install_sct version package

[jcohenadad]

https://sourceforge.net/projects/spinalcordtoolbox/files/3.0/sct_v3.0_beta0.tar.gz/download

julien-macbook:~/Desktop/sct_v3.0_beta0 $ ./install_sct 

Welcome to the SCT installer!

SCT version ......... 3.0_beta0
Installation type ... package
Operating system .... osx

SCT will be installed here: [/Users/julien/sct_3.0_beta0]
Do you agree? yes/no: y
Removing sct and isct softlink from /Users/julien/sct_3.0_beta0/bin
find: /Users/julien/sct_3.0_beta0/bin: No such file or directory
find: /Users/julien/sct_3.0_beta0/bin: No such file or directory

Copying source files from /Users/julien/Desktop/sct_v3.0_beta0 to /Users/julien/sct_3.0_beta0
cp: /Users/julien/sct_3.0_beta0/.: No such file or directory
cp: /Users/julien/Desktop/sct_v3.0_beta0/scripts: unable to copy extended attributes to /Users/julien/sct_3.0_beta0/.: No such file or directory
/Users/julien/Desktop/sct_v3.0_beta0/scripts -> /Users/julien/sct_3.0_beta0/.
cp: /Users/julien/sct_3.0_beta0/./isct_check_detection.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./isct_convert_binary_to_trilinear.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./isct_get_fractional_volume.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./isct_minc2volume-viewer.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./isct_test_ants.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./isct_test_function.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./isct_warpmovie_generator.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./matlab_batcher.sh: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_base_classes.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_gmseg_utils.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_image.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_moco.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_multiatlas_seg.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_nurbs.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_parser.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_pca.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_register.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_register_landmarks.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_register_regularized.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_smooth.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./msct_types.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_apply_transfo.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_average_data_within_mask.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_change_image_type.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_check_atlas_integrity.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_check_dependencies.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_compute_ernst_angle.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_compute_hausdorff_distance.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_compute_mscc.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_compute_mtr.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_compute_snr.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_concat_transfo.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_convert.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_create_mask.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_crop_image.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_denoising_onlm.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dice_coefficient.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dmri_compute_dti.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dmri_concat_bvals.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dmri_concat_bvecs.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dmri_create_noisemask.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dmri_eddy_correct.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dmri_get_bvalue.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dmri_moco.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dmri_separate_b0_and_dwi.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_dmri_transpose_bvecs.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_download_data.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_extract_metric.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_flatten_sagittal.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_flip_data.sh: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_fmri_compute_tsnr.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_fmri_moco.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_get_centerline.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_image.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_invert_image.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_label_utils.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_label_vertebrae.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_maths.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_process_segmentation.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_propseg.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_register_graymatter.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_register_multimodal.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_register_to_template.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_resample.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_segment_graymatter.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_smooth_spinalcord.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_straighten_spinalcord.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_testing.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_utils.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_viewer.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./sct_warp_template.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/./test_regist.py: No such file or directory
cp: /Users/julien/sct_3.0_beta0/.: No such file or directory
/Users/julien/Desktop/sct_v3.0_beta0/install -> /Users/julien/sct_3.0_beta0/install
/Users/julien/Desktop/sct_v3.0_beta0/install/__init__.py -> /Users/julien/sct_3.0_beta0/install/__init__.py
/Users/julien/Desktop/sct_v3.0_beta0/install/build_ants_sct.sh -> /Users/julien/sct_3.0_beta0/install/build_ants_sct.sh
/Users/julien/Desktop/sct_v3.0_beta0/install/check_bash_profile.sh -> /Users/julien/sct_3.0_beta0/install/check_bash_profile.sh
/Users/julien/Desktop/sct_v3.0_beta0/install/compile_ants.py -> /Users/julien/sct_3.0_beta0/install/compile_ants.py
/Users/julien/Desktop/sct_v3.0_beta0/install/compile_external.py -> /Users/julien/sct_3.0_beta0/install/compile_external.py
/Users/julien/Desktop/sct_v3.0_beta0/install/copy_ants_binaries.py -> /Users/julien/sct_3.0_beta0/install/copy_ants_binaries.py
/Users/julien/Desktop/sct_v3.0_beta0/install/create_package.py -> /Users/julien/sct_3.0_beta0/install/create_package.py
/Users/julien/Desktop/sct_v3.0_beta0/install/install_patch.py -> /Users/julien/sct_3.0_beta0/install/install_patch.py
/Users/julien/Desktop/sct_v3.0_beta0/install/make_binaries.sh -> /Users/julien/sct_3.0_beta0/install/make_binaries.sh
/Users/julien/Desktop/sct_v3.0_beta0/install/old -> /Users/julien/sct_3.0_beta0/install/old
/Users/julien/Desktop/sct_v3.0_beta0/install/old/installer.py -> /Users/julien/sct_3.0_beta0/install/old/installer.py
/Users/julien/Desktop/sct_v3.0_beta0/install/requirements -> /Users/julien/sct_3.0_beta0/install/requirements
/Users/julien/Desktop/sct_v3.0_beta0/install/requirements/requirements.py -> /Users/julien/sct_3.0_beta0/install/requirements/requirements.py
