macapype icon indicating copy to clipboard operation
macapype copied to clipboard

Published 20 hours ago • verified publisher icon Macatools

Myelin maps from T1 and t2

Open davidmeunier79 opened this issue 3 years ago • 3 comments

davidmeunier79 avatar Mar 04 '21 23:03 davidmeunier79

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

melinacordeau avatar Mar 17 '21 10:03 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> <OUTPUT IMAGE> 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 <YOURIMAGE> -R | awk '{ print $1 }' max=fslstats <YOURIMAGE> -R | awk '{ print $2 }' scaling=echo "scale=5; 100.0 / ( $max - $min )" | bc fslmaths <YOURIMAGE> -sub $min -mul $scaling YOURIMAGE_rescaled

melinacordeau avatar Mar 17 '21 10:03 melinacordeau

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

davidmeunier79 avatar Mar 17 '21 10:03 davidmeunier79