<commit_before># System wide default fmri analysis programs, for login setup

FMRIBIN=/usr/fmri/bin

PATH64=/usr/fmri/lib64
AFNI=${PATH64}/afni/2010_10_19_1028
CARET=${PATH64}/caret/5.62/bin_linux64
MATLAB=${PATH64}/matlab/2007a/bin
SLICER=${PATH64}/slicer/3.6.3
AIR=${PATH64}/air/5.3.0
IMCONVERT=${PATH64}/imconvert


# FSL variables
export FSLDIR=${PATH64}/fsl/4.1.7
export FSL_DIR=${FSLDIR}
export FSL_BIN=${FSLDIR}/bin
export FSLCONFDIR=${FSLDIR}/config
export FSLLOCKDIR=""
export FSLMACHINELIST=""
export FSLMACHTYPE=""
export FSLMULTIFILEQUIT=TRUE
export FSLOUTPUTTYPE=NIFTI_GZ
export FSLREMOTECALL=""
export FSLTCLSH=${FSL_BIN}/fsltclsh
export FSLWISH=${FSL_BIN}/fslwish

# Freesurfer variables
export FREESURFER_HOME=${PATH64}/freesurfer/5.1.0
FREESURFER_BIN=${FREESURFER_HOME}/bin
export FIX_VERTEX_AREA=""
export FMRI_ANALYSIS_DIR=${FREESURFER_HOME}/fsfast
export FSFAST_HOME=${FREESURFER_HOME}/fsfast
FSFAST_BIN=${FSFAST_HOME}/bin
export FSF_OUTPUT_FORMAT=nii
export FS_OVERRIDE=0
export FUNCTIONALS_DIR=${FREESURFER_HOME}/sessions
export LOCAL_DIR=${FREESURFER_HOME}/local
export MINC_BIN_DIR=${FREESURFER_HOME}/mni/bin
export MINC_LIB_DIR=${FREESURFER_HOME}/mni/lib
export MNI_DATAPATH=${FREESURFER_HOME}/mni/data
export MNI_DIR=${FREESURFER_HOME}/mni
export MNI_PERL5LIB=${FREESURFER_HOME}/mni/lib/perl5/5.8.5
export OS=Linux
export PERL5LIB=${FREESURFER_HOME}/mni/lib/perl5/5.8.5
export SUBJECTS_DIR=${FREESURFER_HOME}/subjects

PATH32=/usr/fmri/lib
NPTK=${PATH32}/nptk/1.8
HAMMER=${PATH32}/hammer/oct-18-2010

if [ "$EUID" != "0" ]; then

    # Path manipulation
    pathmunge ${FMRIBIN} after
    pathmunge ${AFNI} after
    pathmunge ${CARET} after
    pathmunge ${FREESURFER_BIN} after
    pathmunge ${FSFAST_BIN} after
    pathmunge ${FSL_BIN} after
    pathmunge ${MINC_BIN_DIR} after
    pathmunge ${MATLAB} after
    pathmunge ${SLICER} after
    pathmunge ${NPTK} after
    pathmunge ${HAMMER} after
    pathmunge ${AIR} after
    pathmunge ${IMCONVERT} after

fi

export PATH

alias freesurfer43='source /usr/fmri/lib64/freesurfer/fschooser 43'<commit_msg>Add option for new fsl and afni<commit_after># System wide default fmri analysis programs, for login setup

FMRIBIN=/usr/fmri/bin

PATH64=/usr/fmri/lib64
AFNI=${PATH64}/afni/2010_10_19_1028
CARET=${PATH64}/caret/5.62/bin_linux64
MATLAB=${PATH64}/matlab/2007a/bin
SLICER=${PATH64}/slicer/3.6.3
AIR=${PATH64}/air/5.3.0
IMCONVERT=${PATH64}/imconvert


# FSL variables
export FSLDIR=${PATH64}/fsl/4.1.7
export FSL_DIR=${FSLDIR}
export FSL_BIN=${FSLDIR}/bin
export FSLCONFDIR=${FSLDIR}/config
export FSLLOCKDIR=""
export FSLMACHINELIST=""
export FSLMACHTYPE=""
export FSLMULTIFILEQUIT=TRUE
export FSLOUTPUTTYPE=NIFTI_GZ
export FSLREMOTECALL=""
export FSLTCLSH=${FSL_BIN}/fsltclsh
export FSLWISH=${FSL_BIN}/fslwish

# Freesurfer variables
export FREESURFER_HOME=${PATH64}/freesurfer/5.1.0
FREESURFER_BIN=${FREESURFER_HOME}/bin
export FIX_VERTEX_AREA=""
export FMRI_ANALYSIS_DIR=${FREESURFER_HOME}/fsfast
export FSFAST_HOME=${FREESURFER_HOME}/fsfast
FSFAST_BIN=${FSFAST_HOME}/bin
export FSF_OUTPUT_FORMAT=nii
export FS_OVERRIDE=0
export FUNCTIONALS_DIR=${FREESURFER_HOME}/sessions
export LOCAL_DIR=${FREESURFER_HOME}/local
export MINC_BIN_DIR=${FREESURFER_HOME}/mni/bin
export MINC_LIB_DIR=${FREESURFER_HOME}/mni/lib
export MNI_DATAPATH=${FREESURFER_HOME}/mni/data
export MNI_DIR=${FREESURFER_HOME}/mni
export MNI_PERL5LIB=${FREESURFER_HOME}/mni/lib/perl5/5.8.5
export OS=Linux
export PERL5LIB=${FREESURFER_HOME}/mni/lib/perl5/5.8.5
export SUBJECTS_DIR=${FREESURFER_HOME}/subjects

PATH32=/usr/fmri/lib
NPTK=${PATH32}/nptk/1.8
HAMMER=${PATH32}/hammer/oct-18-2010

if [ "$EUID" != "0" ]; then

    # Path manipulation
    pathmunge ${FMRIBIN} after
    pathmunge ${AFNI} after
    pathmunge ${CARET} after
    pathmunge ${FREESURFER_BIN} after
    pathmunge ${FSFAST_BIN} after
    pathmunge ${FSL_BIN} after
    pathmunge ${MINC_BIN_DIR} after
    pathmunge ${MATLAB} after
    pathmunge ${SLICER} after
    pathmunge ${NPTK} after
    pathmunge ${HAMMER} after
    pathmunge ${AIR} after
    pathmunge ${IMCONVERT} after

fi

export PATH

alias freesurfer43='source /usr/fmri/lib64/freesurfer/fschooser 43'
alias fsl5.0.8='source /usr/fmri/lib64/fsl/fsl5.0.8'

afninew () {
    AFNI=${PATH64}/afni/2011_12_21_1014-2015-04-25
    export PATH=$AFNI:$PATH
}
{'fraction_non_alphanumeric': 0.1323325635103926, 'fraction_numerical': 0.046189376443418015, 'mean_word_length': 6.123355263157895, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5418790', 'n_tokens_mistral': 1932, 'n_tokens_neox': 1803, 'n_words': 282}