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arefks bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
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.ipynb_checkpoints e8e54e0207 current state: code is finished for representation il y a 10 mois
AIDAmri @ 8e7f9d3597 13cb663094 added all of the code necessery il y a 9 mois
del bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
mouse_connectivity e8e54e0207 current state: code is finished for representation il y a 10 mois
testData 27a8ac80ee try and error with R studi il y a 1 mois
Big_data_mouse_practical_2020_answer.ipynb e8e54e0207 current state: code is finished for representation il y a 10 mois
GetQuantitativeValues.py d1c8a8c45b code to filter high initital impairments il y a 2 semaines
GetQuantitativeValues_not_parallel.py 71676560e5 sorted and added parallel quantitative value py file il y a 2 mois
GetQuantitativeValues_only_in_CST.py 97e21afc33 added some code il y a 2 semaines
GetQuantitativeValues_only_in_stroke_affected_slices.py 2ea61098ac volcano plots and fa over time il y a 2 semaines
LME.R c039ef3b8d LME il y a 1 mois
README.md 13cb663094 added all of the code necessery il y a 9 mois
correlation_between_bahavior_and_DTI.py 10a414834a visu jobs il y a 3 semaines
correlation_between_bahavior_and_DTI_anovaSpecific.py 132437cf05 final results il y a 7 mois
correlation_fa28_behavior28subtractedbyBaseline.py bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
correlation_fa28subtractedbyBaseline_behavior28subtractedbyBaseline.py bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
extract_atlas_fa_regions.py c4c3bd5b9b stuff for poster, atlas fa valus il y a 2 mois
general_corolation_all_timepoint_together.py c5834f0b56 Adjusted figure sizes il y a 3 semaines
getIncidenceMap.py 1a6c3f835e deleted old things, calculated prediction plots from fa and behaviro, corrected bug in code for replicates when merging il y a 1 mois
heat_maps_correlation.py c9ecfd427e heatmap adjustment il y a 1 mois
incooparate_behavior_data.py 2ea61098ac volcano plots and fa over time il y a 2 semaines
mask2MTPL.py dfaee6412d applied mask2mtpl to whitematter mask il y a 7 mois
merge_csv_sheets.py d1c8a8c45b code to filter high initital impairments il y a 2 semaines
overlayPlot.py 86fce3a119 current state: code is finished for representation il y a 10 mois
plotting_quantitative_dti_values.py bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
plotting_quantitative_dti_values_partions.py 2ea61098ac volcano plots and fa over time il y a 2 semaines
predictive_correlation_chronic_vs_fa_acute.py a76ef52966 figure predictive fa with behaviorr il y a 1 mois
predictive_correlation_fa3_behavior28.py bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
predictive_correlation_fa3_behavior28subtractedbyBaseline.py bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
proof_of_modalities.py 9bcdec0ea4 added overlap percentage csv il y a 8 mois
register_masks.py 748f48e806 changed the flip in the anat step of the registration, changed it back to before il y a 7 mois
remapping_voiting_qc.py 4cf036e11b removed bad qc data from merged with behavior csv il y a 1 mois
single_mask_form_allan_atlas_creator.py 1cd13fc10c added amba regoins to the mix il y a 2 mois
statistical_analysis_of_quantitative_data.py d3c8f1d817 added amba regoins to the mix il y a 2 mois
statsmodel_training.py 63701b1cca code ready for: mixed model analysis and the post hoc tests nad figures with their relevant outputs. also code and results ready for heatmaps of the behavioral and dwi values correlations il y a 7 mois
temp_code.py 062c26905a added new calculation prediction and biomarker approach table style il y a 1 mois
threshold_whitematter.py c5875af414 added white matter mask il y a 7 mois
transpose_csv.py 63701b1cca code ready for: mixed model analysis and the post hoc tests nad figures with their relevant outputs. also code and results ready for heatmaps of the behavioral and dwi values correlations il y a 7 mois
ttest_BL_P28_differences.py 2ea61098ac volcano plots and fa over time il y a 2 semaines
ttest_BL_P3_differences.py 9d24cc2f0d added significance tests il y a 1 semaine
ttest_BL_P7_differences.py 9d24cc2f0d added significance tests il y a 1 semaine
ttest_P3_P7_differences.py 9d24cc2f0d added significance tests il y a 1 semaine
ttest_group_differences.py 2ea61098ac volcano plots and fa over time il y a 2 semaines
viralTracing2MTPL.py 2e82796756 added viraltracin 2 mtpl space filp function il y a 9 mois
visualization_all_timepoints_correlation.py 062c26905a added new calculation prediction and biomarker approach table style il y a 1 mois
visualization_fa_sham_vs_stroke.py 2ea61098ac volcano plots and fa over time il y a 2 semaines
visualization_specific_timepoint_correlation.py bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
vizualization_asymetry_index_fa.py 10a414834a visu jobs il y a 3 semaines
vizualization_fa28_behavior28subtractedbyBaseline.py 10a414834a visu jobs il y a 3 semaines
vizualization_fa28subtractedbyBaseline_behavior28subtractedbyBaseline.py bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
vizualization_fa3_behavior28.py bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
vizualization_fa3_behavior28subtractedbyBaseline.py bdb43f9804 [DATALAD] Recorded changes il y a 1 semaine
volcano_plot.py 2ea61098ac volcano plots and fa over time il y a 2 semaines
volcano_plot_BL_P28_change.py 2ea61098ac volcano plots and fa over time il y a 2 semaines

README.md

AIDAmri code

This is the code used to process raw Bruker data and to apply transformations from the drawn masks to each individual subject. Note that this is a subdataset linked to the GitHub page of AIDAmri.

The link to the exact branch of the code which was used for this process is: AIDAmri - SND_Mask_trafu branch.

Example usage of code

root@9c22c56092e5:/aida/DATA/code# python mask2MTPL.py -i /aida/DATA/output/Tract_Density -o /aida/DATA/output/Nifti_Tract_density_registered