From f85abcb4417f67adb2ce931e4cf538c92853bcde Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 22 Sep 2021 10:18:23 -0400 Subject: [PATCH 1/9] DOCKER: Add FS7 exclusion file --- docker/files/freesurfer7.2-exclude.txt | 51769 +++++++++++++++++++++++ 1 file changed, 51769 insertions(+) create mode 100644 docker/files/freesurfer7.2-exclude.txt diff --git a/docker/files/freesurfer7.2-exclude.txt b/docker/files/freesurfer7.2-exclude.txt new file mode 100644 index 000000000..df14f68f7 --- /dev/null +++ b/docker/files/freesurfer7.2-exclude.txt @@ -0,0 +1,51769 @@ +freesurfer/average +freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh +freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img +freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img.rec +freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.mat +freesurfer/average/3T18yoSchwartzReactN32_as_orig.lst +freesurfer/average/711-2B_as_mni_average_305.4dfp.hdr +freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh +freesurfer/average/711-2B_as_mni_average_305.4dfp.img 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+freesurfer/FreeSurferEnv.sh +freesurfer/SegmentNoLUT.txt +freesurfer/SetUpFreeSurfer.csh +freesurfer/SetUpFreeSurfer.sh +freesurfer/Simple_surface_labels2009.txt +freesurfer/SubCorticalMassLUT.txt +freesurfer/WMParcStatsLUT.txt +freesurfer/build-stamp.txt +freesurfer/sources.csh +freesurfer/sources.sh +freesurfer/tkmeditParcColorsCMA From e63937ccb83e1e29872fe8dc2d031e573e934d04 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 22 Sep 2021 10:19:36 -0400 Subject: [PATCH 2/9] DOCKER: Consolidate exclusions to untouched files/directories --- docker/files/freesurfer7.2-exclude.txt | 50160 +---------------------- 1 file changed, 1 insertion(+), 50159 deletions(-) diff --git a/docker/files/freesurfer7.2-exclude.txt b/docker/files/freesurfer7.2-exclude.txt index df14f68f7..d9069de74 100644 --- a/docker/files/freesurfer7.2-exclude.txt +++ b/docker/files/freesurfer7.2-exclude.txt @@ -1,4 +1,3 @@ -freesurfer/average freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.ifh freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img.rec @@ -9,12 +8,8 @@ freesurfer/average/711-2B_as_mni_average_305.4dfp.ifh freesurfer/average/711-2B_as_mni_average_305.4dfp.img freesurfer/average/711-2B_as_mni_average_305.4dfp.img.rec freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.hdr -freesurfer/average/711-2B_as_mni_average_305_mask.4dfp.ifh 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-freesurfer/average/mult-comp-cor/README freesurfer/average/HippoSF -freesurfer/average/HippoSF/atlas -freesurfer/average/HippoSF/atlas/AtlasDump.mgz -freesurfer/average/HippoSF/atlas/AtlasMesh.gz -freesurfer/average/HippoSF/atlas/compressionLookupTable.txt -freesurfer/average/RB_all_2020-01-02.gca freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca freesurfer/average/RB_all_withskull_2019_10_22.talxfm.mni305.gca -freesurfer/average/RB_all_withskull_2020_01_02.gca freesurfer/average/RLB700_atlas_as_orig.4dfp.hdr freesurfer/average/RLB700_atlas_as_orig.4dfp.ifh freesurfer/average/RLB700_atlas_as_orig.4dfp.img @@ -7441,47 +61,18 @@ freesurfer/average/SVIP_Young_Patient_N12_as_orig.4dfp.ifh freesurfer/average/SVIP_Young_Patient_N12_as_orig.4dfp.img freesurfer/average/SVIP_Young_Patient_N12_as_orig.4dfp.img.rec freesurfer/average/aseg+spmhead+vermis+pons.ixi.gca -freesurfer/average/colortable_BA.txt freesurfer/average/colortable_desikan_killiany.txt 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freesurfer/average/mni_average_305.4dfp.img freesurfer/average/mni_average_305.4dfp.img.rec freesurfer/average/pons.mni152.2mm.mgz -freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs -freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2020-05-13.gcs freesurfer/average/rh.DKTatlas100.gcs freesurfer/average/rh.DKTatlas40.gcs -freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs freesurfer/average/rh.atlas2002_simple.gcs freesurfer/average/rh.atlas2005_simple.gcs freesurfer/average/rh.average.CURVATURE.tif @@ -7506,9 +94,7 @@ freesurfer/average/rh.average.curvature.filled.buckner40.tif freesurfer/average/rh.average.tif freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs freesurfer/average/rh.destrieux.simple.2009-07-29.gcs -freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif freesurfer/average/rh_trans_toSulc.gcs -freesurfer/average/rigidly_aligned_brain_template.tif freesurfer/average/talairach_mixed_with_skull.gca freesurfer/average/tissue_parms.txt freesurfer/average/wmsa_new_eesmith.gca @@ -7517,10 +103,7 @@ freesurfer/average/lh.average.CURVATURE.tif freesurfer/average/lh.average.curvature.filled.buckner40.tif freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs freesurfer/average/lh.destrieux.simple.2009-07-29.gcs -freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif -freesurfer/bin freesurfer/bin/compute_label_volumes.csh -freesurfer/bin/compute_vox2vox freesurfer/bin/connectgraph freesurfer/bin/cor_to_minc freesurfer/bin/cp-dicom @@ -7533,7 +116,6 @@ freesurfer/bin/dcmsplit freesurfer/bin/dcmunpack freesurfer/bin/deface_subject freesurfer/bin/defect-seg -freesurfer/bin/defect2seg freesurfer/bin/dicom-rename freesurfer/bin/diffusionUtils freesurfer/bin/dmri_AnatomiCuts @@ -7566,7 +148,6 @@ freesurfer/bin/dmrirc.multiscan.example freesurfer/bin/dt_recon freesurfer/bin/epidewarp.fsl freesurfer/bin/exportGcam -freesurfer/bin/extract_talairach_avi_QA.awk freesurfer/bin/feat2segstats freesurfer/bin/feat2surf freesurfer/bin/findsession @@ -7590,9 +171,7 @@ freesurfer/bin/fs_install_mcr