aap_parameters_defaults_UEA.xml

<?xml version="1.0" encoding="utf-8"?>
<aap xmlns:xi="http://www.w3.org/2001/XInclude">
    <xi:include href="aap_parameters_defaults.xml" parse="xml"/>
    <local>
        <directory_conventions>
            <fieldmapsdirname desc='Subdirectory in subject dir for fieldmaps' ui='dir'>fieldmaps</fieldmapsdirname>
            <structdirname desc='Subdirectory in subject dir for MRI structurals' ui='dir'>structurals</structdirname>
            <specialseriesdirname desc='Subdirectory in subject dir for special series' ui='text'>specialseries</specialseriesdirname>
            <eventsdirname  desc='Subdirectory in study, subject and/or session for event files' ui='text'>events</eventsdirname>
            <rawdatadir desc='Directories to find raw MRI data' ui='dir_list'>/gpfs/home/ryb17eeu/data</rawdatadir>
            <rawmegdatadir desc='Directory to find raw MEG data' ui='dir'></rawmegdatadir>
            <rawdataafterconversionprefix desc='Prefix of raw data after conversion from DICOM to NIFTI' ui='text'>fMR</rawdataafterconversionprefix>
            <subject_directory_format desc='Format of subject directory' ui='optionlist' options='from subject_directory_names|from data|S#|manual'>3</subject_directory_format>
            <rawseries_usefileorder desc='In raw data, use number in file listing not filtering by series number' ui='yesno'>0</rawseries_usefileorder>
            <selectechonumbers desc='Which echo numbers?' ui='vector_array' range='[1 Inf]'>0</selectechonumbers>
            <outputformat options='splitbymodule|onedirectory' ui='optionlist'>splitbymodule</outputformat>
            <remotefilesystem  desc='Type of files for imaging data' options='none|s3' ui='optionlist'>none</remotefilesystem>
            <dicomfolderstructure desc='Dicom folder structure, "flat" if all files in one directory (e.g., Robarts), "series" if series in separate directory (e.g., CBU)' ui='text'>flat</dicomfolderstructure>
            <subjectoutputformat desc='sprintf formatting string to get subject directory from number' ui='text'>S%02d</subjectoutputformat>
            <seriesoutputformat desc='sprintf formatting string to get series directory from number - at AWS Series_%04d  at CBU Series_%03d*; at CABI *_%d' ui='text'>SER%03d</seriesoutputformat>
            <protocol_fieldmap ui='text'>FieldMapping</protocol_fieldmap>
            <protocol_structural ui='text'>MPRAGE</protocol_structural>
            <protocol_t2 ui='text'>t2_spc</protocol_t2>
            <dicomfilter ui='text'>*</dicomfilter>
            <megsubjectoutputformat desc='sprintf formatting string to get subject directory from number' ui='text'></megsubjectoutputformat>
            <spmdir desc="Path(s) to SPM (>SPM12 r6470 required)" ui="dir">/gpfs/home/ryb17eeu/imaging_pipelines/software/spm12</spmdir>
            <spmtoolsdir desc='Path(s) to SPM tools (colon separated list)' ui='dir'></spmtoolsdir>
            <linuxshell desc='Linux shell used to run linux commands' ui='text'>bash</linuxshell>
            <fsldir desc='Path to fsl' ui='dir'>/gpfs/software/fsl/5.0.10</fsldir>
            <fslsetup desc='Path to fsl setup script, executing before any fsl command' ui='text'>/gpfs/home/ryb17eeu/imaging_pipelines/bin/fsl_bash</fslsetup>
            <fslshell desc='Shell used to run FSL' ui='text'>bash</fslshell>
            <fsloutputtype desc='Output type used by FSL' ui='text'>NIFTI</fsloutputtype>
            <freesurferdir desc='Path to freesurfer' ui='dir'>/gpfs/software/freesurfer/6.0</freesurferdir>        
            <freesurfershell desc='Shell used to run FreeSurfer' ui='text'>bash</freesurfershell>
            <freesurfersetup desc='Path to FreeSurfer setup script, executing before any FreeSurfer command' ui='text'></freesurfersetup>
            <freesurferenvironment desc='Path to FreeSurfer environmental setup script, executing before any FreeSurfer command' ui='text'>/gpfs/software/freesurfer/6.0/FreeSurferEnv.sh;</freesurferenvironment>
