Nick,
Thanks. Yes, I used 'cd packages' and did the installation. After setting the environment and the subjit it works without errors. One more question, can I do a similar conversion for one .orig file having both hemisphere data points and generate one inflated surface or would have to use lh and rh.orig files seperately?
Thanks, Arvind Gururajan
On 13 Jun 2005, Nick Schmansky wrote:
Arvind,
You are right, the MINC installation instructions are mistaken. A 'cd packages' is missing:
mkdir -p packages cd packages <<<<< missing statement tar xvfz mni.$OS.tar.gz
As for the ZM error, is this the name of a subject? If so, preface it with -subjid, like this:
recon-all -smooth1 -subjid ZM
The -smooth1 argument is not one normally used outright, but it will work, once certain variables are set, namely these:
setenv DoCANormalize 0 setenv DoCAReg 0 setenv DoCALabel 0 setenv EditWMwithASeg 0
Nick
On Mon, 2005-06-13 at 12:58 -0500, Arvind Gururajan wrote:
Nick,
Thanks for the clear description. I repeated the exact installation and
got
the same errors. I noticed that the 'current' directory was wrongly
placed
in this path. /usr/pubsw/mni/current. Repeated the same steps again,
but
now installed in the right directory. Getting the following errors:
[root@node1 noarch]# ./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 $ mri_convert --version $ $Header:
/software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v
6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v
96.3
2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v
6.2
1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v
6.1
1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ERROR: Flag ZM unrecognized. -smooth1 ZM
Your feedback will be appreciated.
Thanks, Arvind
On 10 Jun 2005, Nick Schmansky wrote:
--=-yST7vkqiza7BNyzh64R8 Content-Type: text/plain Content-Transfer-Encoding: 7bit
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.cshwill add MINC_BIN_DIR to the path.
Also, where the instructions say to type:
ln -s `which perl` perlbe 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
--=-yST7vkqiza7BNyzh64R8 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 7bit
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 TRANSITIONAL//EN">
<HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=UTF-8"> <META NAME="GENERATOR" CONTENT="GtkHTML/3.3.2"> </head> <BODY> Arvind<BR> <BR> 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 <A
HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.Linux.tar.gz">Linux</a>
and/or <A
HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.SunOS5.tar.gz">SunOS</a
.
', 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:<BR>
<BR> source $FREESURFER_HOME/FreeSurferEnv.csh<BR> <BR> will add MINC_BIN_DIR to the path.<BR> <BR> Also, where the instructions say to type:<BR> <BR> ln -s `which perl` perl <BR> <BR> 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).<BR>
<BR> The important thing is to have perl in the /usr/pubsw/bin directory.
If
its already there, then no need to create a link.<BR>
<BR> Hope this helps.<BR> <BR> Nick<BR> <BR> <BR> <BR> On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: <BLOCKQUOTE TYPE=CITE> <PRE> <FONT COLOR="#000000">Hi Nick,</font>
<FONT COLOR="#000000">I am running it on Linux platform. I followed
the
same
instruction</font> <FONT COLOR="#000000">described here.</font> <FONT COLOR="#000000"><A
HREF="http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html%22%3Ehttp
:/
/surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html</a></font> <FONT COLOR="#000000">and downloaded these two files: NetCDF 3.5.0
and
MINC
1.0 </font>
<FONT COLOR="#000000">I am not sure, if I created the symbolic link correctly.</font> <FONT COLOR="#000000">ln -s 5.8.0 perl - </font> <FONT COLOR="#000000">ln: `perl': File exists [ Same output even the
first
time]</font>
<FONT COLOR="#000000">Also, there are no tools in the path, I
manually
created current/bin and</font> <FONT COLOR="#000000">current/lib. Is there a way to fix this, can I
moved
all the tools to these</font> <FONT COLOR="#000000">two directories?</font>
<FONT COLOR="#000000">Your help is really appreciated.</font>
<FONT COLOR="#000000">Arvind Gururajan</font>
<FONT COLOR="#000000">On 10 Jun 2005, Nick Schmansky wrote:</font> <FONT COLOR="#000000">> Arvind,</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> Hi. On what platform are you running?
Linux?