freesurfer/bin/fs_lib_check freesurfer/bin/fs_run_from_mcr freesurfer/bin/fs_spmreg.glnxa64 -freesurfer/bin/fs_temp_dir freesurfer/bin/fs_temp_file -freesurfer/bin/fs_time freesurfer/bin/fs_tutorial_data freesurfer/bin/fs_update freesurfer/bin/fscalc @@ -7609,14 +188,11 @@ freesurfer/bin/fslorient.fsl freesurfer/bin/fslregister freesurfer/bin/fslswapdim.fsl freesurfer/bin/fspalm -freesurfer/bin/fspython freesurfer/bin/fsr-checkxopts freesurfer/bin/fsr-coreg -freesurfer/bin/fsr-getxopts freesurfer/bin/fsr-import freesurfer/bin/fsvglrun freesurfer/bin/fvcompare -freesurfer/bin/gauss_4dfp freesurfer/bin/gca-apply freesurfer/bin/gcainit freesurfer/bin/gcaprepone @@ -7641,8 +217,6 @@ freesurfer/bin/histo_segment freesurfer/bin/histo_synthesize freesurfer/bin/ico_supersample freesurfer/bin/id.xfm -freesurfer/bin/ifh2hdr -freesurfer/bin/imgreg_4dfp freesurfer/bin/inflate_subject freesurfer/bin/inflate_subject-lh freesurfer/bin/inflate_subject-rh @@ -7684,7 +258,6 @@ freesurfer/bin/long_submit_jobs freesurfer/bin/long_submit_postproc freesurfer/bin/longmc freesurfer/bin/lpcregister -freesurfer/bin/lta_convert freesurfer/bin/lta_diff freesurfer/bin/conf2hires freesurfer/bin/make-segvol-table @@ -7725,16 +298,11 @@ freesurfer/bin/morph_subject-rh freesurfer/bin/morph_subject_on_seychelles freesurfer/bin/morph_tables-lh freesurfer/bin/morph_tables-rh -freesurfer/bin/mpr2mni305 freesurfer/bin/mri-func2sph freesurfer/bin/mri-funcvits freesurfer/bin/mri-sph2surf freesurfer/bin/mri_add_new_tp -freesurfer/bin/mri_add_xform_to_header freesurfer/bin/mri_align_long.csh -freesurfer/bin/mri_and -freesurfer/bin/mri_annotation2label -freesurfer/bin/mri_aparc2aseg freesurfer/bin/mri_aparc2wmseg freesurfer/bin/mri_apply_autoencoder freesurfer/bin/mri_apply_bias @@ -7744,17 +312,11 @@ freesurfer/bin/mri_aseg_edit_train freesurfer/bin/mri_auto_fill freesurfer/bin/mri_average freesurfer/bin/mri_bc_sc_bias_correct -freesurfer/bin/mri_binarize freesurfer/bin/mri_brain_volume -freesurfer/bin/mri_brainvol_stats freesurfer/bin/mri_build_priors -freesurfer/bin/mri_ca_label -freesurfer/bin/mri_ca_normalize -freesurfer/bin/mri_ca_register freesurfer/bin/mri_ca_tissue_parms freesurfer/bin/mri_ca_train freesurfer/bin/mri_cal_renormalize_gca -freesurfer/bin/mri_cc freesurfer/bin/mri_cht2p freesurfer/bin/mri_classify freesurfer/bin/mri_cnr @@ -7763,15 +325,10 @@ freesurfer/bin/mri_compute_bias freesurfer/bin/mri_compute_change_map freesurfer/bin/mri_compute_distances freesurfer/bin/mri_compute_layer_fractions -freesurfer/bin/mri_compute_overlap -freesurfer/bin/mri_compute_seg_overlap freesurfer/bin/mri_compute_structure_transforms freesurfer/bin/mri_compute_volume_fractions freesurfer/bin/mri_compute_volume_intensities -freesurfer/bin/mri_concat freesurfer/bin/mri_concatenate_gcam -freesurfer/bin/mri_concatenate_lta -freesurfer/bin/mri_convert freesurfer/bin/mri_convert_mdh freesurfer/bin/mri_copy_params freesurfer/bin/mri_copy_values @@ -7787,15 +344,12 @@ freesurfer/bin/mri_cvs_requiredfiles.txt freesurfer/bin/mri_dct_align freesurfer/bin/mri_dct_align_binary freesurfer/bin/mri_deface -freesurfer/bin/mri_diff freesurfer/bin/mri_dist_surf_label freesurfer/bin/mri_distance_transform freesurfer/bin/mri_divide_segmentation freesurfer/bin/mri_edit_segmentation freesurfer/bin/mri_edit_segmentation_with_surfaces -freesurfer/bin/mri_edit_wm_with_aseg freesurfer/bin/mri_elastic_energy -freesurfer/bin/mri_em_register freesurfer/bin/mri_estimate_tissue_parms freesurfer/bin/mri_evaluate_morph freesurfer/bin/mri_extract @@ -7806,15 +360,11 @@ freesurfer/bin/mri_extract_largest_CC freesurfer/bin/mri_fcili freesurfer/bin/mri_fdr freesurfer/bin/mri_fieldsign -freesurfer/bin/mri_fill freesurfer/bin/mri_fit_bias freesurfer/bin/mri_fslmat_to_lta freesurfer/bin/mri_fuse_intensity_images -freesurfer/bin/mri_fuse_segmentations -freesurfer/bin/mri_fwhm freesurfer/bin/mri_gca_ambiguous freesurfer/bin/mri_gcab_train -freesurfer/bin/mri_gcut freesurfer/bin/mri_gdfglm freesurfer/bin/mri_glmfit freesurfer/bin/mri_glmfit-sim @@ -7827,12 +377,9 @@ freesurfer/bin/mri_hires_register freesurfer/bin/mri_histo_eq freesurfer/bin/mri_histo_normalize freesurfer/bin/mri_ibmc -freesurfer/bin/mri_info freesurfer/bin/mri_interpolate freesurfer/bin/mri_jacobian freesurfer/bin/mri_joint_density -freesurfer/bin/mri_label2label -freesurfer/bin/mri_label2vol freesurfer/bin/mri_label_accuracy freesurfer/bin/mri_label_histo freesurfer/bin/mri_label_vals @@ -7840,19 +387,15 @@ freesurfer/bin/mri_label_volume freesurfer/bin/mri_linear_align freesurfer/bin/mri_linear_align_binary freesurfer/bin/mri_linear_register -freesurfer/bin/mri_log_likelihood freesurfer/bin/mri_long_normalize freesurfer/bin/mri_make_bem_surfaces freesurfer/bin/mri_make_density_map freesurfer/bin/mri_make_labels freesurfer/bin/mri_make_register freesurfer/bin/mri_make_template -freesurfer/bin/mri_make_uchar freesurfer/bin/mri_map_cpdat freesurfer/bin/mri_maps2csd freesurfer/bin/mri_mark_temporal_lobe -freesurfer/bin/mri_mask -freesurfer/bin/mri_matrix_multiply freesurfer/bin/mri_mc freesurfer/bin/mri_mcsim freesurfer/bin/mri_mergelabels @@ -7861,7 +404,6 @@ freesurfer/bin/mri_modify freesurfer/bin/mri_morphology freesurfer/bin/mri_mosaic freesurfer/bin/mri_motion_correct -freesurfer/bin/mri_motion_correct.fsl freesurfer/bin/mri_motion_correct2 freesurfer/bin/mri_ms_EM freesurfer/bin/mri_ms_EM_with_atlas @@ -7872,25 +414,17 @@ freesurfer/bin/mri_multispectral_segment freesurfer/bin/mri_nl_align freesurfer/bin/mri_nl_align_binary freesurfer/bin/mri_nlfilter -freesurfer/bin/mri_normalize -freesurfer/bin/mri_normalize_tp2 -freesurfer/bin/mri_nu_correct.mni -freesurfer/bin/mri_or freesurfer/bin/mri_paint freesurfer/bin/mri_parse_sdcmdir freesurfer/bin/mri_parselabel freesurfer/bin/mri_partial_ribbon freesurfer/bin/mri_path2label freesurfer/bin/mri_polv -freesurfer/bin/mri_pretess freesurfer/bin/mri_probe_ima freesurfer/bin/mri_probedicom freesurfer/bin/mri_reduce freesurfer/bin/mri_refine_seg freesurfer/bin/mri_register -freesurfer/bin/mri_relabel_hypointensities -freesurfer/bin/mri_relabel_nonwm_hypos -freesurfer/bin/mri_remove_neck freesurfer/bin/mri_reorient_LR.csh freesurfer/bin/mri_rf_label freesurfer/bin/mri_rf_long_label @@ -7898,31 +432,21 @@ freesurfer/bin/mri_rf_long_train freesurfer/bin/mri_rf_train freesurfer/bin/mri_ribbon freesurfer/bin/mri_rigid_register -freesurfer/bin/mri_robust_register -freesurfer/bin/mri_robust_template freesurfer/bin/mri_sbbr freesurfer/bin/mri_seg_diff freesurfer/bin/mri_seg_overlap freesurfer/bin/mri_segcentroids freesurfer/bin/mri_seghead -freesurfer/bin/mri_segment freesurfer/bin/mri_segment_hypothalamic_subunits freesurfer/bin/mri_segment_tumor freesurfer/bin/mri_segment_wm_damage freesurfer/bin/mri_segreg -freesurfer/bin/mri_segstats freesurfer/bin/mri_simulate_atrophy -freesurfer/bin/mri_stats2seg freesurfer/bin/mri_strip_nonwhite freesurfer/bin/mri_strip_subject_info -freesurfer/bin/mri_surf2surf -freesurfer/bin/mri_surf2vol -freesurfer/bin/mri_surf2volseg freesurfer/bin/mri_surfacemask -freesurfer/bin/mri_surfcluster freesurfer/bin/mri_synth_strip freesurfer/bin/mri_synthesize -freesurfer/bin/mri_tessellate freesurfer/bin/mri_threshold freesurfer/bin/mri_topologycorrection freesurfer/bin/mri_train @@ -7935,13 +459,9 @@ freesurfer/bin/mri_validate_skull_stripped freesurfer/bin/mri_vessel_segment freesurfer/bin/mri_vol2label freesurfer/bin/mri_vol2roi -freesurfer/bin/mri_vol2surf -freesurfer/bin/mri_vol2vol freesurfer/bin/mri_volcluster -freesurfer/bin/mri_voldiff freesurfer/bin/mri_volsynth freesurfer/bin/mri_warp_convert -freesurfer/bin/mri_watershed freesurfer/bin/mri_wbc freesurfer/bin/mri_wmfilter freesurfer/bin/mri_xcorr @@ -7951,18 +471,14 @@ freesurfer/bin/mris2rgb freesurfer/bin/mris_AA_shrinkwrap freesurfer/bin/mris_BA_segment freesurfer/bin/mris_add_template -freesurfer/bin/mris_anatomical_stats freesurfer/bin/mris_annot_diff freesurfer/bin/mris_annot_to_segmentation freesurfer/bin/mris_apply_reg freesurfer/bin/mris_aseg_distance -freesurfer/bin/mris_autodet_gwstats freesurfer/bin/mris_average_curvature freesurfer/bin/mris_average_parcellation freesurfer/bin/mris_ca_deform -freesurfer/bin/mris_ca_label freesurfer/bin/mris_ca_train -freesurfer/bin/mris_calc freesurfer/bin/mris_classify_thickness freesurfer/bin/mris_compute_acorr freesurfer/bin/mris_compute_layer_intensities @@ -7972,47 +488,34 @@ freesurfer/bin/mris_compute_overlap freesurfer/bin/mris_compute_parc_overlap freesurfer/bin/mris_compute_volume_fractions freesurfer/bin/mris_congeal -freesurfer/bin/mris_convert freesurfer/bin/mris_copy_header -freesurfer/bin/mris_curvature freesurfer/bin/mris_curvature2image -freesurfer/bin/mris_curvature_stats -freesurfer/bin/mris_defects_pointset freesurfer/bin/mris_deform freesurfer/bin/mris_density -freesurfer/bin/mris_diff freesurfer/bin/mris_distance_map freesurfer/bin/mris_distance_to_label freesurfer/bin/mris_distance_transform -freesurfer/bin/mris_divide_parcellation freesurfer/bin/mris_entropy freesurfer/bin/mris_errors -freesurfer/bin/mris_euler_number freesurfer/bin/mris_expand -freesurfer/bin/mris_extract_main_component freesurfer/bin/mris_extract_patches freesurfer/bin/mris_extract_values freesurfer/bin/mris_exvivo_surfaces freesurfer/bin/mris_fbirn_annot freesurfer/bin/mris_fill freesurfer/bin/mris_find_flat_regions -freesurfer/bin/mris_fix_topology freesurfer/bin/mris_flatten freesurfer/bin/mris_fwhm freesurfer/bin/mris_gradient freesurfer/bin/mris_hausdorff_dist freesurfer/bin/mris_image2vtk -freesurfer/bin/mris_inflate freesurfer/bin/mris_info freesurfer/bin/mris_init_global_tractography freesurfer/bin/mris_intensity_profile freesurfer/bin/mris_interpolate_warp -freesurfer/bin/mris_jacobian -freesurfer/bin/mris_label2annot freesurfer/bin/mris_label_area freesurfer/bin/mris_label_calc freesurfer/bin/mris_label_mode -freesurfer/bin/mris_left_right_register freesurfer/bin/mris_longitudinal_surfaces freesurfer/bin/mris_make_average_surface freesurfer/bin/mris_make_face_parcellation @@ -8032,17 +535,13 @@ freesurfer/bin/mris_multiscale_stats freesurfer/bin/mris_niters2fwhm freesurfer/bin/mris_nudge freesurfer/bin/mris_parcellate_connectivity -freesurfer/bin/mris_place_surface freesurfer/bin/mris_pmake freesurfer/bin/mris_preproc freesurfer/bin/mris_profileClustering freesurfer/bin/mris_refine_surfaces -freesurfer/bin/mris_register freesurfer/bin/mris_register_label_map freesurfer/bin/mris_register_to_label freesurfer/bin/mris_register_to_volume -freesurfer/bin/mris_remesh -freesurfer/bin/mris_remove_intersection freesurfer/bin/mris_remove_negative_vertices freesurfer/bin/mris_remove_variance freesurfer/bin/mris_reposition_surface @@ -8060,26 +559,19 @@ freesurfer/bin/mris_segment_vals freesurfer/bin/mris_segmentation_stats freesurfer/bin/mris_shrinkwrap freesurfer/bin/mris_simulate_atrophy -freesurfer/bin/mris_smooth freesurfer/bin/mris_smooth_intracortical -freesurfer/bin/mris_sphere freesurfer/bin/mris_spherical_average freesurfer/bin/mris_surf2vtk freesurfer/bin/mris_surface_change -freesurfer/bin/mris_surface_stats freesurfer/bin/mris_surface_to_vol_distances freesurfer/bin/mris_svm_classify freesurfer/bin/mris_svm_train freesurfer/bin/mris_talairach -freesurfer/bin/mris_thickness freesurfer/bin/mris_thickness_comparison -freesurfer/bin/mris_thickness_diff -freesurfer/bin/mris_topo_fixer freesurfer/bin/mris_transform freesurfer/bin/mris_translate_annotation freesurfer/bin/mris_transmantle_dysplasia_paths freesurfer/bin/mris_twoclass -freesurfer/bin/mris_volmask freesurfer/bin/mris_volmask_novtk freesurfer/bin/mris_volmask_vtk freesurfer/bin/mris_volsmooth @@ -8088,7 +580,6 @@ freesurfer/bin/mris_w_to_curv freesurfer/bin/mris_warp freesurfer/bin/mris_watershed freesurfer/bin/mris_wm_volume -freesurfer/bin/mrisp_paint freesurfer/bin/mrisp_write freesurfer/bin/ms_refine_subject freesurfer/bin/nmovie_qt @@ -8098,7 +589,6 @@ freesurfer/bin/oct_train freesurfer/bin/optseq2 freesurfer/bin/orientLAS freesurfer/bin/parc_atlas_jackknife_test -freesurfer/bin/pctsurfcon freesurfer/bin/plot_structure_stats.tcl freesurfer/bin/polyorder freesurfer/bin/predict_v1.sh @@ -8113,15 +603,11 @@ freesurfer/bin/quantifyThalamicNuclei.sh freesurfer/bin/rbbr freesurfer/bin/rbftest freesurfer/bin/rca-base-init -freesurfer/bin/rca-config -freesurfer/bin/rca-config2csh freesurfer/bin/rca-long-tp-init freesurfer/bin/rcbf-prep freesurfer/bin/rebuild_gca_atlas.csh -freesurfer/bin/recon-all freesurfer/bin/recon-all-exvivo freesurfer/bin/recon-all.makefile -freesurfer/bin/reconbatchjobs freesurfer/bin/reg-feat2anat freesurfer/bin/reg-mni305.2mm freesurfer/bin/reg2subject @@ -8203,8 +689,6 @@ freesurfer/bin/tal_QC_AZS freesurfer/bin/tal_compare freesurfer/bin/talairach freesurfer/bin/talairach2 -freesurfer/bin/talairach_afd -freesurfer/bin/talairach_avi freesurfer/bin/talairach_mgh freesurfer/bin/talsegprob freesurfer/bin/template @@ -8215,7 +699,6 @@ freesurfer/bin/thickdiffmap freesurfer/bin/tkmedit freesurfer/bin/tkmeditfv freesurfer/bin/tkregister2 -freesurfer/bin/tkregister2_cmdl freesurfer/bin/tkregisterfv freesurfer/bin/tksurfer freesurfer/bin/tksurferfv @@ -8234,7 +717,6 @@ freesurfer/bin/unpackimadir2 freesurfer/bin/unpackmincdir freesurfer/bin/unpacksdcmdir freesurfer/bin/usbtree -freesurfer/bin/vertexvol freesurfer/bin/vno_match_check freesurfer/bin/vol2segavg freesurfer/bin/vol2subfield @@ -8253,14 +735,10 @@ freesurfer/bin/xsanatreg freesurfer/bin/zero_lt_4dfp freesurfer/bin/3dvolreg.afni freesurfer/bin/4dfptoanalyze -freesurfer/bin/AntsDenoiseImageFs -freesurfer/bin/AntsN4BiasFieldCorrectionFs freesurfer/bin/IsLTA freesurfer/bin/SegmentSubfieldsT1Longitudinal freesurfer/bin/SegmentThalamicNuclei freesurfer/bin/Spline3_test -freesurfer/bin/UpdateNeeded -freesurfer/bin/analyzeto4dfp freesurfer/bin/anatomiCutsUtils freesurfer/bin/annot2std freesurfer/bin/aparc2feat @@ -8272,7 +750,6 @@ freesurfer/bin/applyMorph freesurfer/bin/aseg2feat freesurfer/bin/asegstats2table freesurfer/bin/asegstatsdiff -freesurfer/bin/avi2talxfm freesurfer/bin/bblabel freesurfer/bin/bbmask freesurfer/bin/bbregister @@ -8296,2571 +773,23 @@ freesurfer/bin/compute_interrater_variability.csh freesurfer/bin/compute_label_vals.csh freesurfer/bin/qdec freesurfer/diffusion -freesurfer/diffusion/mgh-dti-seqpack -freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti12.gdt -freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti13.gdt -freesurfer/diffusion/mgh-dti-seqpack/gradient_mgh_dti14.gdt 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freesurfer/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot freesurfer/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz @@ -49130,12 +1460,6 @@ freesurfer/subjects/fsaverage/label/lh.aparc.a2009s.annot freesurfer/subjects/fsaverage/label/lh.aparc.annot freesurfer/subjects/fsaverage/label/lh.aparc.label freesurfer/subjects/fsaverage/label/lh.cortex.label -freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.label -freesurfer/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label -freesurfer/subjects/fsaverage/label/lh.hOc1.mpm.vpnl.label -freesurfer/subjects/fsaverage/label/lh.hOc2.mpm.vpnl.label -freesurfer/subjects/fsaverage/label/lh.hOc3v.mpm.vpnl.label -freesurfer/subjects/fsaverage/label/lh.hOc4v.mpm.vpnl.label freesurfer/subjects/fsaverage/label/lh.high-myelin.label freesurfer/subjects/fsaverage/label/lh.oasis.chubs.annot freesurfer/subjects/fsaverage/label/lh.oasis.chubs.ifc.label @@ -49146,42 +1470,12 @@ freesurfer/subjects/fsaverage/label/lh.oasis.chubs.medialpfc.label freesurfer/subjects/fsaverage/label/lh.oasis.chubs.mtl.label freesurfer/subjects/fsaverage/label/lh.oasis.chubs.retrosplenial.label freesurfer/subjects/fsaverage/label/lh.oasis.chubs.tp.label -freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.label -freesurfer/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label -freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.label -freesurfer/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label -freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.label -freesurfer/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label -freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.label -freesurfer/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label -freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.label -freesurfer/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label -freesurfer/subjects/fsaverage/label/rh.BA44_exvivo.label 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freesurfer/subjects/fsaverage/label/rh.PALS_B12.labels.gii freesurfer/subjects/fsaverage/label/rh.PALS_B12_Brodmann.annot freesurfer/subjects/fsaverage/label/rh.PALS_B12_Lobes.annot freesurfer/subjects/fsaverage/label/rh.PALS_B12_OrbitoFrontal.annot freesurfer/subjects/fsaverage/label/rh.PALS_B12_Visuotopic.annot -freesurfer/subjects/fsaverage/label/rh.V1_exvivo.label -freesurfer/subjects/fsaverage/label/rh.V1_exvivo.thresh.label -freesurfer/subjects/fsaverage/label/rh.V2_exvivo.label -freesurfer/subjects/fsaverage/label/rh.V2_exvivo.thresh.label freesurfer/subjects/fsaverage/label/rh.Yeo2011_17NetworksConfidence_N1000.mgz freesurfer/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot freesurfer/subjects/fsaverage/label/rh.Yeo2011_7NetworksConfidence_N1000.mgz @@ -49200,12 +1494,6 @@ freesurfer/subjects/fsaverage/label/rh.aparc.a2009s.annot freesurfer/subjects/fsaverage/label/rh.aparc.annot freesurfer/subjects/fsaverage/label/rh.aparc.label freesurfer/subjects/fsaverage/label/rh.cortex.label -freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.label -freesurfer/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label -freesurfer/subjects/fsaverage/label/rh.hOc1.mpm.vpnl.label -freesurfer/subjects/fsaverage/label/rh.hOc2.mpm.vpnl.label -freesurfer/subjects/fsaverage/label/rh.hOc3v.mpm.vpnl.label -freesurfer/subjects/fsaverage/label/rh.hOc4v.mpm.vpnl.label freesurfer/subjects/fsaverage/label/rh.high-myelin.label freesurfer/subjects/fsaverage/label/rh.oasis.chubs.annot freesurfer/subjects/fsaverage/label/rh.oasis.chubs.ifc.label @@ -49216,15 +1504,10 @@ freesurfer/subjects/fsaverage/label/rh.oasis.chubs.medialpfc.label freesurfer/subjects/fsaverage/label/rh.oasis.chubs.mtl.label freesurfer/subjects/fsaverage/label/rh.oasis.chubs.retrosplenial.label freesurfer/subjects/fsaverage/label/rh.oasis.chubs.tp.label -freesurfer/subjects/fsaverage/label/rh.perirhinal_exvivo.label 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freesurfer/SegmentNoLUT.txt freesurfer/SetUpFreeSurfer.csh freesurfer/SetUpFreeSurfer.sh freesurfer/Simple_surface_labels2009.txt -freesurfer/SubCorticalMassLUT.txt -freesurfer/WMParcStatsLUT.txt -freesurfer/build-stamp.txt -freesurfer/sources.csh freesurfer/sources.sh -freesurfer/tkmeditParcColorsCMA +freesurfer/tkmeditParcColorsCMA \ No newline at end of file From ce036fee9f3b76e2c6fefc4bb5a41741bbc38755 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 22 Sep 2021 10:22:32 -0400 Subject: [PATCH 3/9] DOCKER: Preserve fsaverage{,5,6}, mris_expand --- docker/files/freesurfer7.2-exclude.txt | 157 +------------------------ 1 file changed, 1 insertion(+), 156 deletions(-) diff --git a/docker/files/freesurfer7.2-exclude.txt b/docker/files/freesurfer7.2-exclude.txt index d9069de74..bda6bc10c 100644 --- a/docker/files/freesurfer7.2-exclude.txt +++ b/docker/files/freesurfer7.2-exclude.txt @@ -497,7 +497,6 @@ freesurfer/bin/mris_distance_to_label freesurfer/bin/mris_distance_transform freesurfer/bin/mris_entropy freesurfer/bin/mris_errors -freesurfer/bin/mris_expand freesurfer/bin/mris_extract_patches freesurfer/bin/mris_extract_values freesurfer/bin/mris_exvivo_surfaces @@ -1436,162 +1435,8 @@ freesurfer/subjects/V1_average freesurfer/subjects/bert freesurfer/subjects/cvs_avg35 freesurfer/subjects/cvs_avg35_inMNI152 -freesurfer/subjects/fsaverage/label/lh.Medial_wall.label 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-freesurfer/subjects/fsaverage/mri/T1.mgz -freesurfer/subjects/fsaverage/mri/aparc+aseg.mgz -freesurfer/subjects/fsaverage/mri/aparc.a2005s+aseg.mgz -freesurfer/subjects/fsaverage/mri/aparc.a2009s+aseg.mgz -freesurfer/subjects/fsaverage/mri/aseg.mgz -freesurfer/subjects/fsaverage/mri/brain.mgz -freesurfer/subjects/fsaverage/mri/brainmask.mgz -freesurfer/subjects/fsaverage/mri/lh.ribbon.mgz -freesurfer/subjects/fsaverage/mri/mni305.cor.mgz -freesurfer/subjects/fsaverage/mri/orig.mgz -freesurfer/subjects/fsaverage/mri/p.aseg.mgz -freesurfer/subjects/fsaverage/mri/rh.ribbon.mgz -freesurfer/subjects/fsaverage/mri/ribbon.mgz -freesurfer/subjects/fsaverage/mri/subcort.mask.1mm.README -freesurfer/subjects/fsaverage/mri/subcort.mask.1mm.mgz -freesurfer/subjects/fsaverage/mri/subcort.prob.log -freesurfer/subjects/fsaverage/mri/subcort.prob.mgz -freesurfer/subjects/fsaverage/mri.2mm -freesurfer/subjects/fsaverage/scripts -freesurfer/subjects/fsaverage/surf/lh.orig_avg -freesurfer/subjects/fsaverage/surf/lh.pial -freesurfer/subjects/fsaverage/surf/lh.pial.avg.area.mgh -freesurfer/subjects/fsaverage/surf/lh.pial_avg -freesurfer/subjects/fsaverage/surf/lh.pial_semi_inflated -freesurfer/subjects/fsaverage/surf/lh.smoothwm -freesurfer/subjects/fsaverage/surf/lh.sphere -freesurfer/subjects/fsaverage/surf/lh.sphere.reg.avg -freesurfer/subjects/fsaverage/surf/lh.sulc -freesurfer/subjects/fsaverage/surf/lh.thickness -freesurfer/subjects/fsaverage/surf/lh.white.avg.area.mgh -freesurfer/subjects/fsaverage/surf/lh.white_avg -freesurfer/subjects/fsaverage/surf/lh.white_avg.H -freesurfer/subjects/fsaverage/surf/lh.white_avg.K -freesurfer/subjects/fsaverage/surf/mris_preproc.surface.lh.log -freesurfer/subjects/fsaverage/surf/mris_preproc.surface.rh.log -freesurfer/subjects/fsaverage/surf/rh.area -freesurfer/subjects/fsaverage/surf/rh.avg_curv -freesurfer/subjects/fsaverage/surf/rh.avg_sulc -freesurfer/subjects/fsaverage/surf/rh.avg_thickness -freesurfer/subjects/fsaverage/surf/rh.cortex.patch.3d -freesurfer/subjects/fsaverage/surf/rh.cortex.patch.flat -freesurfer/subjects/fsaverage/surf/rh.curv -freesurfer/subjects/fsaverage/surf/rh.fsaverage_sym.sphere.reg -freesurfer/subjects/fsaverage/surf/rh.inflated -freesurfer/subjects/fsaverage/surf/rh.inflated.H -freesurfer/subjects/fsaverage/surf/rh.inflated.K -freesurfer/subjects/fsaverage/surf/rh.inflated_avg -freesurfer/subjects/fsaverage/surf/rh.inflated_pre -freesurfer/subjects/fsaverage/surf/rh.orig -freesurfer/subjects/fsaverage/surf/rh.orig.avg.area.mgh -freesurfer/subjects/fsaverage/surf/rh.orig_avg -freesurfer/subjects/fsaverage/surf/rh.pial -freesurfer/subjects/fsaverage/surf/rh.pial.avg.area.mgh -freesurfer/subjects/fsaverage/surf/rh.pial_avg -freesurfer/subjects/fsaverage/surf/rh.pial_semi_inflated -freesurfer/subjects/fsaverage/surf/rh.smoothwm -freesurfer/subjects/fsaverage/surf/rh.sphere -freesurfer/subjects/fsaverage/surf/rh.sphere.reg.avg -freesurfer/subjects/fsaverage/surf/rh.sulc -freesurfer/subjects/fsaverage/surf/rh.thickness -freesurfer/subjects/fsaverage/surf/rh.white.avg.area.mgh -freesurfer/subjects/fsaverage/surf/rh.white_avg -freesurfer/subjects/fsaverage/surf/rh.white_avg.H -freesurfer/subjects/fsaverage/surf/rh.white_avg.K -freesurfer/subjects/fsaverage/surf/lh.area -freesurfer/subjects/fsaverage/surf/lh.avg_curv -freesurfer/subjects/fsaverage/surf/lh.avg_sulc -freesurfer/subjects/fsaverage/surf/lh.avg_thickness -freesurfer/subjects/fsaverage/surf/lh.cortex.patch.3d -freesurfer/subjects/fsaverage/surf/lh.cortex.patch.flat -freesurfer/subjects/fsaverage/surf/lh.curv -freesurfer/subjects/fsaverage/surf/lh.fsaverage_sym.sphere.reg -freesurfer/subjects/fsaverage/surf/lh.inflated -freesurfer/subjects/fsaverage/surf/lh.inflated.H -freesurfer/subjects/fsaverage/surf/lh.inflated.K -freesurfer/subjects/fsaverage/surf/lh.inflated_avg -freesurfer/subjects/fsaverage/surf/lh.inflated_pre -freesurfer/subjects/fsaverage/surf/lh.orig -freesurfer/subjects/fsaverage/surf/lh.orig.avg.area.mgh -freesurfer/subjects/fsaverage/xhemi freesurfer/subjects/fsaverage3 freesurfer/subjects/fsaverage4 -freesurfer/subjects/fsaverage5 -freesurfer/subjects/fsaverage6 freesurfer/subjects/fsaverage_sym freesurfer/subjects/lh.EC_average freesurfer/subjects/rh.EC_average @@ -1608,4 +1453,4 @@ freesurfer/SetUpFreeSurfer.csh freesurfer/SetUpFreeSurfer.sh freesurfer/Simple_surface_labels2009.txt freesurfer/sources.sh -freesurfer/tkmeditParcColorsCMA \ No newline at end of file +freesurfer/tkmeditParcColorsCMA From a9f710315f2db809d9c63d38615b92c84e680666 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 22 Sep 2021 10:27:15 -0400 Subject: [PATCH 4/9] DOCKER: Keep licenses in docs/ directory --- docker/files/freesurfer7.2-exclude.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/files/freesurfer7.2-exclude.txt b/docker/files/freesurfer7.2-exclude.txt index bda6bc10c..13c2604ea 100644 --- a/docker/files/freesurfer7.2-exclude.txt +++ b/docker/files/freesurfer7.2-exclude.txt @@ -772,7 +772,7 @@ freesurfer/bin/compute_interrater_variability.csh freesurfer/bin/compute_label_vals.csh freesurfer/bin/qdec freesurfer/diffusion -freesurfer/docs +freesurfer/docs/xml freesurfer/fsfast freesurfer/lib/bem/ic0.tri freesurfer/lib/bem/ic1.tri From 0fc360183b3972d4e45480527cfe80c48f985283 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 22 Sep 2021 13:32:25 -0400 Subject: [PATCH 5/9] DOCKER: Preserve bbregister and subcommands --- docker/files/freesurfer7.2-exclude.txt | 5 ----- 1 file changed, 5 deletions(-) diff --git a/docker/files/freesurfer7.2-exclude.txt b/docker/files/freesurfer7.2-exclude.txt index 13c2604ea..3f9cf42f6 100644 --- a/docker/files/freesurfer7.2-exclude.txt +++ b/docker/files/freesurfer7.2-exclude.txt @@ -333,7 +333,6 @@ freesurfer/bin/mri_convert_mdh freesurfer/bin/mri_copy_params freesurfer/bin/mri_copy_values freesurfer/bin/mri_cor2label -freesurfer/bin/mri_coreg freesurfer/bin/mri_correct_segmentations freesurfer/bin/mri_create_t2combined freesurfer/bin/mri_create_tests @@ -440,7 +439,6 @@ freesurfer/bin/mri_seghead freesurfer/bin/mri_segment_hypothalamic_subunits freesurfer/bin/mri_segment_tumor freesurfer/bin/mri_segment_wm_damage -freesurfer/bin/mri_segreg freesurfer/bin/mri_simulate_atrophy freesurfer/bin/mri_strip_nonwhite freesurfer/bin/mri_strip_subject_info @@ -609,7 +607,6 @@ freesurfer/bin/recon-all-exvivo freesurfer/bin/recon-all.makefile freesurfer/bin/reg-feat2anat freesurfer/bin/reg-mni305.2mm -freesurfer/bin/reg2subject freesurfer/bin/regdat2xfm freesurfer/bin/register.csh freesurfer/bin/register_child @@ -734,7 +731,6 @@ freesurfer/bin/xsanatreg freesurfer/bin/zero_lt_4dfp freesurfer/bin/3dvolreg.afni freesurfer/bin/4dfptoanalyze -freesurfer/bin/IsLTA freesurfer/bin/SegmentSubfieldsT1Longitudinal freesurfer/bin/SegmentThalamicNuclei freesurfer/bin/Spline3_test @@ -751,7 +747,6 @@ freesurfer/bin/asegstats2table freesurfer/bin/asegstatsdiff freesurfer/bin/bblabel freesurfer/bin/bbmask -freesurfer/bin/bbregister freesurfer/bin/bedpostx_mgh freesurfer/bin/bet.fsl freesurfer/bin/beta2sxa From aafda62359e0b683717d333cf2a853e4d4ee7dfc Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Tue, 17 May 2022 14:31:04 -0400 Subject: [PATCH 6/9] DOCKER: Bundle FreeSurfer 7.2.0 --- Dockerfile | 25 ++++--------------------- 1 file changed, 4 insertions(+), 21 deletions(-) diff --git a/Dockerfile b/Dockerfile index 889185cb2..8ffe43594 100644 --- a/Dockerfile +++ b/Dockerfile @@ -48,26 +48,9 @@ ENV DEBIAN_FRONTEND="noninteractive" \ LC_ALL="en_US.UTF-8" # Installing freesurfer -RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz \ - | tar zxv --no-same-owner -C /opt \ - --exclude='freesurfer/diffusion' \ - --exclude='freesurfer/docs' \ - --exclude='freesurfer/fsfast' \ - --exclude='freesurfer/lib/cuda' \ - --exclude='freesurfer/lib/qt' \ - --exclude='freesurfer/matlab' \ - --exclude='freesurfer/mni/share/man' \ - --exclude='freesurfer/subjects/fsaverage_sym' \ - --exclude='freesurfer/subjects/fsaverage3' \ - --exclude='freesurfer/subjects/fsaverage4' \ - --exclude='freesurfer/subjects/cvs_avg35' \ - --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \ - --exclude='freesurfer/subjects/bert' \ - --exclude='freesurfer/subjects/lh.EC_average' \ - --exclude='freesurfer/subjects/rh.EC_average' \ - --exclude='freesurfer/subjects/sample-*.mgz' \ - --exclude='freesurfer/subjects/V1_average' \ - --exclude='freesurfer/trctrain' +COPY docker/files/freesurfer7.2-exclude.txt /usr/local/etc/freesurfer7.2-exclude.txt +RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz \ + | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.2-exclude.txt # Simulate SetUpFreeSurfer.sh ENV FSL_DIR="/opt/fsl-6.0.5.1" \ @@ -85,7 +68,7 @@ ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \ MNI_DATAPATH="$FREESURFER_HOME/mni/data" ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \ MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \ - PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH" + PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH" # FSL 6.0.5.1 RUN apt-get update -qq \ From c6e3d28a69df9197aeea73a03c0dc3cc51579a87 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Wed, 18 May 2022 08:41:00 -0400 Subject: [PATCH 7/9] DOCKER: Restore tools needed by recon-all --- docker/files/freesurfer7.2-exclude.txt | 571 +------------------------ 1 file changed, 1 insertion(+), 570 deletions(-) diff --git a/docker/files/freesurfer7.2-exclude.txt b/docker/files/freesurfer7.2-exclude.txt index 3f9cf42f6..f83bf1d5f 100644 --- a/docker/files/freesurfer7.2-exclude.txt +++ b/docker/files/freesurfer7.2-exclude.txt @@ -259,7 +259,6 @@ freesurfer/bin/long_submit_postproc freesurfer/bin/longmc freesurfer/bin/lpcregister freesurfer/bin/lta_diff -freesurfer/bin/conf2hires freesurfer/bin/make-segvol-table freesurfer/bin/make_average_subcort freesurfer/bin/make_average_subject @@ -301,7 +300,6 @@ freesurfer/bin/morph_tables-rh freesurfer/bin/mri-func2sph freesurfer/bin/mri-funcvits freesurfer/bin/mri-sph2surf -freesurfer/bin/mri_add_new_tp freesurfer/bin/mri_align_long.csh freesurfer/bin/mri_aparc2wmseg freesurfer/bin/mri_apply_autoencoder @@ -320,7 +318,6 @@ freesurfer/bin/mri_cal_renormalize_gca freesurfer/bin/mri_cht2p freesurfer/bin/mri_classify freesurfer/bin/mri_cnr -freesurfer/bin/mri_compile_edits freesurfer/bin/mri_compute_bias freesurfer/bin/mri_compute_change_map freesurfer/bin/mri_compute_distances @@ -342,7 +339,6 @@ freesurfer/bin/mri_cvs_register freesurfer/bin/mri_cvs_requiredfiles.txt freesurfer/bin/mri_dct_align freesurfer/bin/mri_dct_align_binary -freesurfer/bin/mri_deface freesurfer/bin/mri_dist_surf_label freesurfer/bin/mri_distance_transform freesurfer/bin/mri_divide_segmentation @@ -432,7 +428,6 @@ freesurfer/bin/mri_rf_train freesurfer/bin/mri_ribbon freesurfer/bin/mri_rigid_register freesurfer/bin/mri_sbbr -freesurfer/bin/mri_seg_diff freesurfer/bin/mri_seg_overlap freesurfer/bin/mri_segcentroids freesurfer/bin/mri_seghead @@ -471,7 +466,6 @@ freesurfer/bin/mris_BA_segment freesurfer/bin/mris_add_template freesurfer/bin/mris_annot_diff freesurfer/bin/mris_annot_to_segmentation -freesurfer/bin/mris_apply_reg freesurfer/bin/mris_aseg_distance freesurfer/bin/mris_average_curvature freesurfer/bin/mris_average_parcellation @@ -541,7 +535,6 @@ freesurfer/bin/mris_register_to_label freesurfer/bin/mris_register_to_volume freesurfer/bin/mris_remove_negative_vertices freesurfer/bin/mris_remove_variance -freesurfer/bin/mris_reposition_surface freesurfer/bin/mris_resample freesurfer/bin/mris_rescale freesurfer/bin/mris_reverse @@ -557,7 +550,6 @@ freesurfer/bin/mris_segmentation_stats freesurfer/bin/mris_shrinkwrap freesurfer/bin/mris_simulate_atrophy freesurfer/bin/mris_smooth_intracortical -freesurfer/bin/mris_spherical_average freesurfer/bin/mris_surf2vtk freesurfer/bin/mris_surface_change freesurfer/bin/mris_surface_to_vol_distances @@ -575,7 +567,6 @@ freesurfer/bin/mris_volsmooth freesurfer/bin/mris_volume freesurfer/bin/mris_w_to_curv freesurfer/bin/mris_warp -freesurfer/bin/mris_watershed freesurfer/bin/mris_wm_volume freesurfer/bin/mrisp_write freesurfer/bin/ms_refine_subject @@ -599,8 +590,6 @@ freesurfer/bin/quantifyHAsubregions.sh freesurfer/bin/quantifyThalamicNuclei.sh freesurfer/bin/rbbr freesurfer/bin/rbftest -freesurfer/bin/rca-base-init -freesurfer/bin/rca-long-tp-init freesurfer/bin/rcbf-prep freesurfer/bin/rebuild_gca_atlas.csh freesurfer/bin/recon-all-exvivo @@ -629,7 +618,6 @@ freesurfer/bin/run_SegmentSubfieldsT1Longitudinal.sh freesurfer/bin/run_SegmentSubject.sh freesurfer/bin/run_SegmentThalamicNuclei.sh freesurfer/bin/run_mris_preproc -freesurfer/bin/run_samseg freesurfer/bin/run_samseg_long freesurfer/bin/run_segmentSubjectT1T2_autoEstimateAlveusML.sh freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh @@ -683,7 +671,6 @@ freesurfer/bin/t4img_4dfp freesurfer/bin/t4imgs_4dfp freesurfer/bin/tal_QC_AZS freesurfer/bin/tal_compare -freesurfer/bin/talairach freesurfer/bin/talairach2 freesurfer/bin/talairach_mgh freesurfer/bin/talsegprob @@ -713,7 +700,6 @@ freesurfer/bin/unpackimadir2 freesurfer/bin/unpackmincdir freesurfer/bin/unpacksdcmdir freesurfer/bin/usbtree -freesurfer/bin/vno_match_check freesurfer/bin/vol2segavg freesurfer/bin/vol2subfield freesurfer/bin/vol2symsurf @@ -861,569 +847,14 @@ freesurfer/mni/bin/make_model freesurfer/mni/data freesurfer/mni/etc freesurfer/mni/include -freesurfer/mni/lib -freesurfer/mni/lib64 freesurfer/mni/share/N3 freesurfer/mni/share/man freesurfer/mni/share/mni_autoreg -freesurfer/mni/share/perl5/Getopt/Tabular.pod -freesurfer/mni/share/perl5/MNI/Batch.pm -freesurfer/mni/share/perl5/MNI/DataDir.pm -freesurfer/mni/share/perl5/MNI/Spawn.pod -freesurfer/mni/share/perl5/MNI/TagPoint.pm -freesurfer/mni/share/perl5/MNI/TagSet.pm -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/autosplit.ix -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/check_files.al -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/check_input_dirs.al -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/check_output_dirs.al -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/check_output_path.al -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/find_program.al -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/find_programs.al -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/generate_numbered_filename.al -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/statfs.al -freesurfer/mni/share/perl5/auto/MNI/FileUtilities/test_file.al -freesurfer/mni/share/perl5/auto/MNI/MincUtilities -freesurfer/mni/share/perl5/auto/MNI/MiscUtilities -freesurfer/mni/share/perl5/auto/MNI/NumericUtilities -freesurfer/mni/share/perl5/auto/MNI/PathUtilities/autosplit.ix -freesurfer/mni/share/perl5/auto/MNI/PathUtilities/expand_path.al -freesurfer/mni/share/perl5/auto/MNI/PathUtilities/merge_paths.al -freesurfer/mni/share/perl5/auto/MNI/PathUtilities/replace_dir.al -freesurfer/mni/share/perl5/auto/MNI/PathUtilities/replace_ext.al -freesurfer/mni/share/perl5/auto/MNI/PathUtilities/split_path.al -freesurfer/mni/share/perl5/MNI.pm -freesurfer/mni/share/perl5/mni_perllib.pod freesurfer/mni/mni.srcbuild.June2015.tgz freesurfer/mni-1.4 freesurfer/models -freesurfer/python/bin/python3-config -freesurfer/python/bin/python3.6 -freesurfer/python/bin/python3.6-config -freesurfer/python/bin/python3.6m -freesurfer/python/bin/python3.6m-config -freesurfer/python/include -freesurfer/python/lib/pkgconfig -freesurfer/python/lib/python3.6/__future__.py -freesurfer/python/lib/python3.6/__phello__.foo.py -freesurfer/python/lib/python3.6/multiprocessing -freesurfer/python/lib/python3.6/__pycache__ -freesurfer/python/lib/python3.6/_compat_pickle.py -freesurfer/python/lib/python3.6/_compression.py -freesurfer/python/lib/python3.6/_dummy_thread.py -freesurfer/python/lib/python3.6/_markupbase.py -freesurfer/python/lib/python3.6/_osx_support.py -freesurfer/python/lib/python3.6/_pydecimal.py -freesurfer/python/lib/python3.6/_pyio.py -freesurfer/python/lib/python3.6/_strptime.py -freesurfer/python/lib/python3.6/_threading_local.py -freesurfer/python/lib/python3.6/aifc.py 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-freesurfer/python/lib/python3.6/sunau.py -freesurfer/python/lib/python3.6/symbol.py -freesurfer/python/lib/python3.6/tarfile.py -freesurfer/python/lib/python3.6/tempfile.py -freesurfer/python/lib/python3.6/threading.py -freesurfer/python/lib/python3.6/tokenize.py -freesurfer/python/lib/python3.6/tracemalloc.py -freesurfer/python/lib/python3.6/typing.py -freesurfer/python/lib/python3.6/webbrowser.py -freesurfer/python/lib/libcrypto.so.10 -freesurfer/python/lib/liblzma.so.0 -freesurfer/python/lib/libncursesw.so.5 -freesurfer/python/lib/libpanelw.so.5 -freesurfer/python/lib/libpython3.6m.a -freesurfer/python/lib/libreadline.so.6 -freesurfer/python/lib/libssl.so.10 -freesurfer/python/lib/libtinfo.so.5 -freesurfer/python/packages -freesurfer/python/scripts/anatomiCutsUtils -freesurfer/python/scripts/aparcstats2table -freesurfer/python/scripts/asegstats2table -freesurfer/python/scripts/diffusionUtils -freesurfer/python/scripts/dmri_violinPlots -freesurfer/python/scripts/fspalm -freesurfer/python/scripts/gems_compute_binary_atlas_probs -freesurfer/python/scripts/long_mris_slopes -freesurfer/python/scripts/long_qdec_table -freesurfer/python/scripts/long_stats_combine -freesurfer/python/scripts/long_stats_slopes -freesurfer/python/scripts/long_stats_tps -freesurfer/python/scripts/long_submit_jobs -freesurfer/python/scripts/long_submit_postproc -freesurfer/python/scripts/merge_stats_tables -freesurfer/python/scripts/mri_segment_hypothalamic_subunits -freesurfer/python/scripts/mri_synth_strip -freesurfer/python/scripts/qatools.py -freesurfer/python/scripts/run_samseg -freesurfer/python/scripts/run_samseg_long -freesurfer/python/scripts/sbtiv -freesurfer/python/scripts/stattablediff -freesurfer/python/scripts/tractstats2table +freesurfer/python/**/__pycache__ freesurfer/python/share freesurfer/sessions freesurfer/subjects/V1_average From 480021132592528431deb8326a6a4c34c836ecd4 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Thu, 19 May 2022 11:39:02 -0400 Subject: [PATCH 8/9] DOCKER: Add hack for recon-all bug --- Dockerfile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/Dockerfile b/Dockerfile index 8ffe43594..181a95191 100644 --- a/Dockerfile +++ b/Dockerfile @@ -294,6 +294,10 @@ RUN find $HOME -type d -exec chmod go=u {} + && \ find $HOME -type f -exec chmod go=u {} + && \ rm -rf $HOME/.npm $HOME/.conda $HOME/.empty +# HACK for FreeSurfer 7.2.0 +# Fixed in https://github.com/freesurfer/freesurfer/pull/886, so remove on release +ENV FREESURFER="/opt/freesurfer" + ENV IS_DOCKER_8395080871=1 RUN ldconfig From e144b75eb98f21c558c0058d6ab44fd13dcbaba9 Mon Sep 17 00:00:00 2001 From: "Christopher J. Markiewicz" Date: Thu, 19 May 2022 16:43:34 -0400 Subject: [PATCH 9/9] MNT: Require recent nipype with FS 7 support --- setup.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.cfg b/setup.cfg index 3734885af..c6cd91865 100644 --- a/setup.cfg +++ b/setup.cfg @@ -23,7 +23,7 @@ url = https://github.com/nipreps/fmriprep python_requires = >=3.7 install_requires = nibabel >= 3.0 - nipype >= 1.5.1 + nipype >= 1.7.0 nitime nitransforms ~= 21.0.0 niworkflows @ git+https://github.com/nipreps/niworkflows.git@master