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✨ Nifti header orientation checks and decisions for downstream resources #2138
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@sgiavasis , If we have list of all the NIFTI files including atlases and templates, we could do something like this? from nipype import Node, Workflow, Function
from CPAC.pipeline import nipype_pipeline_engine as pe
from nipype.interfaces import afni
from nipype.interfaces.afni import Info
import os
import pandas as pd timeseries_paths = ["/home/biraj/bids_parsing/dataset/anna/raw/sub-PA001/ses-V1W1/func/sub-PA001_ses-V1W1_task-facesmatching_run-1_bold.nii.gz"]*10 def find_orientation(input_file):
import subprocess
cmd_3dinfo = [
"3dinfo",
"-orient", input_file
]
orientation = subprocess.run(cmd_3dinfo, capture_output=True, text=True).stdout.strip().upper()
return orientation
find_orient = Node(Function(input_names=["input_file"],
output_names=["orientation"],
function=find_orientation),
name="find_orient")
reorient_image = Node(interface=afni.Resample(),
name='reorient',
mem_gb=1,
mem_x=(0.0115, 'in_file', 't'))
reorient_image.inputs.outputtype = 'NIFTI_GZ' def check_all_orientations(input_images:list, desired_orientation:str="RPI", reorient=False):
desired_orientation = desired_orientation.upper()
orientations = []
for image in input_images:
find_orient.inputs.input_file = image
orientation = find_orient.run().outputs.orientation
if orientation == desired_orientation:
comment = "Matches desired orientation"
else:
comment = f"Doesnot match the desired orientation: {desired_orientation}"
if reorient:
reorient_image.inputs.in_file = image
reorient_image.inputs.orientation = desired_orientation.upper()
_result = reorient_image.run().outputs.out_file
comment = f"Reoriented to {desired_orientation}"
orientations.append([image,orientation, comment])
return orientations
table = check_all_orientations(
input_images = timeseries_paths,
desired_orientation = "RAI",
reorient = True ) df = pd.DataFrame(table, columns = ['Data', 'Orientation', 'Comment'])
df
|
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Related problem
C-PAC by default updates all incoming data to have its orientation set to
RPI
in the Nifti headers.This matches the atlases and parcellations that come bundled with C-PAC.
However, outside of the errors or warnings that several tools already have bulit-in, there are no strong C-PAC-side catches or guard-rails for the possibility that:
RPI
.Proposed feature
Either:
Acceptance criteria
Alternatives
No response
Additional context
No response
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