Data Analysis and Visualization for High-Resolution Hippocampal Perfusion

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hippocampal_perfusion
hippocampal_perfusion
hippocampal_perfusion
hippocampal_perfusion
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Hippocampal perfusion

This repository contains the data analysis code and (visualization) notebooks related to the preprint:

"Novel insights into hippocampal perfusion using high-resolution, multi-modal 7T MRI"

Code Snippets

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run:
    import numpy as np
    import nibabel as nib

    LR = nib.load(input[0])
    LR_labels = LR.get_fdata()
    LR_relabeled = np.zeros(LR_labels.shape)

    relabeling = [[1, 1],[2, 2],[20, 3],
                  [21, 4],[22, 5],[23, 6]]

    for labels in relabeling:
        LR_relabeled[LR_labels==labels[0]] = labels[1]

    img = nib.Nifti1Image(LR_relabeled.astype(np.int8), header=LR.header, affine=LR.affine)
    nib.save(img, output[0])
SnakeMake numpy nibabel From line 6 of rules/autotop.smk 
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shell:
    'reg_aladin -flo {input.flo} -ref {input.ref} -res {output.warped} -aff {output.xfm_ras} -rigOnly -nac && '
    'c3d_affine_tool {output.xfm_ras} -oitk {output.xfm_itk}'
SnakeMake C3D From line 37 of rules/autotop.smk 
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shell:
    'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} '
    'antsApplyTransforms -d 3 --interpolation NearestNeighbor -i {input.nii} -o {output} -r {input.ref} -t {input.xfm}'
SnakeMake From line 53 of rules/autotop.smk 
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shell:
    "c3d {input} -split -foreach -smooth 0.3mm -endfor -merge -o {output}"
SnakeMake C3D From line 66 of rules/autotop.smk 
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shell:
    "fslmaths {input} -bin {output}"
SnakeMake From line 9 of rules/common.smk 
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shell:
    "{params.merge_cmd}"
SnakeMake From line 29 of rules/common.smk 
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shell:
    "wb_command -metric-reduce {input} MEAN {output.avg} -only-numeric &&"
    "wb_command -metric-reduce {input} STDEV {output.std} -only-numeric &&"
    "wb_command -metric-reduce {input} COV {output.cov} -only-numeric "
SnakeMake From line 40 of rules/common.smk 
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run:
    import numpy as np
    import nibabel as nib
    from scipy.stats import variation 

    metric = nib.load(input[0])
    data = np.zeros((len(metric.darrays[0].data),len(input)))

    gii_merged = nib.gifti.GiftiImage()

    for i,in_metric in enumerate(input):
        data[:,i] = nib.load(in_metric).darrays[0].data
        gii_merged.add_gifti_data_array(
            nib.gifti.GiftiDataArray(data=data[:,i].astype(np.float32)
            )
        )       
    nib.save(gii_merged, output.merged)
    shell("wb_command -set-structure {output.merged} CORTEX_RIGHT")

    metric.darrays[0].data = np.nanmean(data,1)
    nib.save(metric, output.avg)

    metric.darrays[0].data = np.nanstd(data,1)
    nib.save(metric, output.std)

