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Gradient nonlinearity correction step #7

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merged 41 commits into from
Mar 22, 2023
Merged

Gradient nonlinearity correction step #7

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3a87c19
code for lr correction
praitayini Oct 29, 2022
2a0d463
update run_dtiQA for lr correction
praitayini Oct 29, 2022
a76d14f
packages for lr correction
praitayini Oct 29, 2022
f487fcc
update singularity
praitayini Oct 29, 2022
0d02aca
update Singularity
praitayini Oct 29, 2022
a22e5da
update files
praitayini Nov 2, 2022
c62cd15
update nibabel version and gradtensor.sh
praitayini Nov 2, 2022
f21fbec
update venv
praitayini Nov 2, 2022
774e7a1
vis updates
praitayini Nov 2, 2022
2caff3d
update venv
praitayini Nov 4, 2022
da71184
receipe and vis
praitayini Nov 5, 2022
e9978c1
generate btable for LR
praitayini Nov 7, 2022
3a0819e
update vis
praitayini Nov 7, 2022
5ac0e8f
vis fa for gradtensor
praitayini Nov 9, 2022
c80bc33
matlab lib path
praitayini Nov 9, 2022
874a81b
debug complier runtime
praitayini Nov 18, 2022
c06c10e
debug args errors
praitayini Nov 25, 2022
a0a1d8d
matlab runtime call, debug prep inputs, fsl version update eddy function
praitayini Dec 2, 2022
5679604
uncommit mrtrix
praitayini Dec 3, 2022
682c82b
args debug
praitayini Dec 4, 2022
58671ce
debug gradtensor functions
praitayini Dec 5, 2022
0628ea8
debug matlab separately
praitayini Dec 5, 2022
3292d39
variables name fix
praitayini Dec 6, 2022
0c41f4b
debug updates
praitayini Dec 6, 2022
3d2ce3f
update utils typo
praitayini Dec 7, 2022
fa4e4c7
update slice_nii det_matrix function for grad vis
praitayini Dec 8, 2022
631b51a
debug dims for LR
praitayini Dec 8, 2022
7f9bff9
debug grad fa function
praitayini Dec 9, 2022
c039d0b
update run_dtiQA
praitayini Dec 9, 2022
5e9f8ce
fix grad vis
praitayini Dec 9, 2022
5d0cbec
fix vis
praitayini Dec 11, 2022
df30641
fix vis bval intensity
praitayini Dec 12, 2022
284c31e
fix vis
praitayini Dec 12, 2022
b61b706
freesurfer license
praitayini Dec 24, 2022
7d0f53d
old fsl version
praitayini Dec 24, 2022
c73abaa
cleanup and add author
praitayini Dec 30, 2022
442b60f
Update README.md
praitayini Dec 30, 2022
f8500ce
Update README.md
praitayini Dec 30, 2022
a6fa3fe
update singularity
praitayini Jan 18, 2023
81038cb
update keep_intermediates and grad non before preproc renaming
praitayini Feb 4, 2023
ec92307
Update README.md
praitayini Feb 4, 2023
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debug complier runtime
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@praitayini
praitayini committed Nov 18, 2022
commit 874a81bc1c090e48ecd02a84e4e3e06c4dd74a7d
2 changes: 1 addition & 1 deletion src/APPS/gradtensor/gradtensor.sh
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Expand Up @@ -19,7 +19,7 @@ source $abs_path/gradvenv/bin/activate

# Prep inputs for gradtensor to b
echo Preparing the inputs for gradnonlinearity correction
python $abs_path/prep_inputs.py $org_bvec_file $org_bval_file $out_dir
python3.8 $abs_path/prep_inputs.py $org_bvec_file $org_bval_file $out_dir


# Run gradtensor to b #/usr/local/MATLAB/MATLAB_Runtime/v92 \
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2 changes: 1 addition & 1 deletion src/APPS/gradtensor/run_apply_gradtensor_to_b.sh
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Expand Up @@ -18,7 +18,7 @@ else
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/opengl/lib/glnxa64;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT} ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/MATLAB/MATLAB_2017a_Runtime/;
export LD_LIBRARY_PATH;
echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
shift 1
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1 change: 0 additions & 1 deletion src/APPS/gradtensor/utils.py
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@@ -1,4 +1,3 @@
import torch
import logging
import warnings
import numpy as np
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