The recon-all option is no longer working and neither is the other one. I am getting an error.
Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon-all help ERROR: Flag help unrecognized. help Darwin Isaiahs-MacBook-Pro.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Tue Jul 29 21:23:06 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Isaiahs-MacBook-Pro:~ IsaiahSmith$ On Jul 22, 2014, at 4:44 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Isaiah recon-all -i <input file> -s <subject identifier> -sd <dir to put subject in> -all should do the trick. <input file> should be a *single* file in the right dicom series, or a .nii file. Don't use analyze Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello Bruce, Thanks for the response; I tried the inputs from the check freesurfer page. I just tried to do the run recon-all and got the list of possible commands. The input images are unix executable files separately, but I can convert them to .hdr/.img or .nii using mricron. They are MRI images. How do I direct these files to the command? And this is the command to do the things I previously asked, right? Isaiah Hi Isaiah, what are the input images that you have? What format and what imaging sequence? You should be able to just run recon-all on them (check out recon-all -help) cheers Bruce On Tue, 22 Jul 2014, Isaiah C. Smith wrote: Hello All, I was testing to see if the freesurfer program works and it does seem to work for anything besides the free viewer program. I do not know what is wrong with the others; do you have any ideas? Also I am trying to use the inhomogeneity correction, convert the images that I have to 1x1x1 ratio, arrange the directions of the image, and save the program in analyze format. If possible could you outline that process or give me a link that will direct me on the process? Thank you. Your help is really appreciated. Isaiah Smith _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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.
_______________________________________________ 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.
