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

Hi Mark,

I couldn't understand this problem until I upgraded my Mac to 10.6.5 ("Snow Leopard"). It seems that Apple has broken gcc (at least, it no longer works as it does on other systems). The issue seems to be that 10.6.5 no longer supports static linking of libraries. In other words, if you have an object file (mine.o) and a static library sitting in the same directory (libMYLIB.a), then

gcc -o my_executable mine.o -L. -lMYLIB

no longer works. So, the makefiles I provided for Darwin worked fine prior to 10.6.5. A work-around is to treat the static libraries as simple object code:

gcc -o my_executable mine.o libMYLIB.a

This is the strategy I will use for Darwin makefiles on the coming release (v2.0). I will post the new version ASAP.

Best,
Joe