| Thanks for your prompt reply, Doug. I've been checking and following the wiki instructions with regards to setting up proper paths, and I could not find an obvious (to me) problem there. I attach a file with things I have tried and issues I have found. Further advice will be greatly appreciate it. Many thanks, Fidel |
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\pard\tx566\tx1133\tx1700\tx2267\tx2834\tx3401\tx3968\tx4535\tx5102\tx5669\tx6236\tx6803\ql\qnatural\pardirnatural\f0\fs24 \cf0 \ \b #Checked paths on SetUpFreesurfer.sh to make sure they direct to the right spot\ #Run commands to setup FS environment \b0 \ \ a3128u:/Applications FVila$ export FREESURFER_HOME=/Applications/freesurfer\ a3128u:/Applications FVila$ source $FREESURFER_HOME/SetUpFreeSurfer.sh\ -------- freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 --------\ Setting up environment for FreeSurfer/FS-FAST (and FSL)\ FREESURFER_HOME /Applications/freesurfer\ FSFAST_HOME /Applications/freesurfer/fsfast\ FSF_OUTPUT_FORMAT nii.gz\ SUBJECTS_DIR /Applications/freesurfer/subjects\ MNI_DIR /Applications/freesurfer/mni\ FSL_DIR /users/FVila/fsl\ \ \b #Paths point to the right place in terms of HOME, FSFAST, SUBJECTS_DIR, etc \ #Try to run a recon-all -i command \b0 \ \ a3128u:/Applications FVila$ recon-all -i /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid FS_struct.nii.gz \ \ Subject Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0\ Current Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0\ INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects\ Actual FREESURFER_HOME /Applications/freesurfer\ \ \b #I get a list of commands not found \b0 \ \ Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc\ tcsh: talairach_avi: Command not found.\ tcsh: mri_watershed: Command not found.\ tcsh: mri_segment: Command not found.\ tcsh: mri_tessellate: Command not found.\ tcsh: mri_concatenate_lta: Command not found.\ tcsh: mri_normalize_tp2: Command not found.\ tcsh: mris_smooth: Command not found.\ tcsh: mris_inflate: Command not found.\ tcsh: mris_curvature: Command not found.\ tcsh: mris_sphere: Command not found.\ tcsh: mris_fix_topology: Command not found.\ tcsh: mris_topo_fixer: Command not found.\ tcsh: mris_ca_label: Command not found.\ tcsh: mris_euler_number: Command not found.\ tcsh: mris_make_surfaces: Command not found.\ tcsh: mris_register: Command not found.\ tcsh: mris_volmask: Command not found.\ tcsh: mris_anatomical_stats: Command not found.\ tcsh: mrisp_paint: Command not found.\ tcsh: mris_curvature_stats: Command not found.\ tcsh: mris_calc: Command not found.\ tcsh: mri_robust_register: Command not found.\ tcsh: mri_robust_template: Command not found.\ tcsh: mri_segstats: Command not found.\ /Applications/freesurfer/subjects/FS_struct.nii.gz\ \\n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz \\n\ mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz \ $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $\ reading from /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz...\ TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00\ i_ras = (-1, 0, 0)\ j_ras = (0, 1, 0)\ k_ras = (0, 0, 1)\ writing to /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz...\ \ #------------------------------------------\ \ \b #But the recon-all is reported as finished without error. \b0 \ \ recon-all -s FS_struct.nii.gz finished without error at Wed Jul 25 16:46:00 PDT 2012\ done\ \ \ \b #I go into the /freesurfer/bin folder to check whether the commands listed above as not found are actually there... they are missing (??)\ \b0 \ a3128u:/Applications/freesurfer/bin FVila$ ls\ LongQdecTable.py minc2seqinfo mri_motion_correct2\ UpdateNeeded misc.py mri_ms_fitparms\ aparc2feat mkfsdist mri_multispectral_segment\ aparcstats2table mkheadsurf mri_nl_align\ aparcstatsdiff mkima_index.tcl mri_nl_align_binary\ aseg2feat mkmnc_index.tcl mri_nlfilter\ asegstats2table mksubjdirs mri_normalize\ asegstatsdiff mksurfatlas mri_nu_correct.mni\ avi2talxfm mkxsubjreg mri_or\ batchjobs mni152reg mri_paint\ bblabel morph_only_subject mri_parse_sdcmdir\ bbregister morph_only_subject-lh mri_parselabel\ bedpostx_seychelles morph_only_subject-rh mri_partial_ribbon\ beta2sxa morph_rgb-lh mri_polv\ biasfield morph_rgb-rh mri_pretess\ browse-minc-header.tcl morph_subject mri_probe_ima\ bugr morph_subject-lh mri_probedicom\ build_desikan_killiany_gcs.csh morph_subject-rh mri_reduce\ check_siemens_dir morph_subject_on_seychelles mri_reorient_LR.csh\ check_subject morph_tables-lh mri_simulate_atrophy\ clear_fs_env.csh morph_tables-rh mris2rgb\ compute_interrater_variability.csh mri-func2sph mris_extract_main_component\ compute_label_volumes.csh mri-funcvits mris_glm\ connectgraph mri-sph2surf mris_preproc\ cor_to_minc mri_add_new_tp mris_roiCircle\ cp-dicom mri_add_xform_to_header mris_show\ cuda_setup mri_align_long.csh mris_volsmooth\ cudadetect mri_and ms_refine_subject\ cudadetect.bin mri_annotation2label nmovie\ datastruct_utils.py mri_aparc2aseg orient_mri\ dcmdir-info-mgh mri_aparc2wmseg orient_mri.bin\ dcmunpack mri_apply_bias parc_atlas_jackknife_test\ deface_subject mri_aseg_edit_reclassify pctsurfcon\ defect-seg mri_aseg_edit_train petsc_setup\ dicom-rename mri_auto_fill plot_structure_stats.tcl\ dmrirc.example mri_average predict_v1.sh\ dsh mri_binarize progressbar.tcl\ dt_recon mri_build_priors qdec\ epidewarp.fsl mri_ca_label qdec.bin\ extract_talairach_avi_QA.awk mri_ca_normalize qt_setup\ feat2segstats mri_ca_register rbftest\ feat2surf mri_ca_tissue_parms rcbf-prep\ findsession mri_ca_train rebuild_gca_atlas.csh\ fix_subject mri_cal_normalize recon-all\ fix_subject-lh mri_cc recon-all.makefile\ fix_subject-rh mri_cht2p reg-feat2anat\ fix_subject_corrected mri_cnr reg-mni305.2mm\ fix_subject_corrected-lh mri_compile_edits register.csh\ fix_subject_corrected-rh mri_compute_bias register_child\ fix_subject_on_seychelles mri_compute_distances register_elderly_subject\ fixup_mni_paths mri_compute_overlap register_subject\ flip4fsl mri_compute_structure_transforms register_subject_flash\ flirt.newdefault.20080811.sch mri_compute_volume_fractions register_subject_mixed\ fname2ext mri_concat reinflate_subject\ fname2stem mri_convert reinflate_subject-lh\ freesurfer mri_convert_mdh reinflate_subject-rh\ fsPrintHelp mri_copy_params remove_talairach\ fs_lib_check mri_copy_values renormalize_T1_subject\ fs_time mri_cor2label renormalize_subject\ fscalc mri_create_t2combined renormalize_subject_keep_editting\ fscalc.fsl mri_cvs_check repair_siemens_file\ fsfget mri_cvs_data_copy reregister_subject_mixed\ fsfget.tcl mri_cvs_register run-qdec-glm\ fsgd_parser.py mri_cvs_requiredfiles.txt run_mris_preproc\ fshelp mri_dct_align segment_monkey\ fsl_rigid_register mri_dct_align_binary segment_subject\ fsl_sub_seychelles mri_deface segment_subject_notal\ fslregister mri_diff segment_subject_notal2\ fsman mri_edit_segmentation segment_subject_old_skull_strip\ fsr-checkxopts mri_edit_segmentation_with_surfaces segment_subject_sc\ fsr-getxopts mri_em_register segment_subject_talmgh\ fsutils.py mri_estimate_tissue_parms setlabelstat\ get_label_thickness mri_evaluate_morph sfa2fieldsign\ getfullpath mri_extract show_tal\ gifti_test mri_extract_conditions skip_long_make_checks\ gifti_tool mri_extract_label sphere_subject\ grad_unwarp mri_fieldsign sphere_subject-lh\ help_xml_validate mri_fill sphere_subject-rh\ histo_fix_topology mri_fuse_segmentations spm_t_to_b\ histo_segment mri_fwhm spmmat2register\ histo_synthesize mri_gca_ambiguous spmregister\ id.xfm mri_gcab_train sratio\ inflate_subject mri_gcut stem2fname\ inflate_subject-lh mri_gdfglm stim_polar\ inflate_subject-rh mri_glmfit subject_info.py\ inflate_subject3 mri_glmfit-sim tal_compare\ inflate_subject_new mri_hausdorff_dist talairach\ inflate_subject_new-lh mri_head talairach2\ inflate_subject_new-rh mri_hires_register talairach_mgh\ inflate_subject_sc mri_histo_eq talsegprob\ is-surface mri_histo_normalize tcl_setup\ isanalyze mri_info test_fs_tutorial.csh\ isnifti mri_interpolate test_recon-all.csh\ kww_setup mri_jacobian tetgen\ label_child mri_joint_density thickdiffmap\ label_elderly_subject mri_label2label tkmedit\ label_subject mri_label2vol tkregister2\ label_subject_flash mri_label_accuracy tksurfer\ label_subject_mixed mri_label_histo trac-all\ labels_disjoint mri_label_vals trac-paths\ labels_intersect mri_label_volume trac-preproc\ labels_union mri_linear_align tractstats2table\ long_mris_slopes mri_linear_align_binary unpack_ima.tcl\ long_qdec_table mri_linear_register unpack_ima1.tcl\ long_stats_slopes mri_make_bem_surfaces unpack_mnc.tcl\ long_submit_jobs mri_make_register unpackimadir\ lpcregister mri_make_template unpackimadir2\ make-segvol-table mri_make_uchar unpackmincdir\ make_average_subcort mri_map_cpdat unpacksdcmdir\ make_average_subject mri_mark_temporal_lobe