FSv5.1 seems to run fine on 64-bit Mountain Lion, as far as I can tell, but I have not tried GEMS or TRACULA just yet... (I upgraded before installing, in case that matters.)
I use XQuartz for tkmedit, freeview, fslview, etc. So far so good! ~ShannonB -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Monday, September 10, 2012 1:46 PM To: Anthony Dick Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] kvl binaries missing from ppc 5.1 stable release Anthony, Our Leopard build should work on Mountain Lion, although I havent confirmed this. It works on Lion. The Leopard build is 32b, so some stuff which can use >4GB of memory (like mri_cvs_register) will fail due to inability to alloc memory. Nick On Mon, 2012-09-10 at 12:04 -0400, Anthony Dick wrote: > Hello--was just thinking about upgrading to Mountain Lion. Am I to > assume freesurfer will not work if I do this? > > Anthony > > On 9/10/12 11:58 AM, Nick Schmansky wrote: > > 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/freesurf > >> er-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 > > _______________________________________________ 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
