[Freesurfer] Permission denied
Hello, Recently moved freesurfer from one system to another, but I am having trouble executing it. ./csurf: Permission denied. I have license in the right folder. Has anyone experienced the same problem. Thanks, Arvind ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Overlay on cortical surface
Hello all, I was wondering if it possible to overlay functional data on to (pre-generated)cortical surface? Does freesurfer provide an option to functional/surface registration( I dont have any .cor data instead only .orig)? Could anyone please point out how this could be done? Thanks, Arvind Gururajan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tksurfer: Unable to view .orig file
Hi Bruce, I found out what was wrong. If any of you had the same problem, it could be due to this. Vertices for freesurfer are in millimeters, and I had them in meters. Thanks for your help and good luck with the course. Arvind On 22 Jul 2005, Bruce Fischl wrote: Hi Arvind, it's the middle of the FSL/FreeSurfer course, so we're all really busy. Hopefully we'll get to it next week. Bruce On Thu, 21 Jul 2005, Arvind Gururajan wrote: Hi, Could anyone please tell me what could be wrong? What more information do I need to provide? Your help will be really appreciated. Arvind Gururajan On 20 Jul 2005, Arvind Gururajan wrote: Hi Bruce, I had a single file with both hemisphere data points. Was able to make a crude separation into two hemisphere. Probably couldn't have messed up here, I used a different software to visualize them, and it was fairly clean separation. I used the following command to convert from .asc to .orig. mris_convert /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.curv.asc /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.orig .xdebug_tksurfer for the subject is empty, here it is anyways. Thanks for your help. Arvind On 14 Jul 2005, Bruce Fischl wrote: Hi Arvind, you need to give us more info, and the .xdebug_tksurfer files. Bruce On Thu, 14 Jul 2005, Arvind Gururajan wrote: Hi, I have trouble viewing .orig files in Tksurfer. I used mris_convert to generate .orig files from .ascii( with number of vertices and triangles for each hemisphere). Any quick thoughts on what could be wrong ? No error messages. Help would be appreciated. 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tksurfer: Unable to view .orig file
Hi, Could anyone please tell me what could be wrong? What more information do I need to provide? Your help will be really appreciated. Arvind Gururajan On 20 Jul 2005, Arvind Gururajan wrote: Hi Bruce, I had a single file with both hemisphere data points. Was able to make a crude separation into two hemisphere. Probably couldn't have messed up here, I used a different software to visualize them, and it was fairly clean separation. I used the following command to convert from .asc to .orig. mris_convert /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.curv.asc /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.orig .xdebug_tksurfer for the subject is empty, here it is anyways. Thanks for your help. Arvind On 14 Jul 2005, Bruce Fischl wrote: Hi Arvind, you need to give us more info, and the .xdebug_tksurfer files. Bruce On Thu, 14 Jul 2005, Arvind Gururajan wrote: Hi, I have trouble viewing .orig files in Tksurfer. I used mris_convert to generate .orig files from .ascii( with number of vertices and triangles for each hemisphere). Any quick thoughts on what could be wrong ? No error messages. Help would be appreciated. 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
Re: [Freesurfer] Tksurfer: Unable to view .orig file
Hi Bruce, I had a single file with both hemisphere data points. Was able to make a crude separation into two hemisphere. Probably couldn't have messed up here, I used a different software to visualize them, and it was fairly clean separation. I used the following command to convert from .asc to .orig. mris_convert /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.curv.asc /share_data/server/arvind/freesurfer/subjects/ZM/surf/lh.orig .xdebug_tksurfer for the subject is empty, here it is anyways. Thanks for your help. Arvind On 14 Jul 2005, Bruce Fischl wrote: Hi Arvind, you need to give us more info, and the .xdebug_tksurfer files. Bruce On Thu, 14 Jul 2005, Arvind Gururajan wrote: Hi, I have trouble viewing .orig files in Tksurfer. I used mris_convert to generate .orig files from .ascii( with number of vertices and triangles for each hemisphere). Any quick thoughts on what could be wrong ? No error messages. Help would be appreciated. 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 .xdebug_tksurfer Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Tksurfer: Unable to view .orig file
Hi, I have trouble viewing .orig files in Tksurfer. I used mris_convert to generate .orig files from .ascii( with number of vertices and triangles for each hemisphere). Any quick thoughts on what could be wrong ? No error messages. Help would be appreciated. Arvind Gururajan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] General Question
Hello all, I just had a general question about freesurfer. Does freesurfer use Boundary element model for realistic human head (not sphere etc) ? Thanks, Arvind Gururajan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (MNI tools)
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 packagesmissing 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: [EMAIL PROTECTED] 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.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
Re: [Freesurfer] (MNI tools)
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] Inflate from original surface files
Hello, We have already generated a number of original surface files (.orig) in our lab. We were wondering if there is a way to generate the smooth and the inflated surface from the existing .orig files? Could you provide us a seperate tool to do this conversion? Sincerely, Arvind Gururajan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
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 $ 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
