Arvind

I'm suspect that our instructions may be a bit confusing.  The files to download are not the netcdf and minc files from the MNI distribution site, but rather the file mni.Linux.tar.gz from our site (where it says 'Download MNI binaries for Linux and/or SunOS.', click on Linux).  Following the instructions, this will result in an installation of files in the directory /usr/pubsw/packages/mni/current.  Then, the line:

     source $FREESURFER_HOME/FreeSurferEnv.csh

will add  MINC_BIN_DIR to the path.

Also, where the instructions say to type:

     ln -s `which perl` perl

be sure you are using the ` key, which is the far upper left corner key on the keyboard (not to be confused with the ' key).

The important thing is to have perl in the /usr/pubsw/bin directory.  If its already there, then no need to create a link.

Hope this helps.

Nick



On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: 
Hi Nick,

I am running it on Linux platform. I followed the same instruction
described here.
http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html
and downloaded these two files: NetCDF 3.5.0 and MINC 1.0 

I am not sure, if I created the symbolic link correctly.
ln -s 5.8.0 perl - 
ln: `perl': File exists [ Same output even the first time]

Also, there are no tools in the path, I manually created current/bin and
current/lib. Is there a way to fix this, can I moved all the tools to these
two directories?

Your help is really appreciated.

Arvind Gururajan



On 10 Jun 2005, Nick Schmansky wrote:
> Arvind,
> 
> Hi.  On what platform are you running?  Linux?  
> 
> Did you follow the special installation instructions, involving making
> the symbolic links?  Lastly, are the tools in your path?
> 
> If you are feeling brave, an alternative to installing the binaries is
> to compile the MNI package from source on your platform, and install
> those binaries.  Instructions to do this are here:
> 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README
> 
> and the gzip file is here:
> 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz
> 
> 
> Nick
> 
> 
> 
> On Fri, 2005-06-10 at 12:20 -0500, Arvind Gururajan wrote:
> 
> > Hi,
> > 
> > I downloaded the entire MNI package. Although I see all these MNI
files, I
> > still get the same error, file not found. Any clues why this might be? 
> > 
> > 
> > Thanks,
> > 
> > Arvind Gururajan
> >  
> > On 9 Jun 2005, Bruce Fischl wrote:
> > > just download and install the whole MNI package. Much easier than
trying 
> > > to install various pieces....
> > > 
> > > On Thu, 9 Jun 2005, Arvind Gururajan wrote:
> > > 
> > > > Hello,
> > > >
> > > > I am very new to Freesurfer. Could anybody please tell me which
> > specific
> > > > MNI tool, I need to install?
> > > >
> > > >
> > > >>
> > > >> I tried the following command.
> > > >>
> > > >> ./recon-all -smooth1 ZM
> > > >> ########################################
> > > >> program versions used
> > > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $
> > > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $fire
> > > >> mri_convert --version
> > > >> $
> > > >> strings: rawtominc:: No such file or directory
> > > >> strings: Command: No such file or directory
> > > >> strings: not: No such file or directory
> > > >> strings: found.: No such file or directory
> > > >> strings: minctracc:: No such file or directory
> > > >> strings: Command: No such file or directory
> > > >> strings: not: No such file or directory
> > > >> strings: found.: No such file or directory
> > > >> strings: mincresample:: No such file or directory
> > > >> strings: Command: No such file or directory
> > > >> strings: not: No such file or directory
> > > >> strings: found.: No such file or directory
> > > >> strings: mincaverage:: No such file or directory
> > > >> strings: Command: No such file or directory
> > > >> strings: not: No such file or directory
> > > >> strings: found.: No such file or directory
> > > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $
> > > >> mri_convert --version
> > > >> $
> > > >> strings: mritotal:: No such file or directory
> > > >> strings: Command: No such file or directory
> > > >> strings: not: No such file or directory
> > > >> strings: found.: No such file or directory
> > > >> strings: nu_correct:: No such file or directory
> > > >> strings: Command: No such file or directory
> > > >> strings: not: No such file or directory
> > > >> strings: found.: No such file or directory
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> $
> > > >> #######################################
> > > >> ERROR: Flag ZM unrecognized.
> > > >> -smooth1 ZM
> > > >>
> > > >>
> > > >> The folder ZM has only one orig file in the surf directory. There
are
> > no
> > > >> raw data(.COR files). Please let me know your feedback.
> > > >>
> > > >> Sincerely,
> > > >>
> > > >> Arvind Gururajan
> > > >
> > > > _______________________________________________
> > > > 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
> 


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