runPipeline.py

import os
import time

pipelineDirectory = os.getcwd()
sifDirectory = os.path.join(pipelineDirectory, 'SingularitySIFs')
bidsDirectory = os.path.join(pipelineDirectory, 'BIDS')
outputDirectorySRC = os.path.join(pipelineDirectory, 'src')
sifFile = os.path.join(sifDirectory, 'dsistudio_latest.sif')

singularityCommand = f'singularity exec {sifFile}'

## run src process using b10, b2000, b4000 for each subject
for subjID in os.listdir(bidsDirectory):
    if 'sub-' not in subjID: continue
    # source files:
    lowStandard = os.path.join(bidsDirectory, subjID, 'dwi' , f'{subjID}_dir-std_acq-lowb_dwi.nii.gz')
    midStandard = os.path.join(bidsDirectory, subjID, 'dwi' , f'{subjID}_dir-std_acq-midb_dwi.nii.gz')
    highSandard = os.path.join(bidsDirectory, subjID, 'dwi' , f'{subjID}_dir-std_acq-highb_dwi.nii.gz')
    # output file:
    subjectSRCDir = os.path.join(outputDirectorySRC, subjID)
    try:
        os.mkdir(subjectSRCDir)
    except FileExistsError:
        print(f'\nsrc action already complete for subject: {subjID}!\n')
        continue
    stdOutFile = os.path.join(subjectSRCDir, f'{subjID}_dir-std.src.gz')
    srcCommandStandard = f'dsi_studio --action=src --source={lowStandard} --other_source={midStandard},{highSandard} --output={stdOutFile}'

    # reversed source files:
    lowReverse = os.path.join(bidsDirectory, subjID, 'dwi' , f'{subjID}_dir-rev_acq-lowb_dwi.nii.gz')
    midReverse = os.path.join(bidsDirectory, subjID, 'dwi' , f'{subjID}_dir-rev_acq-midb_dwi.nii.gz')
    highReverse = os.path.join(bidsDirectory, subjID, 'dwi' , f'{subjID}_dir-rev_acq-highb_dwi.nii.gz')
    # reversed output file:
    revOutFile = os.path.join(subjectSRCDir, f'{subjID}_dir-rev.src.gz')

    srcCommandReversed = f'dsi_studio --action=src --source={lowReverse} --other_source={midReverse},{highReverse} --output={revOutFile}'

    fullCommandStandard = f'{singularityCommand} {srcCommandStandard}' # appending standard command to singularity image execution command
    print(f'\nRunning DSI Studio src standard action for subject: {subjID}.....\n')
    os.system(fullCommandStandard)
    print(f'\n{subjID} standard src exited!\n')

    fullCommandReversed = f'{singularityCommand} {srcCommandReversed}' # appending reversed command to singularity image execution command
    print(f'\nRunning DSI Studio src reversed action for subject: {subjID}.....\n')
    os.system(fullCommandReversed)
    print(f'\n{subjID} reversed src exited!\n')

reconOutputDirectory = os.path.join(pipelineDirectory, 'fib')
for subjID in os.listdir(outputDirectorySRC):
    start = time.time()
    
    subjRecOutDirectory = os.path.join(reconOutputDirectory, subjID) # fib/subject/
    subjSrcInDirectory = os.path.join(outputDirectorySRC, subjID) # src/subject/
    # src files for input
    for file in os.listdir(subjSrcInDirectory):
        if 'rev' in file:
            revFileName = file
        elif 'std' in file:
            stdFileName = file
    srcFileS = os.path.join(subjSrcInDirectory, stdFileName)
    srcFileR = os.path.join(subjSrcInDirectory, revFileName)
    fibFileOutput = os.path.join(subjRecOutDirectory, f'{subjID}_rec.icbm152_adult.qsdr.1.25.fib.gz')

    try:
        os.mkdir(subjRecOutDirectory)
    except FileExistsError:
        print(f'\nrecon action already complete for subject: {subjID}.....\n')
        continue

    settings = '--method=7 --param0=1.25 --template=0 --qsdr_reso=2.0' # optional settings flags
    reconCommand = f'dsi_studio --action=rec --source={srcFileS} --rev_pe={srcFileR} --output={fibFileOutput} {settings}'

    fullRecCommand = f'{singularityCommand} {reconCommand}'
    print(f'\nRunning DSI Studio recon action for subject: {subjID}.....\n')
    os.chdir(os.path.join(outputDirectorySRC, subjID))
    os.system(fullRecCommand)
    end = time.time()
    print(f'\n{subjID} recon exited in {end - start} seconds!\n')
    os.chdir(pipelineDirectory)