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Aswendt_Lab
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2024_Ruthe_SND
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2024_Ruthe_SND
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code
arefks 3321dce0e3 volcano plots 2 هفته پیش
..
.ipynb_checkpoints e8e54e0207 current state: code is finished for representation 10 ماه پیش
AIDAmri @ 8e7f9d3597 13cb663094 added all of the code necessery 9 ماه پیش
del 71676560e5 sorted and added parallel quantitative value py file 1 ماه پیش
mouse_connectivity e8e54e0207 current state: code is finished for representation 10 ماه پیش
testData 27a8ac80ee try and error with R studi 1 ماه پیش
Big_data_mouse_practical_2020_answer.ipynb e8e54e0207 current state: code is finished for representation 10 ماه پیش
GetQuantitativeValues.py d1c8a8c45b code to filter high initital impairments 2 هفته پیش
GetQuantitativeValues_not_parallel.py 71676560e5 sorted and added parallel quantitative value py file 1 ماه پیش
LME.R c039ef3b8d LME 1 ماه پیش
README.md 13cb663094 added all of the code necessery 9 ماه پیش
correlation_between_bahavior_and_DTI.py 10a414834a visu jobs 2 هفته پیش
correlation_between_bahavior_and_DTI_anovaSpecific.py 132437cf05 final results 7 ماه پیش
correlation_fa28_behavior28subtractedbyBaseline.py e1c2b12287 visu jobs 2 هفته پیش
correlation_fa28subtractedbyBaseline_behavior28subtractedbyBaseline.py 10a414834a visu jobs 2 هفته پیش
extract_atlas_fa_regions.py c4c3bd5b9b stuff for poster, atlas fa valus 2 ماه پیش
general_corolation_all_timepoint_together.py c5834f0b56 Adjusted figure sizes 2 هفته پیش
getIncidenceMap.py 1a6c3f835e deleted old things, calculated prediction plots from fa and behaviro, corrected bug in code for replicates when merging 4 هفته پیش
heat_maps_correlation.py c9ecfd427e heatmap adjustment 1 ماه پیش
incooparate_behavior_data.py d1c8a8c45b code to filter high initital impairments 2 هفته پیش
mask2MTPL.py dfaee6412d applied mask2mtpl to whitematter mask 7 ماه پیش
merge_csv_sheets.py d1c8a8c45b code to filter high initital impairments 2 هفته پیش
overlayPlot.py 86fce3a119 current state: code is finished for representation 10 ماه پیش
plotting_quantitative_dti_values.py 3321dce0e3 volcano plots 2 هفته پیش
predictive_correlation_chronic_vs_fa_acute.py a76ef52966 figure predictive fa with behaviorr 1 ماه پیش
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 هفته پیش
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 هفته پیش
proof_of_modalities.py 9bcdec0ea4 added overlap percentage csv 7 ماه پیش
register_masks.py 748f48e806 changed the flip in the anat step of the registration, changed it back to before 7 ماه پیش
remapping_voiting_qc.py 4cf036e11b removed bad qc data from merged with behavior csv 1 ماه پیش
single_mask_form_allan_atlas_creator.py 1cd13fc10c added amba regoins to the mix 1 ماه پیش
statistical_analysis_of_quantitative_data.py d3c8f1d817 added amba regoins to the mix 1 ماه پیش
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 ماه پیش
temp_code.py 062c26905a added new calculation prediction and biomarker approach table style 1 ماه پیش
threshold_whitematter.py c5875af414 added white matter mask 7 ماه پیش
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 ماه پیش
ttest_group_differences.py 3321dce0e3 volcano plots 2 هفته پیش
viralTracing2MTPL.py 2e82796756 added viraltracin 2 mtpl space filp function 9 ماه پیش
visualization_all_timepoints_correlation.py 062c26905a added new calculation prediction and biomarker approach table style 1 ماه پیش
visualization_fa_sham_vs_stroke.py c5834f0b56 Adjusted figure sizes 2 هفته پیش
visualization_general_correlation_correlation.py c5834f0b56 Adjusted figure sizes 2 هفته پیش
visualization_predictive_correlation.py a486c1adc0 adjusted fa correlation figure 1 ماه پیش
visualization_specific_timepoint_correlation.py 10a414834a visu jobs 2 هفته پیش
vizualization_asymetry_index_fa.py 10a414834a visu jobs 2 هفته پیش
vizualization_fa28_behavior28subtractedbyBaseline.py 10a414834a visu jobs 2 هفته پیش
vizualization_fa28subtractedbyBaseline_behavior28subtractedbyBaseline.py 10a414834a visu jobs 2 هفته پیش
volcano_plot.py 3321dce0e3 volcano plots 2 هفته پیش

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