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

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