            <neuromagdir desc='Path to Neuromag' ui='dir'></neuromagdir>
            <eeglabdir desc='Path to EEGLAB toolbox' ui='dir'></eeglabdir>
            <GIFTdir desc='Path to GIFT toolbox' ui='dir'></GIFTdir>
            <templatedir desc='Path to folder with various templates (e.g. for aamod_freesurfer_deface)' ui='dir'></templatedir>
            <ANTSdir desc='Path to Advanced Normalisation Tools (ANTS)' ui='dir'></ANTSdir>
            <fieldtripdir desc='Path to fieltrip toolbox' ui='dir'></fieldtripdir>
            <BrainWaveletdir desc='Path to BrainWavelet toolbox' ui='dir'>/gpfs/home/ryb17eeu/imaging_pipelines/software/BrainWavelet_v2.0</BrainWaveletdir>
            <DCMTKdir desc='Path to DICOM Toolkit' ui='dir'></DCMTKdir>
            <FaceMaskingdir desc='Path to FaceMasking (WUSTL NRG)' ui='dir'></FaceMaskingdir>
            <allowremotecache desc='Allow local caching of files from remote server' ui='optionlist'>1</allowremotecache>
            <poolprofile desc='Cluster Profile and (optional) initial submit argument (e.g. asking for specific queue or resource) separated with colon' ui='text'>LSF2016b: -q long-ib:source /etc/profile; module add container/matlab/R2018; export MALLOC_ARENA_MAX=4; singularity exec /gpfs/software/singularity/2.3.2/gcc/images/matlab_6.7.img /usr/local/MATLAB/R2018a/bin/</poolprofile>
            <mailerserver desc='E-mail address and password (colon-sepertated) for the mailer account for sending notifications' ui='text'>aamailer.uea@gmail.com:aamailer</mailerserver>
        </directory_conventions>
        <options>
            <maximumretry desc='Maximum number of (re)tries to retrieve file' ui='double'>5</maximumretry>            
            <NIFTI4D desc="Use NIFTI-4D instead of NIFTI-3D" ui="yesno">1</NIFTI4D> 
            <wheretoprocess desc='where to do processing' options='localsingle|localparallel|aws|qsub' ui='optionlist'>qsub</wheretoprocess>
            <garbagecollection desc='Perform garbage collection after the analysis' ui='yesno'>1</garbagecollection>
            <aaworkercleanup desc='Remove aaworker folders older then the specified number of days (Empty means no cleanup)' ui='double'>7</aaworkercleanup>
            <aaworkermaximumretry desc='Maximum number of (re)tries to submit job to the scheduler' ui='double'>6</aaworkermaximumretry>
            <aaworkerwaitbeforeretry desc='If job has been pendign for longer than this value, aa re-ubmit it to the scheduler if aaworkermaximumretry > 1' ui='double'>3600</aaworkerwaitbeforeretry>
            <aaparallel desc='Settings for parallel execution on a cluster (if applicable)' ui='none'>
                <numberofworkers desc='Requested number of workers' ui='double'>8</numberofworkers>
                <memory desc='Requested amount of memory in GB' ui='double'>4</memory>
                <walltime desc='Maximum amount of time (in hours) to run a job' ui='double'>24</walltime>
            </aaparallel>
            <restorepath desc='Restore linux and MATLAB path upon closing' ui='yesno'>1</restorepath>
            <diagnostic_videos desc='Enable diagnostic videos (matlab not stable on some platforms)' ui='yesno'>1</diagnostic_videos>
            <autoidentifystructural desc='Automatically identify structurals?' ui='yesno'>0</autoidentifystructural>
            <autoidentifyfieldmaps desc='Automatically identify field maps?' ui='yesno'>0</autoidentifyfieldmaps>
            <autoidentifyfieldmaps_number desc='If field maps exist, how many are there? Positive or negatve number indicates fieldmap after or before EPI, respectively' ui='double'>-1</autoidentifyfieldmaps_number>
            <autoidentifyt2 desc='Automatically identify T2?' ui='yesno'>0</autoidentifyt2>		
            <autoidentifytmaps desc='Automatically identify t maps?' ui='yesno'>0</autoidentifytmaps>
        </options>
    </local>
</aap>