EDIT: Nevermind, I just noticed you provided Darwin-i386 binaries that are working just fine. Thanks.


Hi Joseph,

I'm attempting to compile the jip executables on OS X 10.5.8 Intel.

It looks like all the required libraries compiled fine, but I get this error when trying to compile jip, jip-display, and jip-align.

Can you point me in the right direction to get this working?
Thanks,
Mark

It looks like I'm missing a library, but I have no idea which. All the prerequisite libraries compiled fine:

Undefined symbols:
"_free_fcomplex_vector", referenced from:
_install_stack in jip-front.o
_free_stack in jip-front.o
_ishift_pixels in jip-align.o
_register_volume in jip-align.o
_register_volume in jip-align.o
_smooth_volumes in jip-average.o
_fft_volume in jip-transfilt.o
_fft_volume in jip-transfilt.o
_ft_1d in jip-transfilt.o
_ft_time in jip-transfilt.o
_edge_filter in jip-transfilt.o
_read_xdisplay_file in jip-io.o
_clip_stack in jip-reorder.o
_pad_stack in jip-reorder.o
_reverse_slice_order in jip-reorder.o
_reorder_slices in jip-reorder.o
"_Gauss", referenced from:
_register_volume in jip-align.o
_register_volume in jip-align.o
_register_volume in jip-align.o
"_unsigned_short_vector", referenced from:
_read_xdisplay_file in jip-io.o
_write_output_file in jip-io.o
"_free_short_vector", referenced from:
_magnitude_window_together in jip-magcor.o
_magnitude_window_together in jip-magcor.o
_scale_volumes in jip-magcor.o
_scale_volumes in jip-magcor.o
_normalize_volumes in jip-magcor.o
_normalize_volumes in jip-magcor.o
_read_xdisplay_file in jip-io.o
_read_xdisplay_file in jip-io.o
_write_output_file in jip-io.o
_write_slices in jip-io.o
_glm_assess_global_F_variance in jip-glm.o
_scatter_plot in jip-maps.o
"_float_vector", referenced from:
_read_map_array in jip-front.o
_register_volume in jip-align.o
_register_volume in jip-align.o
_register_volume in jip-align.o
_magnitude_window in jip-magcor.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_create_overlay_from_bitmap in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_read_xdisplay_file in jip-io.o
_read_xdisplay_file in jip-io.o
_read_xdisplay_file in jip-io.o
_write_output_file in jip-io.o
_write_slices in jip-io.o
_fill_weighted_histogram in jip-stats.o
_glm_remove_or_correct_baseline in jip-glm.o
_glm_remove_or_correct_baseline in jip-glm.o
_glm_histogram_unbiased in jip-glm.o
_glm_histogram_unbiased in jip-glm.o
_glm_histogram_unbiased_residue in jip-glm.o
_glm_histogram_unbiased_residue in jip-glm.o
_glm_create_residue in jip-glm.o
_glm_create_residue in jip-glm.o
_glm_fit_events in jip-glm.o
_glm_fit_events in jip-glm.o
_glm_maximal_effect in jip-glm.o
_glm_maximal_effect in jip-glm.o
_glm_create_residual_variance in jip-glm.o
_glm_create_residual_variance in jip-glm.o
_glm_create_AR_maps in jip-glm.o
_glm_create_AR_maps in jip-glm.o
_glm_assess_global_F_variance in jip-glm.o
_glm_assess_global_F_variance in jip-glm.o
_map_snr in jip-maps.o
_map_snr in jip-maps.o
_map_t2 in jip-maps.o
_map_t2 in jip-maps.o
_GLM_read_hrf_file in glm.o
_GLM_read_hrf_file in glm.o
_GLM_read_hrf_file in glm.o
_GLM_read_event_file in glm.o
_GLM_read_event_file in glm.o
_GLM_read_table_file in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_calculate_AR_coefficient in glm.o
_GLM_calculate_AR_coefficient in glm.o
_GLM_calculate_whitening_filter in glm.o
_GLMInternal_convolve_paradigm_IRF in glm.o
_GLM_calculate_F in glm.o
_GLM_set_time_constant in glm.o
_GLM_set_time_constant in glm.o
_GLM_get_maximal_effect_size in glm.o
_GLM_delete_1_stimulus in glm.o
_GLM_delete_1_stimulus in glm.o
_GLMInternal_whiten_data in glm.o
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
