nimh-dsst dsst-defacing-pipeline issues

nimh-dsst / dsst-defacing-pipeline

Defacing algorithm to improve and evaluate accuracy for large datasets.

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issues

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Add --mode derivative,inplace option

#46 yarikoptic opened 3 months ago
0
Should exit with non-0 exit code in case of failing, and likely even upon initial fail to run AFNI / fsl tools

#45 yarikoptic opened 3 months ago
1
Should just skip a subject without anatomical

#44 yarikoptic opened 3 months ago
0
Should not look under non-bids folders, or in particular under folder names with leading period

#43 yarikoptic opened 3 months ago
0
Blows up with `KeyError: 'ses-02'` whenever that subject does not have T1w in any other session but one

#42 yarikoptic opened 3 months ago
0
Gentoo based Dockerfile (presumably reproducible) to provide bids-app

#41 yarikoptic opened 5 months ago
7
fsleyes render not working

#40 Arshitha closed 4 months ago
2
major changes

#39 Arshitha closed 3 weeks ago
2
-p flag not working

#38 Arshitha closed 3 weeks ago
2
Adding DOI badge

#37 Arshitha closed 9 months ago
0
Reduce environment size

#36 dmoracze opened 1 year ago
1
final polish before defaced dataset is ready to be shared

#35 Arshitha closed 9 months ago
0
Add an option to merge non-anat contents of orig dataset to defaced dataset

#34 Arshitha closed 9 months ago
0
Add an anonymization flag

#33 Arshitha closed 9 months ago
2
integrating generate renders to pipeline

#32 Arshitha closed 1 year ago
6
Eric testing

#31 Arshitha closed 1 year ago
0
Integrate into bids tree

#30 Arshitha closed 1 year ago
1
Create pylint.yml

#29 Arshitha opened 1 year ago
0
Update generate_renders.py

#28 ericearl closed 1 year ago
1
Pipeline modified to enhance user-friendliness

#27 Arshitha closed 1 year ago
0
Add a flag to dsst_defacing_wf.py cli to start swarm jobs from within the script

#26 Arshitha closed 1 year ago
1
Generate modality specific 3D renders

#25 Arshitha opened 1 year ago
0
Turn into Docker container for BIDS App

#24 ericearl opened 1 year ago
1
Use python logging module instead of print statements to control verbosity

#23 ericearl opened 1 year ago
0
Parallelize fsleyes render as well

#22 ericearl closed 1 year ago
1
BIDS App preparation and serial/parallel behavior

#21 ericearl closed 1 year ago
3
parallel execution at session level

#20 Arshitha closed 1 year ago
2
Add progress bar while defacing is in progress

#19 Arshitha opened 1 year ago
1
Replace FSL commands with AFNI equivalents

#18 Arshitha opened 1 year ago
0
merging main to code refactoring

#17 Arshitha closed 1 year ago
0
Improve summary output information

#16 Arshitha closed 1 year ago
1
replace NIH HPC module load commands

#15 Arshitha closed 1 year ago
1
Add docstrings for functions in deface.py and register.py

#14 Arshitha opened 1 year ago
0
printing helpful summary info to stdout

#13 Arshitha closed 1 year ago
1
adding a snippet of example bids tree to the README

#12 Arshitha closed 1 year ago
1
adding examples of scripts' outputs

#11 Arshitha closed 1 year ago
0
Add flag feature to automatically use all images as primary rather than doing the whole primary T1w dance and pony show

#10 dmoracze closed 1 year ago
2
Flesh out the QC workflow, in text and sample images

#9 dmoracze opened 1 year ago
0
Option to use all scans as primary for subject without a T1w instead of skipping over them

#8 dmoracze closed 3 weeks ago
2
Add more helpful output to terminal

#7 dmoracze closed 1 year ago
1
Add example mapping file

#6 dmoracze closed 1 year ago
2
In README describe what the input dataset looks like (eg BIDS valid or, if not what?)

#5 dmoracze closed 1 year ago
1
Pradeep's last name is spelled incorrectly in the README

#4 ericearl closed 1 year ago
1
redesign the workflow using the same functions

#3 Arshitha closed 1 year ago
0
Update 01_defacing

#2 ericearl closed 2 years ago
2
Update 02_improve_defacing_accuracy.py

#1 ericearl closed 2 years ago
1