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arefks 3321dce0e3 volcano plots 2 týždňov pred
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.ipynb_checkpoints e8e54e0207 current state: code is finished for representation 10 mesiacov pred
AIDAmri @ 8e7f9d3597 13cb663094 added all of the code necessery 9 mesiacov pred
del 71676560e5 sorted and added parallel quantitative value py file 1 mesiac pred
mouse_connectivity e8e54e0207 current state: code is finished for representation 10 mesiacov pred
testData 27a8ac80ee try and error with R studi 1 mesiac pred
Big_data_mouse_practical_2020_answer.ipynb e8e54e0207 current state: code is finished for representation 10 mesiacov pred
GetQuantitativeValues.py d1c8a8c45b code to filter high initital impairments 2 týždňov pred
GetQuantitativeValues_not_parallel.py 71676560e5 sorted and added parallel quantitative value py file 1 mesiac pred
LME.R c039ef3b8d LME 1 mesiac pred
README.md 13cb663094 added all of the code necessery 9 mesiacov pred
correlation_between_bahavior_and_DTI.py 10a414834a visu jobs 2 týždňov pred
correlation_between_bahavior_and_DTI_anovaSpecific.py 132437cf05 final results 7 mesiacov pred
correlation_fa28_behavior28subtractedbyBaseline.py e1c2b12287 visu jobs 2 týždňov pred
correlation_fa28subtractedbyBaseline_behavior28subtractedbyBaseline.py 10a414834a visu jobs 2 týždňov pred
extract_atlas_fa_regions.py c4c3bd5b9b stuff for poster, atlas fa valus 2 mesiacov pred
general_corolation_all_timepoint_together.py c5834f0b56 Adjusted figure sizes 2 týždňov pred
getIncidenceMap.py 1a6c3f835e deleted old things, calculated prediction plots from fa and behaviro, corrected bug in code for replicates when merging 4 týždňov pred
heat_maps_correlation.py c9ecfd427e heatmap adjustment 1 mesiac pred
incooparate_behavior_data.py d1c8a8c45b code to filter high initital impairments 2 týždňov pred
mask2MTPL.py dfaee6412d applied mask2mtpl to whitematter mask 7 mesiacov pred
merge_csv_sheets.py d1c8a8c45b code to filter high initital impairments 2 týždňov pred
overlayPlot.py 86fce3a119 current state: code is finished for representation 10 mesiacov pred
plotting_quantitative_dti_values.py 3321dce0e3 volcano plots 2 týždňov pred
predictive_correlation_chronic_vs_fa_acute.py a76ef52966 figure predictive fa with behaviorr 1 mesiac pred
predictive_correlation_fa3_behavior28.py 1a6c3f835e deleted old things, calculated prediction plots from fa and behaviro, corrected bug in code for replicates when merging 4 týždňov pred
predictive_correlation_fa3_behavior28subtractedbyBaseline.py 1a6c3f835e deleted old things, calculated prediction plots from fa and behaviro, corrected bug in code for replicates when merging 4 týždňov pred
proof_of_modalities.py 9bcdec0ea4 added overlap percentage csv 7 mesiacov pred
register_masks.py 748f48e806 changed the flip in the anat step of the registration, changed it back to before 7 mesiacov pred
remapping_voiting_qc.py 4cf036e11b removed bad qc data from merged with behavior csv 1 mesiac pred
single_mask_form_allan_atlas_creator.py 1cd13fc10c added amba regoins to the mix 1 mesiac pred
statistical_analysis_of_quantitative_data.py d3c8f1d817 added amba regoins to the mix 1 mesiac pred
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 7 mesiacov pred
temp_code.py 062c26905a added new calculation prediction and biomarker approach table style 1 mesiac pred
threshold_whitematter.py c5875af414 added white matter mask 7 mesiacov pred
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 7 mesiacov pred
ttest_group_differences.py 3321dce0e3 volcano plots 2 týždňov pred
viralTracing2MTPL.py 2e82796756 added viraltracin 2 mtpl space filp function 9 mesiacov pred
visualization_all_timepoints_correlation.py 062c26905a added new calculation prediction and biomarker approach table style 1 mesiac pred
visualization_fa_sham_vs_stroke.py c5834f0b56 Adjusted figure sizes 2 týždňov pred
visualization_general_correlation_correlation.py c5834f0b56 Adjusted figure sizes 2 týždňov pred
visualization_predictive_correlation.py a486c1adc0 adjusted fa correlation figure 1 mesiac pred
visualization_specific_timepoint_correlation.py 10a414834a visu jobs 2 týždňov pred
vizualization_asymetry_index_fa.py 10a414834a visu jobs 2 týždňov pred
vizualization_fa28_behavior28subtractedbyBaseline.py 10a414834a visu jobs 2 týždňov pred
vizualization_fa28subtractedbyBaseline_behavior28subtractedbyBaseline.py 10a414834a visu jobs 2 týždňov pred
volcano_plot.py 3321dce0e3 volcano plots 2 týždňov pred

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