"_short_vector", referenced from:
_magnitude_window_together in jip-magcor.o
_scale_volumes in jip-magcor.o
_normalize_volumes in jip-magcor.o
_read_xdisplay_file in jip-io.o
_read_xdisplay_file in jip-io.o
_write_output_file in jip-io.o
_write_slices in jip-io.o
_glm_assess_global_F_variance in jip-glm.o
_scatter_plot in jip-maps.o
"_ipoint3d_vector", referenced from:
_magnitude_window in jip-magcor.o
_magnitude_window_together in jip-magcor.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_create_overlay_from_bitmap in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_glm_fit_events in jip-glm.o
"_downsample_stack", referenced from:
_downsample_stacks in jip-align.o
"_Convert_Voxel_to_Space", referenced from:
_register_volume in jip-align.o
"_fcomplex_vector", referenced from:
_install_stack in jip-front.o
_ishift_pixels in jip-align.o
_register_volume in jip-align.o
_register_volume in jip-align.o
_smooth_volumes in jip-average.o
_fft_volume in jip-transfilt.o
_fft_volume in jip-transfilt.o
_ft_1d in jip-transfilt.o
_ft_time in jip-transfilt.o
_edge_filter in jip-transfilt.o
_read_xdisplay_file in jip-io.o
_clip_stack in jip-reorder.o
_pad_stack in jip-reorder.o
_reverse_slice_order in jip-reorder.o
_reorder_slices in jip-reorder.o
"_free_float_matrix", referenced from:
_GLM_read_control_file in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLMInternal_calculate_AR_mixing_matrix in glm.o
_GLMInternal_calculate_AR_mixing_matrix in glm.o
_GLMInternal_calculate_AR_mixing_matrix in glm.o
_GLM_calculate_whitening_filter in glm.o
_GLM_calculate_whitening_filter in glm.o
_GLM_define_conditions in glm.o
_GLM_define_conditions in glm.o
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
"_ham_sinc", referenced from:
_register_volume in jip-align.o
_register_volume in jip-align.o
_register_volume in jip-align.o
"_int_vector", referenced from:
_set_variable in jip-front.o
_read_slice_order in jip-front.o
_print_help_page in jip-front.o
_print_help_page in jip-front.o
_average_stacks in jip-average.o
_fill_histogram in jip-stats.o
_fill_weighted_histogram in jip-stats.o
_fill_weighted_histogram in jip-stats.o
_glm_histogram_unbiased in jip-glm.o
_glm_histogram_unbiased_residue in jip-glm.o
_glm_histogram_unbiased_residue in jip-glm.o
_glm_fit_events in jip-glm.o
_map_snr in jip-maps.o
_GLM_read_table_file in glm.o
_GLM_define_basis_functions in glm.o
_GLM_initialize in glm.o
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
"_swap_x", referenced from:
_fft_volume in jip-transfilt.o
_fft_volume in jip-transfilt.o
_fft_volume in jip-transfilt.o
_fft_volume in jip-transfilt.o
_ft_1d in jip-transfilt.o
_ft_1d in jip-transfilt.o
_ft_time in jip-transfilt.o
_ft_time in jip-transfilt.o
"_help_menu", referenced from:
_act_on_command in jip-front.o
"_float_matrix", referenced from:
_GLM_read_table_file in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLMInternal_whiten_model in glm.o
_GLMInternal_calculate_AR_mixing_matrix in glm.o
_GLMInternal_calculate_AR_mixing_matrix in glm.o
_GLMInternal_calculate_AR_mixing_matrix in glm.o
_GLM_calculate_whitening_filter in glm.o
_GLM_calculate_whitening_filter in glm.o
_GLM_define_conditions in glm.o
_GLM_define_conditions in glm.o
_GLM_define_table_event_interactive in glm.o
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
"_ibeta", referenced from:
_GLM_calculate_F in glm.o
"_free_long_vector", referenced from:
_read_xdisplay_file in jip-io.o
"_free_int_vector", referenced from:
_set_variable in jip-front.o
_read_slice_order in jip-front.o
_fill_histogram in jip-stats.o
_fill_weighted_histogram in jip-stats.o
_fill_weighted_histogram in jip-stats.o
_glm_histogram_unbiased in jip-glm.o