    metric.darrays[0].data = np.nanstd(data,1)/np.nanmean(data,1)
    nib.save(metric, output.cov)
SnakeMake numpy scipy nibabel From line 54 of rules/common.smk 
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shell:
    "wb_command -metric-gradient {input.midthickness} {input.metric} {output} -presmooth {params.sigma} -average-normals"
SnakeMake From line 103 of rules/common.smk 
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shell: "mris_convert {input} {output}"
SnakeMake From line 7 of rules/hcp-mmp.smk 
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shell: "mri_convert {input} {output}"
SnakeMake From line 15 of rules/hcp-mmp.smk 
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shell: 'mri_info {input} --tkr2scanner > {output}'
SnakeMake From line 23 of rules/hcp-mmp.smk 
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shell: 'wb_command -surface-apply-affine {input.surf} {input.tkr2scanner} {output}'
SnakeMake From line 33 of rules/hcp-mmp.smk 
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shell: 'wb_command -surface-resample {input.surf} {input.current_sphere} {input.new_sphere} {params.method} {output}'
SnakeMake From line 46 of rules/hcp-mmp.smk 
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shell: 'wb_command -surface-cortex-layer {input.white} {input.pial} 0.5 {output}'
SnakeMake From line 56 of rules/hcp-mmp.smk 
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shell:
    "wb_command -surface-generate-inflated {input} {output.inflated} {output.very_inflated} -iterations-scale 0.75"
SnakeMake From line 66 of rules/hcp-mmp.smk 
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shell: 
    """
    wb_command -label-resample {input.label} {input.current_sphere} {input.new_sphere} {params.method} {output} -area-surfs {input.current_surf} {input.new_surf}
    """
SnakeMake From line 82 of rules/hcp-mmp.smk 
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shell:
    'wb_command -label-to-volume-mapping {input.label} {input.surf} {input.vol_ref} {output}'
    ' -ribbon-constrained {input.white_surf} {input.pial_surf} -greedy'
SnakeMake From line 98 of rules/hcp-mmp.smk 
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shell:
    "wb_command -surface-vertex-areas {input} {output}"
SnakeMake From line 7 of rules/morphology.smk 
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shell:
    "wb_command -surface-vertex-areas {input} {output}"
SnakeMake From line 15 of rules/morphology.smk 
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shell:    
    """
    wb_command -metric-math x/y {output} -var x {input.native} -var y {input.unfolded}
    """
SnakeMake From line 25 of rules/morphology.smk 
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shell:
    "wb_command -surface-smoothing {input} {params.strength} {params.iterations} {output}"
SnakeMake From line 39 of rules/morphology.smk 
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shell:
    "wb_command -surface-curvature {input} -mean {output}"
SnakeMake From line 47 of rules/morphology.smk 
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shell:
    "wb_command -surface-to-surface-3d-distance {input.outer} {input.inner} {output}"
SnakeMake From line 58 of rules/morphology.smk 
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shell:    
    "wb_command -surface-to-surface-3d-distance {input.avg} {input.subject} {output.distance} -vectors {output.displacement} && "
    "wb_command -metric-math 'metric' {output.distance} -fixnan 0 -var metric {output.distance} && "
    "wb_command -metric-math 'metric' {output.displacement} -fixnan 0 -var metric {output.displacement}"
SnakeMake From line 72 of rules/morphology.smk 
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shell:
    """
    jupyter nbconvert \
        --TagRemovePreprocessor.enabled=True \
        --TagRemovePreprocessor.remove_cell_tags snakemake-job-properties \
        --to html {input}
    """
SnakeMake From line 95 of rules/morphology.smk 
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shell:
    "bash ./{params.script} {wildcards.subject} {input.gradcorrect} {params.mp2rage_correction}"
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shell:
    "bash ./{params.script} -i {input.inv2} -u {input.t1w} -o `dirname {output}`"
SnakeMake From line 29 of rules/mp2rage.smk 
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shell:
    "bash {params.script} -i {input}"
SnakeMake From line 44 of rules/mp2rage.smk 
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shell:
    "cp {input.nii} {output.nii} && cp {input.json} {output.json}"
SnakeMake From line 56 of rules/mp2rage.smk 
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    shell:
        "bash scripts/skullstripping/skullstrip.sh {params.script} {input} `realpath {output}` " #&> {log} {params.out_dir}  

# Apply the brain mask
rule apply_brain_mask:
    input: 
        t1w = rules.mprageise.output,
        brain_mask = rules.skull_stripping.output
    output: 'results/freesurfer/sub-{subject}/mri/orig/001.mgz'
    group: 'preprocessing'
    singularity: config['singularity_freesurfer']
    shell:
        "mri_mask {input.t1w} {input.brain_mask} {output}"
SnakeMake From line 70 of rules/mp2rage.smk 
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shell:
    "export SUBJECTS_DIR={params.sd} && "
    "recon-all -all -s sub-{wildcards.subject} -no-wsgcaatlas -notal-check -threads 8"
SnakeMake RECON From line 101 of rules/mp2rage.smk 
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shell:
    "c3d_affine_tool -ref {input.ref} -src {input.src} {input.xfm} -fsl2ras -oitk {output}"
SnakeMake C3D From line 116 of rules/mp2rage.smk 
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shell:
    "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
    "antsApplyTransforms -d 3 --interpolation Linear -i {input.nii} -o {output} -r {input.ref} -t {input.xfm2crop} -t {input.xfm2ref} -t {input.xfm2tse}"
SnakeMake From line 134 of rules/mp2rage.smk 
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shell:
    "c3d {input} -flip x -o  {output}"
SnakeMake C3D From line 144 of rules/mp2rage.smk 
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shell:
    "wb_command -volume-to-surface-mapping {input.nii} {input.midthickness} {output} -ribbon-constrained {input.outer} {input.inner} -volume-roi {input.ribbon}"
SnakeMake From line 161 of rules/mp2rage.smk 
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shell:
    "wb_command -metric-math '(t1w/t2w)' {output} -var t1w {input.t1w} -var t2w {input.t2w} -fixnan 0"
SnakeMake From line 174 of rules/mp2rage.smk 
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shell:
    "c3d_affine_tool -ref {input.ref} -src {input.src} {input.xfm} -fsl2ras -oitk {output}"
SnakeMake C3D From line 13 of rules/perfusion.smk 
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shell:
    """
    ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads}
    antsApplyTransforms -d 3 --interpolation Linear -i {input.nii} -o {output} -r {input.ref} \
        -t {input.xfm2crop} -t {input.xfm2ref} -t {input.xfm2tse}
    """
SnakeMake From line 27 of rules/perfusion.smk 
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shell:
    "c3d {input} -flip x -o {output}"
SnakeMake C3D From line 39 of rules/perfusion.smk 
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shell:
    """
    if [ {wildcards.tpl_res} = 'hires' ] ; then 
        wb_command -volume-to-surface-mapping {input.nii} {input.midthickness} {output} \
            -ribbon-constrained {input.outer} {input.inner} -volume-roi {input.ribbon}
    else
        wb_command -volume-to-surface-mapping {input.nii} {input.midthickness} {output} \
            -trilinear
    fi
    """
SnakeMake From line 52 of rules/perfusion.smk 
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shell:
    "AverageImages 3 {output} 0 {input}"
SnakeMake From line 68 of rules/perfusion.smk 
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shell:
    """
    ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads}
    antsApplyTransforms -d 3 --interpolation Linear -i {input.nii} -o {output} -r {input.ref} \
        -t {input.xfm2crop} -t {input.xfm2ref} -t {input.xfm2tse}
    """
SnakeMake From line 82 of rules/perfusion.smk 
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shell:
    "c3d {input} -flip x -o {output}"
SnakeMake C3D From line 94 of rules/perfusion.smk 
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shell:
    """
    if [ {wildcards.tpl_res} = 'hires' ] ; then 
        wb_command -volume-to-surface-mapping {input.nii} {input.midthickness} {output} \
            -ribbon-constrained {input.outer} {input.inner} -volume-roi {input.ribbon}
    else
        wb_command -volume-to-surface-mapping {input.nii} {input.midthickness} {output} \
            -trilinear
    fi
    """
SnakeMake From line 107 of rules/perfusion.smk 
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shell:
    "fslsplit {input} {params.prefix} -t"
SnakeMake From line 126 of rules/perfusion.smk 
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shell:
    """
    hemi={wildcards.hemi}
    in_dir=`dirname {input.nii}`
    out_dir=`dirname {output}`
    for file in $in_dir/*.nii.gz ; do
        out_file=`basename $file`
        antsApplyTransforms -d 3 --interpolation Linear -i $file -o $out_dir/$out_file -r {input.ref}  -t {input.xfm2crop} -t {input.xfm2ref} -t {input.xfm2tse}
    done
    """
SnakeMake From line 139 of rules/perfusion.smk 
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shell:
    """
    in_dir=`dirname {input}`
    out_dir=`dirname {output}`
    for file in $in_dir/*.nii.gz ; do
        out_file=`basename $file`
        c4d $file -flip x -o $out_dir/$out_file
    done
    """
SnakeMake From line 155 of rules/perfusion.smk 
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shell:
    """
    in_dir=`dirname {input.nii}`
    out_dir=`dirname {output}`
    exclude="0098 0197 0296 0395 0494 0593 0692 0791"
    for file in $in_dir/*.nii.gz ; do
        fname=`basename $file .nii.gz`
        vol=${{fname:10:4}}   

