added t1w preprocess pipeline #331

tclose · 2024-10-01T08:47:28Z

Adds the T1-weighted preprocessing pipeline

…ended

…pipelines into t1w-preproc

…ow functions in tasks

…ng pipeline

…d py to reflect this

… create one in the CWD

…with labelsgmfix

tclose and others added 30 commits October 1, 2024 18:47

added t1w preprocess pipeline

969ac27

added t1-preprocessing pipeline from communities repository

a86d415

added in parcellations from mrtrix3 label directory

0e80109

cleaned up t1w-preprocess yaml

7a05476

added arkiev as an author

1a6b191

updated syntax for pipeline2app make

e32fde2

removed version file from git repo

4ab86a8

updated tests to use latest package and class names

8b72aae

added mypy config to pyproject

cbc3797

cleaned up t1-weighted preproc python code

e4a6f6e

deletec debug_specific_case.py

662cfb9

added all_parcs command to t1-preproc spec

244bf15

debugging github action

08595a0

fixed up specs to have multiple commands

f709a59

removed t1w_preproc from command names as image name will now be prep…

857cc65

…ended

collated all parcellations to a single directory before returning

46b65e9

debugging preprocess spec

5441eee

:Merge branch 't1w-preproc' of github.com:Australian-Imaging-Service/…

5a2d358

…pipelines into t1w-preproc

fixed up reference to single_parc in all_parcs workflow

e8bfa8d

fixed reference to all_parcs

b1780ca

added freesurfer to image, updated freesurfer home and renamed workfl…

70a43d1

…ow functions in tasks

added freesurfer neurodocker template

ccc29bc

added test to load preprocess yaml

3530246

updated bids apps specs to reference frametree instead of arcana

e2830a3

removed fsaverage5 from exclude paths passed to freesurfer template

32920e3

added parcellations and surfaces required for t1-weighted preprocessi…

e28139f

…ng pipeline

reverted location of lut directories to freesurfer home

9df14a6

renamed neurodocker template optional_args to args

4970956

streamlined versions

6454ca4

updated location of source files for Yeo and HCPMMP1, updated yaml an…

c4f27ae

…d py to reflect this

adsouza added 25 commits October 29, 2024 15:17

updated path of yeo .annot files

b5ab30a

test excluding aparc parcellation

7c7a890

FS changed batch from 16 to 8 to check if memory is causing crash

102e106

revert back to default batch of 16

6c8b3f6

created dependencies for lh annot -> rh annot -> mri_a2a_task

d8658aa

changed mandatory to false in mri_s2s

21e8db7

reintroduced aparc to list

df6667f

changes values to items in collate_parcs

a8ee17e

set the default for out_dir to None in the method signature and then…

c07d29b

… create one in the CWD

moved collect_parcs to the constructor node

f08133d

made out_dir os var

6050ed9

added out_dir to collate_parcs FunctionTask

1593a5e

added in missing return wf to all_parcs

79ded64

fixed up location of collate_parcs, i.e. within all_parcs workflow

f688029

Added in updated Yeo mrtrix LUT

e6d1919

updated Yeo in neuro-parcellations

214eb31

updated annot short for Yeo parcs

7481b6f

updated annot short for HCPMMP1

49d2765

updated schaeffer to include LH and RH medial wall

2cc088e

added annotname to mri_a2a_task_originals

31c4afc

update mri_s2s and mri_a2a originals with dummy dependency subject dir

7b90c87

fixed bug in mri_a2a with missing "originals"

8557071

node name fix

4fb79ff

updated lh rh medial wall for aparc

287dccd

replaced l_ and r_ with left- and right-, respectively, to fix error …

66d459c

…with labelsgmfix

tclose merged commit e2bba58 into main Dec 12, 2024
2 of 3 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

added t1w preprocess pipeline #331

added t1w preprocess pipeline #331

tclose commented Oct 1, 2024 •

edited

Loading

added t1w preprocess pipeline #331

added t1w preprocess pipeline #331

Conversation

tclose commented Oct 1, 2024 • edited Loading

tclose commented Oct 1, 2024 •

edited

Loading