</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> Did you follow the special installation instructions, involving making</font> <FONT COLOR="#000000">> the symbolic links? Lastly, are the tools in
your
path?</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> If you are feeling brave, an alternative to installing the binaries is</font> <FONT COLOR="#000000">> to compile the MNI package from source on
your
platform, and install</font> <FONT COLOR="#000000">> those binaries. Instructions to do this are here:</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> <A
HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README">ftp://
su
rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README</a></font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> and the gzip file is here:</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> <A
HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz">ftp://
su
rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz</a></font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> Nick</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> On Fri, 2005-06-10 at 12:20 -0500, Arvind Gururajan wrote:</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> > Hi,</font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > I downloaded the entire MNI package.
Although
I see all these MNI</font> <FONT COLOR="#000000">files, I</font> <FONT COLOR="#000000">> > still get the same error, file not found.
Any
clues why this might be? </font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > Thanks,</font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > Arvind Gururajan</font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > On 9 Jun 2005, Bruce Fischl wrote:</font> <FONT COLOR="#000000">> > > just download and install the whole MNI package. Much easier than</font> <FONT COLOR="#000000">trying </font> <FONT COLOR="#000000">> > > to install various pieces....</font> <FONT COLOR="#000000">> > > </font> <FONT COLOR="#000000">> > > On Thu, 9 Jun 2005, Arvind Gururajan wrote:</font> <FONT COLOR="#000000">> > > </font> <FONT COLOR="#000000">> > > > Hello,</font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > > I am very new to Freesurfer. Could anybody please tell me which</font> <FONT COLOR="#000000">> > specific</font> <FONT COLOR="#000000">> > > > MNI tool, I need to install?</font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> I tried the following command.</font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> ./recon-all -smooth1 ZM</font> <FONT COLOR="#000000">> > > >> ########################################</font> <FONT COLOR="#000000">> > > >> program versions used</font> <FONT COLOR="#000000">> > > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $</font> <FONT COLOR="#000000">> > > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $fire</font> <FONT COLOR="#000000">> > > >> mri_convert --version</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> strings: rawtominc:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: minctracc:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: mincresample:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: mincaverage:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $</font> <FONT COLOR="#000000">> > > >> mri_convert --version</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> strings: mritotal:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: nu_correct:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> #######################################</font> <FONT COLOR="#000000">> > > >> ERROR: Flag ZM unrecognized.</font> <FONT COLOR="#000000">> > > >> -smooth1 ZM</font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> The folder ZM has only one orig file in the surf directory. There</font> <FONT COLOR="#000000">are</font> <FONT COLOR="#000000">> > no</font> <FONT COLOR="#000000">> > > >> raw data(.COR files). Please let me know your feedback.</font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> Sincerely,</font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> Arvind Gururajan</font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > > _______________________________________________</font> <FONT COLOR="#000000">> > > > Freesurfer mailing list</font> <FONT COLOR="#000000">> > > > <A
HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu
</
A></font> <FONT COLOR="#000000">> > > > <A
HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%22%3Ehttps:/
/m
ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a></font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > _______________________________________________</font> <FONT COLOR="#000000">> > > Freesurfer mailing list</font> <FONT COLOR="#000000">> > > <A
HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu
</
A></font> <FONT COLOR="#000000">> > > <A
HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%22%3Ehttps:/
/m
ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a></font> <FONT COLOR="#000000">> > > </font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > _______________________________________________</font> <FONT COLOR="#000000">> > Freesurfer mailing list</font> <FONT COLOR="#000000">> > <A
HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu
</
A></font> <FONT COLOR="#000000">> > <A
HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%22%3Ehttps:/
/m
ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a></font> <FONT COLOR="#000000">> </font>
<FONT
COLOR="#000000">_______________________________________________</font>
<FONT COLOR="#000000">Freesurfer mailing list</font> <FONT COLOR="#000000"><A
HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu
</
A></font> <FONT COLOR="#000000"><A
HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%22%3Ehttps:/
/m
ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a></font> </pre>
</blockquote> </body> </html>
--=-yST7vkqiza7BNyzh64R8--
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Arvind,
no, you need to keep the hemispheres separate.
Bruce
On Mon, 13 Jun 2005, Arvind Gururajan wrote:
Nick,
Thanks. Yes, I used 'cd packages' and did the installation. After setting the environment and the subjit it works without errors. One more question, can I do a similar conversion for one .orig file having both hemisphere data points and generate one inflated surface or would have to use lh and rh.orig files seperately?
