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

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