All of new 2nd order ROIs+code

[alachancesc]

No description provided.

[mdesco]

Beaucoup de petites modifications à faire stp.

Peux-tu me copier-coller ta commande que tu utilises pour tester stp? Comme je t'avais demander, ça va me permettre de tester tes bdo plus facilement vers la fin.

e.g.
scil_tractogram_filter_by_roi TGN_2nd_order_VTTT_Controlat_vPSN_R.trk test_R.trk --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_1.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_2.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_3.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_4.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_5.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_6.bdo 'any' 'exclude' -f

[alachancesc]

"> Beaucoup de petites modifications à faire stp.

Peux-tu me copier-coller ta commande que tu utilises pour tester stp? Comme je t'avais demander, ça va me permettre de tester tes bdo plus facilement vers la fin.

e.g. scil_tractogram_filter_by_roi TGN_2nd_order_VTTT_Controlat_vPSN_R.trk test_R.trk --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_1.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_2.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_3.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_4.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_5.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/VTTT_Controlat/VTTT_Controlat_vPSN_6.bdo 'any' 'exclude' -f"

Désolé pour les bug, j'utilisais juste git status après avoir push mes fichiers sur ma branche, mais je devrais le faire systématiquement.

J'ai essayé de tester le script sur mon Mac en revenant hier, mais il affiche toujours :

/Users/antoinelachance/Desktop/Recherche TGN/MAIN/atlases_final/trks/TGN_2nd_order_DTTT_Ipsilat_dPSN_R.trk
test_R.trk
--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_1.bdo 'any' 'exclude'
--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_2.bdo 'any' 'exclude'
--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_3.bdo 'any' 'exclude'
--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_4.bdo 'any' 'exclude'
--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_5.bdo 'any' 'exclude'
--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_6.bdo 'any' 'exclude'
--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_7.bdo 'any' 'exclude'
--bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_8.bdo 'any' 'exclude'
-f

usage: scil_tractogram_filter_by_roi [-h] [--drawn_roi DRAWN_ROI [DRAWN_ROI ...]] [--atlas_roi ATLAS_ROI [ATLAS_ROI ...]] [--bdo BDO [BDO ...]] [--x_plane X_PLANE [X_PLANE ...]]
[--y_plane Y_PLANE [Y_PLANE ...]] [--z_plane Z_PLANE [Z_PLANE ...]] [--filtering_list FILTERING_LIST] [--overwrite_distance OVERWRITE_DISTANCE [OVERWRITE_DISTANCE ...]]
[--save_masks_atlas_roi SAVE_MASKS_ATLAS_ROI] [--no_empty] [--display_counts] [--save_rejected FILENAME] [--indent INDENT] [--sort_keys] [--reference REFERENCE]
[-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
in_tractogram out_tractogram
scil_tractogram_filter_by_roi: error: unrecognized arguments: test_R.trk

J'aurais dû demander avant de faire la PR... Désolé

[alachancesc]

la vraie commande qui marche pour moi
scil_tractogram_filter_by_roi /home/local/USHERBROOKE/laca6352/s/atlases_final/trks/TGN_2nd_order_DTTT_Ipsilat_dPSN_R.trk test_R.trk --bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_1.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_2.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_3.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_4.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_5.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_6.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_7.bdo 'any' 'exclude' --bdo ${mni_dir}/MNI/from_${nside}/new_ROIs/DTTT_Ipsilat_dPSN_8.bdo 'any' 'exclude' -f

[mdesco]

This PR is no longer compatible with latest first-order.sh

@nasrin100 can you adjust with the help of @arnaudbore please?

thanks

[mdesco]

Adjust indentation

[mdesco]

This path needs to be adjusted... final is now final_merged/final I think