Thanks, Arvind Gururajan
On 13 Jun 2005, Nick Schmansky wrote:
Arvind,
You are right, the MINC installation instructions are mistaken. A 'cd packages' is missing:
mkdir -p packages cd packages <<<<< missing statement tar xvfz mni.$OS.tar.gz
As for the ZM error, is this the name of a subject? If so, preface it with -subjid, like this:
recon-all -smooth1 -subjid ZM
The -smooth1 argument is not one normally used outright, but it will work, once certain variables are set, namely these:
setenv DoCANormalize 0 setenv DoCAReg 0 setenv DoCALabel 0 setenv EditWMwithASeg 0
Nick
On Mon, 2005-06-13 at 12:58 -0500, Arvind Gururajan wrote:
Nick,
Thanks for the clear description. I repeated the exact installation and
got
the same errors. I noticed that the 'current' directory was wrongly
placed
in this path. /usr/pubsw/mni/current. Repeated the same steps again,
but
now installed in the right directory. Getting the following errors:
[root@node1 noarch]# ./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 $ mri_convert --version $ $Header:
/software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v
6.3 1999/10/19 14:45:31 neelin Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v
96.3
2000/03/15 08:42:41 stever Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v
6.2
1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v
6.1
1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ERROR: Flag ZM unrecognized. -smooth1 ZM
Your feedback will be appreciated.
Thanks, Arvind
On 10 Jun 2005, Nick Schmansky wrote:
--=-yST7vkqiza7BNyzh64R8 Content-Type: text/plain Content-Transfer-Encoding: 7bit
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.cshwill add MINC_BIN_DIR to the path.
Also, where the instructions say to type:
ln -s `which perl` perlbe 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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<HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html; CHARSET=UTF-8"> <META NAME="GENERATOR" CONTENT="GtkHTML/3.3.2"> </head> <BODY> Arvind<BR> <BR> 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 <A
HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.Linux.tar.gz">Linux</a>
and/or <A
HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.SunOS5.tar.gz">SunOS</a
.
', 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:<BR>
<BR> source $FREESURFER_HOME/FreeSurferEnv.csh<BR> <BR> will add MINC_BIN_DIR to the path.<BR> <BR> Also, where the instructions say to type:<BR> <BR> ln -s `which perl` perl <BR> <BR> 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).<BR>
<BR> The important thing is to have perl in the /usr/pubsw/bin directory.
If
its already there, then no need to create a link.<BR>
<BR> Hope this helps.<BR> <BR> Nick<BR> <BR> <BR> <BR> On Fri, 2005-06-10 at 16:51 -0500, Arvind Gururajan wrote: <BLOCKQUOTE TYPE=CITE> <PRE> <FONT COLOR="#000000">Hi Nick,</font>
<FONT COLOR="#000000">I am running it on Linux platform. I followed
the
same
instruction</font> <FONT COLOR="#000000">described here.</font> <FONT COLOR="#000000"><A
HREF="http://surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html%22%3Ehttp
:/
/surfer.nmr.mgh.harvard.edu/freesurfer/minc-download.html</a></font> <FONT COLOR="#000000">and downloaded these two files: NetCDF 3.5.0
and
MINC
1.0 </font>
<FONT COLOR="#000000">I am not sure, if I created the symbolic link correctly.</font> <FONT COLOR="#000000">ln -s 5.8.0 perl - </font> <FONT COLOR="#000000">ln: `perl': File exists [ Same output even the
first
time]</font>
<FONT COLOR="#000000">Also, there are no tools in the path, I
manually
created current/bin and</font> <FONT COLOR="#000000">current/lib. Is there a way to fix this, can I
moved
all the tools to these</font> <FONT COLOR="#000000">two directories?</font>
<FONT COLOR="#000000">Your help is really appreciated.</font>
<FONT COLOR="#000000">Arvind Gururajan</font>
<FONT COLOR="#000000">On 10 Jun 2005, Nick Schmansky wrote:</font> <FONT COLOR="#000000">> Arvind,</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> Hi. On what platform are you running?
Linux?