        if [[ $exclude != *$vol* ]] ; then
            out_file=${{fname}}.shape.gii
            wb_command -volume-to-surface-mapping $file {input.midthickness} $out_dir/$out_file -trilinear
        fi
    done
    """
SnakeMake From line 175 of rules/perfusion.smk 
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shell:
    "{params.merge_cmd}"
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shell:
    """
    ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads}
    antsApplyTransforms -d 3 --interpolation Linear -i {input.nii} -o {output} -r {input.nii} -t {input.xfm}
    """
SnakeMake From line 212 of rules/perfusion.smk 
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shell:
    """           
    wb_command -volume-to-surface-mapping {input.nii} {input.midthickness} {output} -trilinear        
    """
SnakeMake From line 227 of rules/perfusion.smk 
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shell:
    "mri_convert {input.t1w} {output} -nc -rl {input.fs}"
SnakeMake From line 9 of rules/sa2rage.smk 
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shell:   
    "reg_aladin -flo {input.src} -ref {input.ref} -aff {output.xfm} -rigOnly -nac"
SnakeMake From line 23 of rules/sa2rage.smk 
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shell:
    "c3d_affine_tool {input.xfm} -oitk {output}"
SnakeMake C3D From line 36 of rules/sa2rage.smk 
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shell:
    "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
    "antsApplyTransforms -d 3 --interpolation Linear -i {input.nii} -o {output} -r {input.ref} -t {input.xfm2crop} -t {input.xfm2ref} -t {input.xfm2tse} -t {input.xfm2hires}"
SnakeMake From line 55 of rules/sa2rage.smk 
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shell:
    "c3d {input} -flip x -o  {output}"
SnakeMake C3D From line 65 of rules/sa2rage.smk 
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shell:
    "wb_command -volume-to-surface-mapping {input.nii} {input.midthickness} {output} -ribbon-constrained {input.outer} {input.inner} -volume-roi {input.ribbon}"
SnakeMake From line 82 of rules/sa2rage.smk 
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shell:
    "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} "
    "antsApplyTransforms -d 3 --interpolation Linear -i {input.nii} -o {output} -r {input.ref}  -t {input.xfm} -t {input.init}"
SnakeMake From line 14 of rules/t2w.smk 
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shell:
    "c3d {input} -flip x -o  {output}"
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shell:
    "wb_command -volume-to-surface-mapping {input.nii} {input.midthickness} {output} -ribbon-constrained {input.outer} {input.inner} -volume-roi {input.ribbon}"
SnakeMake From line 41 of rules/t2w.smk
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/royhaast/hippocampal_perfusion
Name: hippocampal_perfusion
Version: 1
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Copyright: Public Domain
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