Myelin maps from T1 and t2

[macatools]

Myelin maps from T1 and t2

[melinacordeau]

#T1/T2:
fslmaths
<.../test_pipeline_single_indiv_params_ANTS/full_ants_subpipes/brain_segment_from_mask_pipe/masked_correct_bias_pipe/_session_01_subject_Moussaka/restore_mask_T1/avg_sub-Moussaka_ses-01_acq-0p5mm_run-01_T1w_roi_corrected_noise_corrected_maths_masked.nii.gz>
-div
<.../test_pipeline_single_indiv_params_ANTS/full_ants_subpipes/brain_segment_from_mask_pipe/masked_correct_bias_pipe/_session_01_subject_Moussaka/restore_mask_T2/sub-Moussaka_ses-01_acq-0p5mm_run-01_T2w_roi_corrected_noise_corrected_flirt_maths_masked.nii>
#GMmask T1/T2:
fslmaths <INPUT_IMAGE(T1/T2)> -mas <GM_mask>
NB: GM_MASK = .../test_pipeline_single_indiv_params_ANTS/full_ants_subpipes/brain_segment_from_mask_pipe/segment_atropos_pipe/_session_01_subject_Moussaka/threshold_gm/ )
#rescale myelinmap masked :
min=fslstats -R | awk '{ print $1 }'
max=fslstats -R | awk '{ print $2 }'
scaling=echo "scale=5; 100.0 / ( $max - $min )" | bc
fslmaths -sub $min -mul $scaling YOURIMAGE_rescaled

[melinacordeau]

https://framateam.org/mars-hackat2019/pl/dae98q56tifminr67789o4jtjy

[davidmeunier79]

https://www.biorxiv.org/content/10.1101/2020.09.08.286518v2.full