Fidel, Sorry, but the GEMS tools are not built for our mac powerpc distribution. we no longer support that platform (or at least we dont make an effort to build the entire freesurfer toolset on it). Our focus is now on getting a 64b Mac (Mountain) Lion build working.
Nick > Hi Nick, > > I run recon-all and worked well, but then I added the hippo-subfields > flag and quitted with errors. The hippo-subfields.log says > "kvlSegmentHippocamlSubfields.sh: Command not found". > > I went into the bin folder and all the kvl files are missing. > > Advice will be appreciate it. > > Thanks, > > Fidel > > > On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote: > > Fidel, > > I don't know why those files are missing from the Tiger ppc > distribution, > but i confirmed that indeed they are. Here is a tarball of the > distribution which contains everything: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz > > save it to your /Applications directory, and then from the Terminal > type: > > cd /Applications > sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz > > you dont need to remove your existing install. > > Nick > > > >> Hi, >> >> I'm reposting this, hoping Nick has returned and can provide some >> guidance. >> >> Thanks, >> >> Fidel >> >> On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote: >> >>> This is strange, it must be something that is specific to the PPC >>> Mac distribution. Nick is going to have to deal with this, but he >>> won't be back until Mon. Can you wait that long? >>> doug >>> >>> On 07/31/2012 06:01 PM, Fidel Vila wrote: >>>>> 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 >>>>> >>>> >>>> >>> >>> -- >>> 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 >> >> >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
