Unable to track Right superior longitudinal fasciculus

Software Support
1

Hello pyAFQ experts,

I’m trying to run py AFQ to track the right superior longitudinal fasciculus, I’m using this structure:
add_custom_bundle.py

I added the right SLF to the left SLF(already used in the example):

bundles = abd.BundleDict({
“L_SLF1”: {
“include”: [
template_dir + ‘SFgL.nii.gz’,
template_dir + ‘PaL.nii.gz’],
“exclude”: [
template_dir + ‘SLFt_roi2_L.nii.gz’],

    "cross_midline": False,

    "mahal": {
        "clean_rounds": 20,
        "length_threshold": 4,
        "distance_threshold": 2}
},
"L_SLF2": {
    "include": [
        template_dir + 'MFgL.nii.gz',
        template_dir + 'PaL.nii.gz'],
    "exclude": [
        template_dir + 'SLFt_roi2_L.nii.gz'],

    "cross_midline": False,

    "mahal": {
        "clean_rounds": 20,
        "length_threshold": 4,
        "distance_threshold": 2}
},
"L_SLF3": {
    "include": [
        template_dir + 'PrgL.nii.gz',
        template_dir + 'PaL.nii.gz'],
    "exclude": [
        template_dir + 'SLFt_roi2_L.nii.gz'],

    "cross_midline": False,

    "mahal": {
        "clean_rounds": 20,
        "length_threshold": 4,
        "distance_threshold": 2}
}
"R_SLF1": {
    "include": [
        template_dir + 'SFgR.nii.gz',
        template_dir + 'PaR.nii.gz'],
    "exclude": [
        template_dir + 'SLFt_roi2_R.nii.gz'],

    "cross_midline": False,

    "mahal": {
        "clean_rounds": 20,
        "length_threshold": 4,
        "distance_threshold": 2}
},
"R_SLF2": {
    "include": [
        template_dir + 'MFgR.nii.gz',
        template_dir + 'PaR.nii.gz'],
    "exclude": [
        template_dir + 'SLFt_roi2_R.nii.gz'],

    "cross_midline": False,

    "mahal": {
        "clean_rounds": 20,
        "length_threshold": 4,
        "distance_threshold": 2}
},
"R_SLF3": {
    "include": [
        template_dir + 'PrgR.nii.gz',
        template_dir + 'PaR.nii.gz'],
    "exclude": [
        template_dir + 'SLFt_roi2_R.nii.gz'],

    "cross_midline": False,

    "mahal": {
        "clean_rounds": 20,
        "length_threshold": 4,
        "distance_threshold": 2}
}

})

The rest of the code is the same as the example (add_custom_bundle.py), but when it comes to the cleaning step, it removes all the streams in the first cleaning round, I also get the same results for other tracks when tracking the fibers in the cerebellar peduncles. I want to know if there is something wrong with my default parameters or if it’s totally normal to get zero streams for some fibers.

Bests,
Masood