> And there is nothing in /Applications/freesurfer/bin? There are 357 items in /Applications/freesurfer/bin
> Are there any files in the other directories? Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license) The executable files missing in /Applications/freesurfer/bin seem to be: talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in /Applications/ freesurfer/bin folder) retrieves no matching pattern. The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all. > Do you have permission to install it in that location? I do. Could this be related to compillation of files for the May 2011 5.1. stable release for ppc? Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities... Regards, Fidel On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote: > And there is nothing in /Applications/freesurfer/bin? Are there any > files in the other directories? Do you have permission to install it > in that location? If nothing is in the bin dir, then there is no > need to try recon-all, it will always fail. > doug > > > > On 07/31/2012 04:05 PM, Fidel Vila wrote: >> Hi Doug, >> >> I re-installed freesurfer, and I still get the same error message >> (terminal output attached); bin files are still missing from bin >> folder. >> >> Shall I report this as a bug? >> >> Regards, >> >> Fidel >> >> >> >> >> On 25-Jul-12, at 8:22 PM, Douglas Greve wrote: >> >>> did you set up your environment so that your path environment >>> variable has all the proper paths in it? Look at the wiki for >>> instructions. >>> doug >>> >>> On 7/25/12 7:57 PM, Fidel Vila wrote: >>>> Hi Freesurfer experts, >>>> >>>> I recently installed FS (PowerPC architecture version available >>>> on FS website) on a Mac OS X 10.4.11 and I get the attached >>>> output error when running recon-all. >>>> >>>> Advice on how to troubleshoot this would be appreciate. >>>> >>>> Thanks, >>>> >>>> Fidel >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> The information in this e-mail is intended only for the person to >>> whom it is >>> addressed. If you believe this e-mail was sent to you in error and >>> the e-mail >>> contains patient information, please contact the Partners >>> Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> but does not contain patient information, please contact the >>> sender and properly >>> dispose of the e-mail. >>> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
