Hi, Thank you. It seems to be working. The command returns, however, that there is nothing to be done in all three autorecons individually. What should that mean, considering the error in autorecon2? Regards
Pedro Rosa On 21 Aug 2013, at 04:16 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > Getting 'make' on Mac systems requires installing XCode AND Command Line > Tool. You can download these from Apple using the following link: > > https://developer.apple.com/downloads > > FYI: This will require opening a developer account (free) if you do not > already have one. > > -Zeke > > > > On 08/21/2013 12:33 PM, Douglas N Greve wrote: >> >> Yea, I don't think mac os comes with it by default. If you want to use >> this functionality, you'll have to install it. Zeke, can you point him >> in the right direction? >> >> to get back to your original problem, I think I gave you the wrong >> version of mri_segstats. What version of mac os do you have? If I get >> you the right version, then you might not need the make option. >> >> doug >> >> >> On 08/21/2013 12:06 PM, Pedro Rosa wrote: >>> Hi, >>> I could not find the make file. I am using Mac OS (most recent). >>> Thanks >>> >>> Pedro Rosa >>> >>> On 21 Aug 2013, at 10:51 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> wrote: >>> >>>> You will need to add the "make" program to your path. In Linux, it is >>>> usually in /usr/bin >>>> doug >>>> >>>> >>>> On 08/20/2013 10:12 PM, Pedro Rosa wrote: >>>>> Hi, >>>>> Sorry for that! >>>>> I tried using several targets: all / autorecon1-2-3, and for all I get >>>>> 'make: command not found.' >>>>> I used recon-all -s subject -make target >>>>> Thank you again, >>>>> Pedro Rosa >>>>> >>>>> On 20 Aug 2013, at 12:34 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>>> They should be fine. BTW, you can run >>>>>> >>>>>> recon-all -s subject -make all >>>>>> >>>>>> and it will only run the parts that need to be run >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> On 08/20/2013 12:13 PM, Pedro Rosa wrote: >>>>>>> Hi, >>>>>>> I am mainly interested in using the wmparc.mgz files. Are they alright >>>>>>> in the subjects with this error in autorecon2? It would be better if I >>>>>>> could use this processing, as doing it again in 80 subjects would take >>>>>>> a lot of time. Autorecon 1 and 3 ended without errors for all subjects. >>>>>>> I inspected the wmparc.mgz files as labels using Slicer 4, and they >>>>>>> seem fine. >>>>>>> Thanks, >>>>>>> Pedro Rosa. >>>>>>> >>>>>>> On 20 Aug 2013, at 10:28 AM, Douglas N Greve >>>>>>> <gr...@nmr.mgh.harvard.edu> wrote: >>>>>>> >>>>>>>> Hi Pedro, see the release notes for the issue >>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes >>>>>>>> doug >>>>>>>> >>>>>>>> On 08/19/2013 10:06 PM, Pedro Rosa wrote: >>>>>>>>> Hi experts, >>>>>>>>> I am processing several subjects, and they all ended up with the same >>>>>>>>> error at the autorecon2: ribbon.mgz could not be opened. I ran at >>>>>>>>> first the autorecon1 to check the skull striping, and then autorecon2 >>>>>>>>> and 3. Autorecon3 always finished without error. I attached a log >>>>>>>>> file. >>>>>>>>> >>>>>>>>> >>>>>>>>> Any help is appreciated. >>>>>>>>> Regards, >>>>>>>>> Pedro Rosa. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> -- >>>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: >>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> 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