/Users/julien/Desktop/sct_v3.0_beta0/install/requirements/requirementsConda.txt -> /Users/julien/sct_3.0_beta0/install/requirements/requirementsConda.txt
/Users/julien/Desktop/sct_v3.0_beta0/install/requirements/requirementsPip.txt -> /Users/julien/sct_3.0_beta0/install/requirements/requirementsPip.txt
/Users/julien/Desktop/sct_v3.0_beta0/install/sct_env -> /Users/julien/sct_3.0_beta0/install/sct_env
/Users/julien/Desktop/sct_v3.0_beta0/install/sct_launcher -> /Users/julien/sct_3.0_beta0/install/sct_launcher
/Users/julien/Desktop/sct_v3.0_beta0/install/update_bin.sh -> /Users/julien/sct_3.0_beta0/install/update_bin.sh
/Users/julien/Desktop/sct_v3.0_beta0/testing -> /Users/julien/sct_3.0_beta0/./testing
/Users/julien/Desktop/sct_v3.0_beta0/testing/notes.txt -> /Users/julien/sct_3.0_beta0/./testing/notes.txt
/Users/julien/Desktop/sct_v3.0_beta0/testing/sct_crop -> /Users/julien/sct_3.0_beta0/./testing/sct_crop
/Users/julien/Desktop/sct_v3.0_beta0/testing/sct_crop/test_sct_crop.sh -> /Users/julien/sct_3.0_beta0/./testing/sct_crop/test_sct_crop.sh
/Users/julien/Desktop/sct_v3.0_beta0/testing/sct_dmri_separate_b0_and_dwi -> /Users/julien/sct_3.0_beta0/./testing/sct_dmri_separate_b0_and_dwi
/Users/julien/Desktop/sct_v3.0_beta0/testing/sct_dmri_separate_b0_and_dwi/test_sct_dmri_separate_b0_and_dwi.sh -> /Users/julien/sct_3.0_beta0/./testing/sct_dmri_separate_b0_and_dwi/test_sct_dmri_separate_b0_and_dwi.sh
/Users/julien/Desktop/sct_v3.0_beta0/testing/sct_icv -> /Users/julien/sct_3.0_beta0/./testing/sct_icv
/Users/julien/Desktop/sct_v3.0_beta0/testing/sct_icv/batch_testing_icv.sh -> /Users/julien/sct_3.0_beta0/./testing/sct_icv/batch_testing_icv.sh
/Users/julien/Desktop/sct_v3.0_beta0/testing/sct_label_utils -> /Users/julien/sct_3.0_beta0/./testing/sct_label_utils
/Users/julien/Desktop/sct_v3.0_beta0/testing/sct_label_utils/test_sct_label_utils.sh -> /Users/julien/sct_3.0_beta0/./testing/sct_label_utils/test_sct_label_utils.sh
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_debug_off.py -> /Users/julien/sct_3.0_beta0/./testing/test_debug_off.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_apply_transfo.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_apply_transfo.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_check_atlas_integrity.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_check_atlas_integrity.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_compute_mtr.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_compute_mtr.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_concat_transfo.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_concat_transfo.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_convert.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_convert.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_convert_binary_to_trilinear.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_convert_binary_to_trilinear.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_create_mask.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_create_mask.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_crop_image.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_crop_image.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_denoising_onlm.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_denoising_onlm.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_dmri_compute_dti.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_dmri_compute_dti.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_dmri_create_noisemask.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_dmri_create_noisemask.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_dmri_get_bvalue.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_dmri_get_bvalue.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_dmri_moco.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_dmri_moco.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_dmri_separate_b0_and_dwi.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_dmri_separate_b0_and_dwi.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_dmri_transpose_bvecs.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_dmri_transpose_bvecs.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_documentation.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_documentation.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_extract_metric.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_extract_metric.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_flatten_sagittal.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_flatten_sagittal.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_fmri_compute_tsnr.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_fmri_compute_tsnr.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_fmri_moco.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_fmri_moco.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_get_centerline.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_get_centerline.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_image.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_image.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_label_utils.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_label_utils.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_label_vertebrae.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_label_vertebrae.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_maths.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_maths.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_orientation.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_orientation.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_process_segmentation.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_process_segmentation.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_propseg.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_propseg.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_register_graymatter.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_register_graymatter.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_register_multimodal.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_register_multimodal.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_register_to_template.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_register_to_template.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_resample.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_resample.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_segment_graymatter.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_segment_graymatter.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_smooth_spinalcord.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_smooth_spinalcord.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_straighten_spinalcord.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_straighten_spinalcord.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/test_sct_warp_template.py -> /Users/julien/sct_3.0_beta0/./testing/test_sct_warp_template.py
/Users/julien/Desktop/sct_v3.0_beta0/testing/testing_sct_propseg.py -> /Users/julien/sct_3.0_beta0/./testing/testing_sct_propseg.py

ERROR: Cannot cd into SCT folder. SCT_DIR=/Users/julien/sct_3.0_beta0

[poquirion]

@jcohenadad I can't reproduce. Have you fixed it in : 8ffe66c (HEAD -> master, origin/master, origin/HEAD) install_sct: fixed bug on package installation [Julien Cohen-Adad] ?

[poquirion]

Ok, got it

[poquirion]

made a pull request