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
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