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IUSCA
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IUSM-ConnPipe
Refactored version of the IU School of Medicine neuroscience connectivity pipeline that executes pre-processing of anatomical, functional, and diffusion Magnetic Resonance Imaging data (written in Python and Bash).
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path_DWI_EDDY variable needs rename to EDDYpath in line 89 and 90 of DWI_A_eddy.sh
#161
echumin
opened
3 months ago
0
redundant rT1_brain_dof6_brr.nii.gz generation
#160
echumin
opened
3 months ago
0
nuisasnce regression folders being created even if nuisance regression is set to false
#159
echumin
opened
4 months ago
0
pulling Andrea's updates from main into my latest fsl version testing on Quartz
#158
echumin
closed
4 months ago
0
Update eddy
#157
aiavenak
closed
4 months ago
0
T1a updates
#156
aiavenak
closed
4 months ago
0
fixed T1_A to allow skipping T1 denoising
#155
aiavenak
closed
4 months ago
0
Dwib finetune
#154
aiavenak
closed
4 months ago
0
Dtifit finetune
#153
aiavenak
closed
4 months ago
0
stopped tracking pycache files
#152
aiavenak
closed
5 months ago
0
Fix logs
#151
aiavenak
closed
5 months ago
0
small changes to DWI. Cannot get past the 5ttgen command in line #87 …
#150
aiavenak
closed
5 months ago
0
Fix regression
#149
aiavenak
closed
5 months ago
0
renamed main and config files; added DVAR data to BPF output so that …
#148
aiavenak
closed
5 months ago
0
Fix regression
#147
aiavenak
closed
5 months ago
0
Fix regression
#146
aiavenak
closed
6 months ago
0
DWI_B ants registration for T1->DWI for tractography
#145
echumin
closed
6 months ago
0
everything working up to AROMA
#144
aiavenak
closed
6 months ago
0
Bidsywork finetune
#143
aiavenak
closed
6 months ago
0
added T1_A flag that allows the user to use fsl's robustfov for cropping
#142
aiavenak
closed
1 year ago
0
fixed issue with file names on EPIj with j>1
#141
aiavenak
closed
1 year ago
0
Fix multi session unwarp
#140
aiavenak
closed
1 year ago
0
Fix multi session unwarp
#139
aiavenak
closed
1 year ago
0
changing parcellations after T1_B has been run
#138
aiavenak
closed
7 months ago
1
added option to select number of dilations to cerebellum
#137
aiavenak
closed
2 years ago
0
Fix multi session unwarp
#136
aiavenak
closed
2 years ago
0
Handle BIDS data format with source and raw directories read-only
#135
aiavenak
opened
2 years ago
0
Handle various cases for multiple EPI and Field Map sessions.
#134
aiavenak
closed
7 months ago
1
User-defined subcortical parcellation is not being used
#133
aiavenak
closed
7 months ago
1
Find alternatives to saving data in .mat format
#132
aiavenak
closed
7 months ago
1
Deprecation warning fo python get_data()
#131
echumin
closed
7 months ago
1
Test running ConnPipe on various systems
#130
aiavenak
closed
7 months ago
1
Test Data transfer times
#129
aiavenak
closed
7 months ago
0
Adni3
#128
aiavenak
closed
2 years ago
0
Dicom file checks do not follow directory links
#127
echumin
closed
7 months ago
1
fixed typo
#126
aiavenak
closed
2 years ago
0
Adni3
#125
aiavenak
closed
2 years ago
0
updated t1_B
#124
aiavenak
closed
2 years ago
0
Adni3
#123
aiavenak
closed
2 years ago
0
fixed issues with parcellation masking - cerebellum and subcortical
#122
aiavenak
closed
2 years ago
0
Add reho alff
#121
aiavenak
closed
2 years ago
0
feature request: change or add a function version of main.sh
#120
echumin
closed
7 months ago
1
comment: CSFvent parc in config
#119
echumin
closed
7 months ago
1
Cortical parcellation in the cerebellum
#118
echumin
closed
2 years ago
0
Issue: subcortical parcellations spreading into the cortex
#117
echumin
closed
2 years ago
0
User provided subcortical parcellation boundary problem
#116
echumin
closed
2 years ago
0
Comment: Brain stem in brain mask
#115
echumin
opened
2 years ago
1
organizational question: betQC brain
#114
echumin
closed
7 months ago
0
minor edit: move a flag
#113
echumin
closed
7 months ago
1
added new options for ALFF and ReHo
#112
aiavenak
closed
2 years ago
0
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