_glm_histogram_unbiased_residue in jip-glm.o
_map_snr in jip-maps.o
_GLM_read_table_file in glm.o
_GLM_define_basis_functions in glm.o
_GLM_initialize in glm.o
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
"_scale_and_shift_to_mat44", referenced from:
_ishift_pixels in jip-align.o
_register_volume in jip-align.o
_write_nifti_header in jip-io.o
_clip_stack in jip-reorder.o
_read_nifti_header in libIO.a(io.o)
_read_xdisplay_header in libIO.a(io.o)
_read_freesurfer_header in libIO.a(io.o)
"_free_unsigned_short_vector", referenced from:
_read_xdisplay_file in jip-io.o
_write_output_file in jip-io.o
"_get_line_with_comment", referenced from:
_main in jip-front.o
_main in jip-front.o
_main in jip-front.o
_print_help_page in jip-front.o
_print_help_page in jip-front.o
_print_help_page in jip-front.o
_print_help_page in jip-front.o
_print_help_page in jip-front.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_GLM_read_control_file in glm.o
_GLM_read_control_file in glm.o
_GLM_read_hrf_file in glm.o
_GLM_read_hrf_file in glm.o
_GLM_read_hrf_file in glm.o
_GLM_read_event_file in glm.o
_GLM_read_event_file in glm.o
_GLM_read_event_file in glm.o
_GLM_read_table_file in glm.o
_GLM_read_table_file in glm.o
_GLM_read_table_file in glm.o
_GLM_read_table_file in glm.o
_read_xdisplay_header in libIO.a(io.o)
_read_xdisplay_header in libIO.a(io.o)
_read_freesurfer_header in libIO.a(io.o)
"_long_vector", referenced from:
_read_xdisplay_file in jip-io.o
"_int_matrix", referenced from:
_GLM_define_conditions in glm.o
"_invert_mat44", referenced from:
_ishift_pixels in jip-align.o
_register_volume in jip-align.o
_clip_stack in jip-reorder.o
_read_volume_header in libIO.a(io.o)
"_general_affine_to_mat44", referenced from:
_read_nifti_header in libIO.a(io.o)
"_centered_xyz_to_ijk", referenced from:
_register_volume in jip-align.o
"_free_ipoint3d_vector", referenced from:
_magnitude_window in jip-magcor.o
_magnitude_window_together in jip-magcor.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_delete_overlay in jip-ovl.o
_create_overlay_from_bitmap in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_glm_fit_events in jip-glm.o
"_centered_ijk_to_xyz", referenced from:
_register_volume in jip-align.o
"_free_int_matrix", referenced from:
_GLM_define_conditions in glm.o
"_next_non_white", referenced from:
_do_command in jip-front.o
_do_command in jip-front.o
_strip_com_arguments in jip-front.o
_strip_com_arguments in jip-front.o
_strip_com_arguments in jip-front.o
_strip_com_arguments in jip-front.o
_strip_com_arguments in jip-front.o
_strip_com_arguments in jip-front.o
_strip_com_arguments in jip-front.o
_strip_com_arguments in jip-front.o
_strip_com_arguments in jip-front.o
_decode_volume_list in jip-front.o
_decode_volume_list in jip-front.o
_decode_comparison_list in jip-front.o
_decode_string_and_comparison_list in jip-front.o
_decode_int_and_comparison_list in jip-front.o
_decode_read_special in jip-front.o
_decode_string_and_list in jip-front.o
_decode_int_and_list in jip-front.o
_decode_int_string_and_list in jip-front.o
_decode_2strings_and_list in jip-front.o
_decode_real_string_and_list in jip-front.o
_decode_real_string_and_comparison_list in jip-front.o
_decode_real_and_list in jip-front.o
_decode_euler_and_list in jip-front.o
_decode_2reals_and_list in jip-front.o
_decode_2reals_and_list in jip-front.o
_decode_4reals_string_and_list in jip-front.o
_decode_4reals_string_and_list in jip-front.o
_decode_4reals_string_and_list in jip-front.o
_decode_4reals_string_and_list in jip-front.o
_decode_3reals_and_list in jip-front.o
_decode_3reals_and_list in jip-front.o
_decode_3reals_and_list in jip-front.o
