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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Arvind Gururajan -
Nick Schmansky