arefks 97e21afc33 added some code		пре 1 недеља
..
.ipynb_checkpoints	e8e54e0207 current state: code is finished for representation	пре 10 месеци
AIDAmri @ 8e7f9d3597	13cb663094 added all of the code necessery	пре 9 месеци
del	71676560e5 sorted and added parallel quantitative value py file	пре 1 месец
mouse_connectivity	e8e54e0207 current state: code is finished for representation	пре 10 месеци
testData	27a8ac80ee try and error with R studi	пре 1 месец
Big_data_mouse_practical_2020_answer.ipynb	e8e54e0207 current state: code is finished for representation	пре 10 месеци
GetQuantitativeValues.py	d1c8a8c45b code to filter high initital impairments	пре 2 недеља
GetQuantitativeValues_not_parallel.py	71676560e5 sorted and added parallel quantitative value py file	пре 1 месец
GetQuantitativeValues_only_in_CST.py	97e21afc33 added some code	пре 1 недеља
GetQuantitativeValues_only_in_stroke_affected_slices.py	97e21afc33 added some code	пре 1 недеља
LME.R	c039ef3b8d LME	пре 1 месец
README.md	13cb663094 added all of the code necessery	пре 9 месеци
correlation_between_bahavior_and_DTI.py	10a414834a visu jobs	пре 2 недеља
correlation_between_bahavior_and_DTI_anovaSpecific.py	132437cf05 final results	пре 7 месеци
correlation_fa28_behavior28subtractedbyBaseline.py	e1c2b12287 visu jobs	пре 2 недеља
correlation_fa28subtractedbyBaseline_behavior28subtractedbyBaseline.py	10a414834a visu jobs	пре 2 недеља
extract_atlas_fa_regions.py	c4c3bd5b9b stuff for poster, atlas fa valus	пре 2 месеци
general_corolation_all_timepoint_together.py	c5834f0b56 Adjusted figure sizes	пре 2 недеља
getIncidenceMap.py	1a6c3f835e deleted old things, calculated prediction plots from fa and behaviro, corrected bug in code for replicates when merging	пре 4 недеља
heat_maps_correlation.py	c9ecfd427e heatmap adjustment	пре 1 месец
incooparate_behavior_data.py	d1c8a8c45b code to filter high initital impairments	пре 2 недеља
mask2MTPL.py	dfaee6412d applied mask2mtpl to whitematter mask	пре 7 месеци
merge_csv_sheets.py	d1c8a8c45b code to filter high initital impairments	пре 2 недеља
overlayPlot.py	86fce3a119 current state: code is finished for representation	пре 10 месеци
plotting_quantitative_dti_values.py	924c18ada6 continued with pp	пре 1 недеља
plotting_quantitative_dti_values_partions.py	97e21afc33 added some code	пре 1 недеља
predictive_correlation_chronic_vs_fa_acute.py	a76ef52966 figure predictive fa with behaviorr	пре 1 месец
predictive_correlation_fa3_behavior28.py	1a6c3f835e deleted old things, calculated prediction plots from fa and behaviro, corrected bug in code for replicates when merging	пре 4 недеља
predictive_correlation_fa3_behavior28subtractedbyBaseline.py	1a6c3f835e deleted old things, calculated prediction plots from fa and behaviro, corrected bug in code for replicates when merging	пре 4 недеља
proof_of_modalities.py	9bcdec0ea4 added overlap percentage csv	пре 7 месеци
register_masks.py	748f48e806 changed the flip in the anat step of the registration, changed it back to before	пре 7 месеци
remapping_voiting_qc.py	4cf036e11b removed bad qc data from merged with behavior csv	пре 1 месец
single_mask_form_allan_atlas_creator.py	1cd13fc10c added amba regoins to the mix	пре 1 месец
statistical_analysis_of_quantitative_data.py	d3c8f1d817 added amba regoins to the mix	пре 1 месец
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	пре 7 месеци
temp_code.py	062c26905a added new calculation prediction and biomarker approach table style	пре 1 месец
threshold_whitematter.py	c5875af414 added white matter mask	пре 7 месеци
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	пре 7 месеци
ttest_group_differences.py	0acc779668 ttest_sig_stroke_vs_sham	пре 1 недеља
viralTracing2MTPL.py	2e82796756 added viraltracin 2 mtpl space filp function	пре 9 месеци
visualization_all_timepoints_correlation.py	062c26905a added new calculation prediction and biomarker approach table style	пре 1 месец
visualization_fa_sham_vs_stroke.py	c5834f0b56 Adjusted figure sizes	пре 2 недеља
visualization_general_correlation_correlation.py	c5834f0b56 Adjusted figure sizes	пре 2 недеља
visualization_predictive_correlation.py	a486c1adc0 adjusted fa correlation figure	пре 1 месец
visualization_specific_timepoint_correlation.py	10a414834a visu jobs	пре 2 недеља
vizualization_asymetry_index_fa.py	10a414834a visu jobs	пре 2 недеља
vizualization_fa28_behavior28subtractedbyBaseline.py	10a414834a visu jobs	пре 2 недеља
vizualization_fa28subtractedbyBaseline_behavior28subtractedbyBaseline.py	10a414834a visu jobs	пре 2 недеља
volcano_plot.py	e76431ef07 Quantitiative values at stroke specific locations	пре 1 недеља

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

README.md

AIDAmri code

Example usage of code