</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> Did you follow the special installation instructions, involving making</font> <FONT COLOR="#000000">> the symbolic links? Lastly, are the tools in
your
path?</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> If you are feeling brave, an alternative to installing the binaries is</font> <FONT COLOR="#000000">> to compile the MNI package from source on
your
platform, and install</font> <FONT COLOR="#000000">> those binaries. Instructions to do this are here:</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> <A
HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README">ftp://
su
rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.README</a></font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> and the gzip file is here:</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> <A
HREF="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz">ftp://
su
rfer.nmr.mgh.harvard.edu/pub/dist/mni.srcbuild.tar.gz</a></font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> Nick</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> On Fri, 2005-06-10 at 12:20 -0500, Arvind Gururajan wrote:</font> <FONT COLOR="#000000">> </font> <FONT COLOR="#000000">> > Hi,</font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > I downloaded the entire MNI package.
Although
I see all these MNI</font> <FONT COLOR="#000000">files, I</font> <FONT COLOR="#000000">> > still get the same error, file not found.
Any
clues why this might be? </font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > Thanks,</font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > Arvind Gururajan</font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > On 9 Jun 2005, Bruce Fischl wrote:</font> <FONT COLOR="#000000">> > > just download and install the whole MNI package. Much easier than</font> <FONT COLOR="#000000">trying </font> <FONT COLOR="#000000">> > > to install various pieces....</font> <FONT COLOR="#000000">> > > </font> <FONT COLOR="#000000">> > > On Thu, 9 Jun 2005, Arvind Gururajan wrote:</font> <FONT COLOR="#000000">> > > </font> <FONT COLOR="#000000">> > > > Hello,</font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > > I am very new to Freesurfer. Could anybody please tell me which</font> <FONT COLOR="#000000">> > specific</font> <FONT COLOR="#000000">> > > > MNI tool, I need to install?</font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> I tried the following command.</font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> ./recon-all -smooth1 ZM</font> <FONT COLOR="#000000">> > > >> ########################################</font> <FONT COLOR="#000000">> > > >> program versions used</font> <FONT COLOR="#000000">> > > >> $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $</font> <FONT COLOR="#000000">> > > >> $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $fire</font> <FONT COLOR="#000000">> > > >> mri_convert --version</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> strings: rawtominc:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: minctracc:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: mincresample:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: mincaverage:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $</font> <FONT COLOR="#000000">> > > >> mri_convert --version</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> strings: mritotal:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: nu_correct:: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: Command: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: not: No such file or directory</font> <FONT COLOR="#000000">> > > >> strings: found.: No such file or directory</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> $</font> <FONT COLOR="#000000">> > > >> #######################################</font> <FONT COLOR="#000000">> > > >> ERROR: Flag ZM unrecognized.</font> <FONT COLOR="#000000">> > > >> -smooth1 ZM</font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> The folder ZM has only one orig file in the surf directory. There</font> <FONT COLOR="#000000">are</font> <FONT COLOR="#000000">> > no</font> <FONT COLOR="#000000">> > > >> raw data(.COR files). Please let me know your feedback.</font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> Sincerely,</font> <FONT COLOR="#000000">> > > >></font> <FONT COLOR="#000000">> > > >> Arvind Gururajan</font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > > _______________________________________________</font> <FONT COLOR="#000000">> > > > Freesurfer mailing list</font> <FONT COLOR="#000000">> > > > <A
HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu
</
A></font> <FONT COLOR="#000000">> > > > <A
HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%22%3Ehttps:/
/m
ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a></font> <FONT COLOR="#000000">> > > ></font> <FONT COLOR="#000000">> > > _______________________________________________</font> <FONT COLOR="#000000">> > > Freesurfer mailing list</font> <FONT COLOR="#000000">> > > <A
HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu
</
A></font> <FONT COLOR="#000000">> > > <A
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/m
ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a></font> <FONT COLOR="#000000">> > > </font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > </font> <FONT COLOR="#000000">> > _______________________________________________</font> <FONT COLOR="#000000">> > Freesurfer mailing list</font> <FONT COLOR="#000000">> > <A
HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu
</
A></font> <FONT COLOR="#000000">> > <A
HREF="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%22%3Ehttps:/
/m
ail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a></font> <FONT COLOR="#000000">> </font>
<FONT
COLOR="#000000">_______________________________________________</font>
<FONT COLOR="#000000">Freesurfer mailing list</font> <FONT COLOR="#000000"><A
HREF="mailto:Freesurfer@nmr.mgh.harvard.edu">Freesurfer@nmr.mgh.harvard.edu
</
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-
Arvind Gururajan -
Bruce Fischl