Hello Bruce, The I am a little confused with the results of the recon-all command? Does the recon-all -help explain the file placement?
Isaiah > On Jul 30, 2014, at 6:21 AM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > wrote: > > Hi Isaiah > > remove the space. It should be: > > recon-all > > cheers > Bruce >> On Wed, 30 Jul 2014, Isaiah C. Smith wrote: >> >> The command is not found. >> Last login: Tue Jul 29 17:42:52 on ttys001 >> -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /Applications/freesurfer >> FSFAST_HOME /Applications/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR /Applications/freesurfer/subjects >> MNI_DIR /Applications/freesurfer/mni >> Isaiahs-MacBook-Pro:~ IsaiahSmith$ recon- all -i os005a1001.nii -s Practice >> -sd/Users/IsaiahSmith/Documents/LABData/MRIFolder/CfMRI01/CfMRI0124May2012/SRS >> 00001 -all >> -bash: recon-: command not found >> Isaiahs-MacBook-Pro:~ IsaiahSmith$ -bash: os005a1001.nii: No such file or >> directory >> On Jul 22, 2014, at 4:44 PM, Bruce Fischl <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 >> >> 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 >> >> 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. > _______________________________________________ > 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
