For now I only need brainmask.mgz and wmparc.mgz, so Yes. In case I need other files in the future (i.e. mri_segstats) I plan to run all processing again. Thanks a lot! Pedro Rosa
On 23 Aug 2013, at 11:36 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > 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