_decode_3reals_string_and_list in jip-front.o
_decode_3reals_string_and_list in jip-front.o
_decode_3reals_string_and_list in jip-front.o
_decode_2ints_string_and_list in jip-front.o
_decode_2ints_string_and_list in jip-front.o
_read_slice_order in jip-front.o
_read_slice_order in jip-front.o
_read_map_array in jip-front.o
_read_map_array in jip-front.o
_GLM_read_control_file in glm.o
_GLM_read_control_file in glm.o
_GLMInternal_decode_keyword in glm.o
_GLM_read_table_file in glm.o
_GLM_read_table_file in glm.o
_GLM_define_conditions in glm.o
_GLM_define_conditions in glm.o
_decode_xdisplay_header_keyword in libIO.a(io.o)
_decode_freesurfer_header_keyword in libIO.a(io.o)
"_is_power_of_2", referenced from:
_fft_volumes in jip-transfilt.o
_fft_volumes in jip-transfilt.o
_clip_stacks in jip-reorder.o
_clip_stacks in jip-reorder.o
_clip_stacks in jip-reorder.o
_pad_stacks in jip-reorder.o
_pad_stacks in jip-reorder.o
_pad_stacks in jip-reorder.o
_pad_2n_stacks in jip-reorder.o
_pad_2n_stacks in jip-reorder.o
"_free_float_vector", referenced from:
_read_map_array in jip-front.o
_register_volume in jip-align.o
_register_volume in jip-align.o
_register_volume in jip-align.o
_magnitude_window in jip-magcor.o
_magnitude_window in jip-magcor.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_read_ovl_file in jip-ovl.o
_delete_overlay in jip-ovl.o
_create_overlay_from_bitmap in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_mirror_overlay_in_x in jip-ovl.o
_read_xdisplay_file in jip-io.o
_read_xdisplay_file in jip-io.o
_read_xdisplay_file in jip-io.o
_write_output_file in jip-io.o
_write_slices in jip-io.o
_fill_weighted_histogram in jip-stats.o
_glm_remove_or_correct_baseline in jip-glm.o
_glm_remove_or_correct_baseline in jip-glm.o
_glm_histogram_unbiased in jip-glm.o
_glm_histogram_unbiased in jip-glm.o
_glm_histogram_unbiased_residue in jip-glm.o
_glm_histogram_unbiased_residue in jip-glm.o
_glm_create_residue in jip-glm.o
_glm_create_residue in jip-glm.o
_glm_fit_events in jip-glm.o
_glm_fit_events in jip-glm.o
_glm_maximal_effect in jip-glm.o
_glm_maximal_effect in jip-glm.o
_glm_create_residual_variance in jip-glm.o
_glm_create_residual_variance in jip-glm.o
_glm_create_AR_maps in jip-glm.o
_glm_create_AR_maps in jip-glm.o
_glm_assess_global_F_variance in jip-glm.o
_glm_assess_global_F_variance in jip-glm.o
_map_snr in jip-maps.o
_map_snr in jip-maps.o
_map_t2 in jip-maps.o
_map_t2 in jip-maps.o
_GLM_read_control_file in glm.o
_GLM_read_control_file in glm.o
_GLM_read_hrf_file in glm.o
_GLM_read_hrf_file in glm.o
_GLM_read_hrf_file in glm.o
_GLM_read_table_file in glm.o
_GLM_define_basis_functions in glm.o
_GLM_define_basis_functions in glm.o
_GLM_calculate_AR_coefficient in glm.o
_GLM_calculate_AR_coefficient in glm.o
_GLM_calculate_whitening_filter in glm.o
_GLMInternal_convolve_paradigm_IRF in glm.o
_GLM_calculate_F in glm.o
_GLM_set_time_constant in glm.o
_GLM_set_time_constant in glm.o
_GLM_get_maximal_effect_size in glm.o
_GLM_delete_1_stimulus in glm.o
_GLM_delete_1_stimulus in glm.o
_GLMInternal_whiten_data in glm.o
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
"_rInvertSquareMatrix", referenced from:
_GLMInternal_whiten_model in glm.o
_GLMInternal_whiten_model in glm.o
_GLMInternal_calculate_AR_mixing_matrix in glm.o
_GLM_calculate_whitening_filter in glm.o
_GLM_define_conditions in glm.o
_PolynomialDefineGLM in libJIPFIT.a(jip-fit.o)
_GeneralDefineGLM in libJIPFIT.a(jip-fit.o)
"_Convert_Space_to_rVoxel", referenced from:
_register_volume in jip-align.o
"_Trace_of_Matrix", referenced from:
_GLMInternal_calculate_AR_mixing_matrix in glm.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [jip] Error 1