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Add group directives to mrtpipelines.smk #12

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Nov 2, 2022
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Add group directives to mrtpipelines.smk #12

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8012344
Add group directives to mrtpipelines.smk
kaitj Oct 28, 2022
c258563
Fix group directive usage
kaitj Nov 2, 2022
36529fd
add reasoning for step size
kaitj Nov 2, 2022
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19 changes: 7 additions & 12 deletions dbsc/config/snakebids.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,9 @@ derivatives: False # Search in bids/derivatives if True; can also be path(s) to

# List of analysis levels in bids app
analysis_levels: &analysis_levels
- participant
- participant1
- group
- participant2

# Mapping from analysis_level to set of target rules or files
targets_by_analysis_level:
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Need to update this to reflect participant1 and participant2 analysis levels.

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Fixed this in c258563 - this is actually still suppose to be participant and group. Got this part mixed up with the group directive usage within the .smk file.

Expand Down Expand Up @@ -93,8 +94,8 @@ parse_args:
nargs: "+"

--step:
help: '(Mrtrix3) set the step size of the algorithm in mm
(default: 0.35mm)'
help: '(Mrtrix3) set the step size of the algorithm in mm. Should set to
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If we're going to include this recommendation it would be good to briefly explain why or give a reference.

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Added reasoning in 36529fd

4 steps per voxel (e.g. 1/4 * voxel size). (default: 0.35mm)'
default: 0.35

--sl_count:
Expand All @@ -114,17 +115,10 @@ parse_args:
node is found within this radius, the streamline endpoint is not
assigned to any node. (default: 1.5mm)'
default: 1.5

--exclude_gm:
help: 'Exclude streamlines passing through other GM nodes along its
trajectory (default: True)'
default: True
action: 'store_false'

#-----------------------------------------------------#

# Workflow specific config
# Space (MNI152, MNINlin2009bAsym)
# Spaces available (MNI152, MNINlin2009bAsym)
space: MNI152

zona_bb_subcortex:
Expand All @@ -137,11 +131,12 @@ zona_bb_subcortex:
seg: 'resources/MNI2009b/sub-SNSX32NLin2020Asym_space-MNINlin2009bAsym_ZonaBBSubCorSeg.nii.gz'
exclude: 'resources/MNI152/sub-SNSX32NLin2020Asym_space-MNINlin2009bAsym_desc-exclude_ROI.nii.gz'

# NOTE: This may not be needed with labelmerge
freesurfer:
labels: 'resources/freesurfer/fs_labels.csv'

# Containers
# Note: Update from latest to use specific tags
# NOTE: Update from latest to use specific tags
singularity:
freesurfer: "docker://pwighton/freesurfer:7.2.0"
neuroglia-core: "docker://khanlab/neuroglia-core:latest"
Expand Down
30 changes: 20 additions & 10 deletions dbsc/workflow/rules/mrtpipelines.smk
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Expand Up @@ -56,6 +56,7 @@ rule nii_to_mif:
shell:
'mrconvert -nthreads {threads} -fslgrad {input.bvecs} {input.bvals} {input.dwi} {output.dwi} '
'mrconvert -nthreads {threads} {input.mask} {output.mask}'
group: participant1


rule estimate_response:
Expand Down Expand Up @@ -91,8 +92,9 @@ rule estimate_response:
config['singularity']['mrtpipelines']
shell:
'dwi2response dhollander {input.dwi} {output.sfwm} {output.gm} {output.csf} -nthreads {threads}'
group: participant1


# TODO: Add check for pre-computed group response function
rule avg_response:
"""Compute average response function"""
input:
Expand Down Expand Up @@ -122,6 +124,7 @@ rule avg_response:
config['singularity']['mrtpipelines']
shell:
'average_response {input.sfwm} {output.avg_sfwm} {input.gm} {output.avg_gm} {input.csf} {output.csf}'
group: group


rule compute_fod:
Expand Down Expand Up @@ -161,10 +164,11 @@ rule compute_fod:
config['singularity']['mrtpipelines']
shell:
'if [ {params.shell} == "" ] && [ {params.lmax} == "" ]; then'
' dwi2fod -nthreads {params.threads} -shell {params.shell} -lmax {params.lmax} -mask {input.mask} msmt_csd {input.dwi} {input.avg_sfwm} {output.wm_fod} {input.avg_gm} {output.gm_fod} {input.avg_csf} {output.csf} '
'else '
' dwi2fod -nthreads {params.threads} -mask {input.mask} msmt_csd {input.dwi} {input.avg_sfwm} {output.wm_fod} {input.avg_gm} {output.gm_fod} {input.avg_csf} {output.avg_csf} '
'else '
' dwi2fod -nthreads {params.threads} -shell {params.shell} -lmax {params.lmax} -mask {input.mask} msmt_csd {input.dwi} {input.avg_sfwm} {output.wm_fod} {input.avg_gm} {output.gm_fod} {input.avg_csf} {output.csf} '
'fi'
group: participant2


