifti volume for series ${seriesNumber}..."
    echo ""
    bxh2analyze --nii -b -s ${tempDir}/fmriSeries${seriesNumber}.bxh ${tempDir}/fmriSeries${seriesNumber}
    echo ""
    echo "...done."
    echo ""
    echo "Reorienting series ${seriesNumber} nifti volume to match FSL's MNI 152 template..."
    echo ""
    fslreorient2std ${tempDir}/fmriSeries${seriesNumber}.nii ${tempDir}/fmriSeries${seriesNumber}_MNI
    echo ""
    echo "...done."
    echo ""
    done

    ls -l ${tempDir}
    echo ""


    #############################################################################
    # STEP 5: Inspect 4D images using FSLVIEW before moving on to generating the
    # intensity QC reports.
    #
    echo ""
    echo "Now opening fslview to confirm that each reoriented _MNI volume has"
    echo "orientation consistent with the MNI152 template..."
    fslview ${tempDir}/*_MNI* &

    echo ""
    echo "If you are happy with what you seen in fslview, hit "
    echo -n "Enter to continue. (or CTRL-C to quit)"
    read


    #############################################################################
    # STEP 6: Execute FBIRN's fmriqa_generate.pl to generate the QC report for these
    # runs:
    #
    echo ""
    echo "Creating QC report for series ${fmriSeriesList}:"
    echo ""
    # ...first we make a list of bxh files ordered according to their appearance in the ${fmriSeriesList} defined above:
    orderedListBXH=''
    for seriesNumber in ${fmriSeriesList}; do
    orderedListBXH="${orderedListBXH} ${tempDir}/fmriSeries${seriesNumber}.bxh "
    done
    # ...and then we execute the command that creates qc report:
    qcReportOutDir=${tempDir}/qcReport-FBIRN
    # ...don't mkdir: the fmriqa_generate.pl command will create it.
    fmriqa_generate.pl ${orderedListBXH} ${qcReportOutDir}
    echo ""
    echo "...done."
    echo ""


    #############################################################################
    # STEP 7: cleaning up
    #
    echo "To inspect the QC report just point your web browser at file://${qcReportOutDir}/index.html"
    echo ""
    echo "If you are happy with the conversion and QC results, copy the output files"
    echo "from the temporary ${tempDir} to your project folder. "
    echo "Something like:"
    echo ""

    echo "mkdir -p /data/birc/Atlanta/${projectName}/06.acqfiles/${participant}/${session}/${sequences}"
    echo "mkdir -p /data/birc/Atlanta/${projectName}/08.QC/${participant}/${session}/${sequences}"
    echo "cp ${tempDir}/*.nii* /data/birc/Atlanta/${projectName}/06.acqfiles/${participant}/${session}/${sequences}"
    echo "cp ${tempDir}/*.bxh /data/birc/Atlanta/${projectName}/06.acqfiles/${participant}/${session}/${sequences}"
    echo "cp -r ${qcReportOutDir} /data/birc/Atlanta/${projectName}/08.QC/${participant}/${session}/${sequences}"
    echo ""
    echo "...then the last step is for you to delete your temporary directory ${tempDir} ."
    echo ""
    du -sh ${tempDir}
    #tree -L 1 ${tempDir}
    echo ""
    echo ""