#Checked paths on SetUpFreesurfer.sh to make sure they direct to the right spot
#Run commands to setup FS environment
 
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

#Paths point to the right place in terms of HOME, FSFAST, SUBJECTS_DIR, etc 
#Try to run a recon-all -i command

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

#I get a list of commands not found

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...

#------------------------------------------

#But the recon-all is reported as finished without error.

recon-all -s FS_struct.nii.gz finished without error at Wed Jul 25 16:46:00 PDT 2012
done

#I go into the /freesurfer/bin folder to check whether the commands listed above as not found are actually there... they are missing (??)

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

#I copy the bin folder from another machine, and I check the bin files are there
#I run a recon-all -i subject again

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

#This time the file is found but it says is 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
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

# 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