rule normalise_fod:
Expand Down Expand Up @@ -204,7 +208,7 @@ rule normalise_fod:
config['singularity']['mrtpipelines']
shell:
'mtnormalise -nthreads {params.threads} -mask {input.mask} {input.wm_fod} {output.wm_fod} {input.gm_fod} {output.gm_fod} {input.csf_fod} {output.csf_fod}'

group: participant2

# DTI (Tensor) Processing
rule dwi_normalise:
Expand All @@ -226,6 +230,7 @@ rule dwi_normalise:
config['singularity']['mrtpipelines']
shell:
'dwinormalise -nthreads {params.threads} {input.dwi} {input.mask} {output.dwi}'
group: participant1


rule compute_tensor:
Expand Down Expand Up @@ -279,6 +284,7 @@ rule compute_tensor:
shell:
'dwi2tensor -nthreads {params.threads} -mask {input.mask} {input.dwi} {output.dti}'
'tensor2metric -nthreads {params.threads} -mask {input.mask} {output.dti} -fa {output.fa} -ad {output.ad} -rd {output.rd} -adc {output.md}'
group: participant1


# Tractography processing
Expand Down Expand Up @@ -306,6 +312,7 @@ rule gen_tractography:
config['singularity']['mrtpipelines']
shell:
'tckgen -nthreads {params.threads} -algorithm iFOD2 -step {params.step} -select {params.sl_count} -exclude {input.cortical_ribbon} -exclude {input.convex_hull} -include {input.subcortical_seg} -mask {input.mask} -seed_image {input.mask} {input.fod} {output.tck}'
group: participant2

rule weight_tractography:
input:
Expand Down Expand Up @@ -335,11 +342,12 @@ rule weight_tractography:
config['singularity']['mrtpipelines']
shell:
'tcksift2 -nthreads {params.threads} -out_mu {output.mu} {input.tck} {input.fod} {output.weights}'
group: participant2

# ADD OPTION TO OUTPUT TDI MAP
# TODO: ADD OPTION TO OUTPUT TDI MAP

# Connectivity map
# ADD OPTION TO MULTIPLY BY MU COEFFICIENT
# TODO: ADD OPTION TO MULTIPLY BY MU COEFFICIENT
rule connectome_map:
input:
weights=rules.weight_tractography.output.weights,
Expand Down Expand Up @@ -369,9 +377,8 @@ rule connectome_map:
config['singularity']['mrtpipelines']
shell:
'tck2connectome -nthreads {params.threads} -zero_diagonal -stat_edge sum -assignment_radial_search {params.radius} -tck_weights_in {input.weights} -out_assignments {output.sl_assignment} -symmetric {input.tck} {input.subcortical_seg} {output.node_weights} '
group: participant2

# Remove streamlines passing through other GM ROI
if config['exclude_gm']:
rule extract_tck:
input:
node_weights=rules.connectome_map.output.node_weights,
Expand Down Expand Up @@ -407,8 +414,9 @@ if config['exclude_gm']:
' nodes=$nodes,$i '
'done '
'connectome2tck -nthreads {params.threads} -nodes $nodes -exclusive -filters_per_edge -tck_weights_in {input.node_weights} -prefix_tck_weights_out {output.edge_weight} {input.tck} {input.sl_assignment} {output.edge_tck} '
group: participant2


# NOTE: Pass labelmerge split segs here?
rule create_roi_mask:
# EXPAND OVER NODE1 IN RULE ALL
input:
Expand Down Expand Up @@ -500,7 +508,7 @@ if config['exclude_gm']:
shell:
'mrcalc -nthreads {params.threads} {input.subcortical_seg} 0 -neq {input.roi1} -sub {input.roi2} -sub {input.lZI} -sub {input.rZI} -sub {output.filter_mask} '
'tckedit -nthreads {params.therads} -exclude {output.filter_mask} -tck_weights_in {input.weights} -tck_weights_out {output.filtered_weights} {input.tck} {output.filtered_tck} '

group: participant2

rule combine_filtered:
input:
Expand Down Expand Up @@ -528,6 +536,7 @@ if config['exclude_gm']:
shell:
'tckedit {input.tck} {output.combined_tck} '
'cat {input.weights} >> {output.combined_weights} '
group: participant2

rule filtered_connectome_map:
input:
Expand Down Expand Up @@ -558,3 +567,4 @@ if config['exclude_gm']:
config['singularity']['mrtpipelines']
shell:
'tck2connectome -nthreads {params.threads} -zero_diagonal -stat_edge sum -assignment_radial_search {params.radius} -tck_weights_in {input.weights} -out_assignments {output.sl_assignment} -symmetric {input.tck} {input.subcortical_seg} {output.node_weights} -force'
group: participant2