unpacksdcmdir.tcl\ make_average_surface mri_mask usbtree\ make_average_volume mri_matrix_multiply vno_match_check\ make_cortex_label mri_mc vtk_setup\ map_all_labels mri_mcsim wfilemask\ map_all_labels-lh mri_mergelabels wm-anat-snr\ map_central_sulcus mri_mi_nl_align xfmrot\ map_to_base mri_modify xhemireg\ meanval mri_motion_correct xmlToHtml\ merge_stats_tables mri_motion_correct.fsl xsanatreg\ \ \ \b #I copy the bin folder from another machine, and I check the bin files are there\ #I run a recon-all -i subject again \b0 \ \ a3128u:/Applications FVila$ recon-all -i /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid FS_struct.nii.gz \ Subject Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0\ Current Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0\ INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects\ Actual FREESURFER_HOME /Applications/freesurfer\ \ \b #This time the file is found but it says is not executable.\ \b0 \ Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc\ tcsh: /Applications/freesurfer/bin/mri_convert: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_convert: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_make_uchar: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_normalize: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_watershed: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_gcut: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_segment: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_label2label: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_em_register: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_ca_normalize: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_ca_register: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_ca_label: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_pretess: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_fill: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_tessellate: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_concatenate_lta: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_smooth: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_inflate: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_curvature: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_sphere: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_fix_topology: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_topo_fixer: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_ca_label: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_euler_number: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_make_surfaces: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_register: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_volmask: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_anatomical_stats: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mrisp_paint: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_curvature_stats: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mris_calc: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_robust_register: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_robust_template: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_and: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_or: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_fuse_segmentations: Exec format error. Binary file not executable.\ tcsh: /Applications/freesurfer/bin/mri_segstats: Exec format error. Binary file not executable.\ /Applications/freesurfer/subjects/FS_struct.nii.gz\ \\n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz \\n\ tcsh: /Applications/freesurfer/bin/mri_convert: Exec format error. Binary file not executable.\ Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc\ \ recon-all -s FS_struct.nii.gz exited with ERRORS at Thu Jul 26 09:16:57 PDT 2012\ \ For more details, see the log file /Applications/freesurfer/subjects/FS_struct.nii.gz/scripts/recon-all.log\ To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting\ \ \b # I chmod +x to the list of files reported as not executable, but made no difference. Same error as above is given. \ #At this point I'm not sure what to do next. \ #I wonder why the bin files are missing in the first place, because I'm under the impression that I installed the package the right way.\ # ?Advice, ?comments, ?suggestions \b0 \ \ \ }
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
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