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Macatools / macapype

PNH segmentation pipelines based on nipype
https://macatools.github.io/macapype/
BSD 3-Clause "New" or "Revised" License
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Myelin maps from T1 and t2 #120

Open davidmeunier79 opened 3 years ago

melinacordeau commented 3 years ago

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

melinacordeau commented 3 years ago

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 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

davidmeunier79 commented 3 years ago

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