Skip to content

BUG FIX: the --bold_autobox, --oblique2card, and RAS reorientation of… #521

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Gab-D-G merged 1 commit into from
Oct 3, 2026
Merged

BUG FIX: the --bold_autobox, --oblique2card, and RAS reorientation of… #521

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 24 additions & 2 deletions rabies/preprocess_pkg/main_wf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -175,11 +175,18 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
MATCHING INPUTS TO MAIN ITERABLES
'''

# the original input BOLD file, used for naming outputs and for the datasink
select_input_bold_node = pe.Node(Function(input_names=['scan_info', 'run', 'joined_scan_info', 'joined_run', 'joined_file_list'],
output_names=['selected_file'],
function=match_iterables),
name='select_input_bold')

# the BOLD file formatted by prep_input_wf (oblique correction, RAS, autobox), which is fed to preprocessing
format_bold_node = pe.Node(Function(input_names=['scan_info', 'run', 'joined_scan_info', 'joined_run', 'joined_file_list'],
output_names=['selected_file'],
function=match_iterables),
name='format_bold')

workflow.connect([
(prep_input_wf, select_input_bold_node, [
("outputnode.input_bold_list", "joined_file_list"),
Expand All @@ -188,11 +195,20 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
(main_split, select_input_bold_node, [
("scan_info", "scan_info"),
]),
(prep_input_wf, format_bold_node, [
("outputnode.prep_bold_list", "joined_file_list"),
("outputnode.joined_scan_info", "joined_scan_info"),
]),
(main_split, format_bold_node, [
("scan_info", "scan_info"),
]),
])

if opts.bold_only:
select_input_bold_node.inputs.run = None
select_input_bold_node.inputs.joined_run = None
format_bold_node.inputs.run = None
format_bold_node.inputs.joined_run = None
else:
run_split = pe.Node(niu.IdentityInterface(fields=['run', 'split_name']),
name="run_split")
Expand All @@ -209,6 +225,12 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
(run_split, select_input_bold_node, [
("run", "run"),
]),
(prep_input_wf, format_bold_node, [
("outputnode.joined_run", "joined_run"),
]),
(run_split, format_bold_node, [
("run", "run"),
]),
])

format_anat_node = pe.Node(Function(input_names=['scan_info', 'run', 'joined_scan_info', 'joined_run', 'joined_file_list'],
Expand Down Expand Up @@ -318,7 +340,7 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):

# MAIN WORKFLOW STRUCTURE #######################################################
workflow.connect([
(select_input_bold_node, bold_main_wf, [
(format_bold_node, bold_main_wf, [
("selected_file", "inputnode.bold_file"),
]),
(resample_template_node, template_diagnosis, [
Expand Down Expand Up @@ -468,7 +490,7 @@ def init_main_wf(data_dir_path, output_folder, opts, name='main_wf'):
("registration_template", "template_inputnode.template_anat"),
("registration_mask", "template_inputnode.template_mask"),
]),
(select_input_bold_node, inho_cor_bold_main_wf, [
(format_bold_node, inho_cor_bold_main_wf, [
("selected_file", "inputnode.bold_file"),
]),
(EPI_target_buffer, inho_cor_bold_main_wf, [
Expand Down
Loading