Are all the files you need there? If not, what is missing?
On 08/22/2013 07:41 PM, Pedro Rosa wrote: > 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 > -- 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
