Hello Freesurfer Developers,
We are attempting to install freesurfer as one of our standard image processing packages at the Mental Health Clinical Research Center Image Processing Lab at The University of Iowa. Our environment consists of Redhat EL3WS, Redhat EL4WS, and MacOSX 10.4 operating systems.
I could only find a matching MacOSX version of the software. Will the Redhat series of OS be supported?
Additionally, I am attempting to install freesurfer on Mac OS X 10.4, but after the installer spends several minutes installing, it reports "There were errors installing the software" "Please try installing again".
Your help and advise is greatly appreciated.
Thanks, Hans J. Johnson, PhD Director of Image Processing The Department of Psychiatry, The University of Iowa
Hans,
Hello, Does your Mac OS X Tiger freesurfer installation work despite the reported error? I suspect that the problem is that it failed to write the 'receipt' to the /Library/Receipt directory, which requires Administrator privileges.
This is the only part of the install (as currently implemented) that necessitates Admin privileges, but does not (currently) prompt for it.
If, following the running of the command: 'source /Users/Shared/freesurfer/SetUpFreeSurfer.csh' you are able to run freesurfer commands (such as recon-all --help), then the installation proceeded correctly. BTW, 'recon-all --help' is the epicenter of freesurfer, and the best place to begin working with the tools (although an updated tutorial is soon to be made available).
However, if you need to re-install, then at the point where the error is displayed, before closing that box, click on the upper-bar menu item 'Window->Installer Log', which will show the error in more detail.
This Mac installation is a bit in-flux as we prepare for an official release in a couple weeks, so I apologize for the troubles. Linux distributions with decent install instructions will also be forthcoming (in the upcoming release).
Any suggestions are appreciated.
------------------------------------------------------------------------ Nick Schmansky, Engineer email: nicks at nmr.mgh.harvard.edu MGH/MIT/HMS Martinos Center for Biomedical Imaging 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 USA ------------------------------------------------------------------------
On Wed, 2005-07-27 at 07:52 -0500, Hans Johnson wrote:
Hello Freesurfer Developers,
We are attempting to install freesurfer as one of our standard image processing packages at the Mental Health Clinical Research Center Image Processing Lab at The University of Iowa. Our environment consists of Redhat EL3WS, Redhat EL4WS, and MacOSX 10.4 operating systems.
I could only find a matching MacOSX version of the software. Will the Redhat series of OS be supported?
Additionally, I am attempting to install freesurfer on Mac OS X 10.4, but after the installer spends several minutes installing, it reports "There were errors installing the software" "Please try installing again".
Your help and advise is greatly appreciated.
Thanks, Hans J. Johnson, PhD Director of Image Processing The Department of Psychiatry, The University of Iowa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick,
It does seem that the freesurfer files are installed on my Mac.
Just some minor notes:
1) Bash/POSIX shell is not supported. 'source /Users/Shared/freesurfer/SetUpFreeSurfer.csh' 2) After changing to tcsh and resourcing 'source /Users/Shared/freesurfer/SetUpFreeSurfer.csh' the PATH does not include /Users/Shared/freesurfer/bin. 3) During sourcing, warnings are presented about MINC_BIN_DIR and MINC_LIB_DIR not being defined. If they are included with freesurfer, they should be set automatically, if not, the warning message should indicate where to get the package.
I have not actually ran any data yet.
Thank you for your help.
Hans
On 7/27/05 8:32 AM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Hans,
Hello, Does your Mac OS X Tiger freesurfer installation work despite the reported error? I suspect that the problem is that it failed to write the 'receipt' to the /Library/Receipt directory, which requires Administrator privileges.
This is the only part of the install (as currently implemented) that necessitates Admin privileges, but does not (currently) prompt for it.
If, following the running of the command: 'source /Users/Shared/freesurfer/SetUpFreeSurfer.csh' you are able to run freesurfer commands (such as recon-all --help), then the installation proceeded correctly. BTW, 'recon-all --help' is the epicenter of freesurfer, and the best place to begin working with the tools (although an updated tutorial is soon to be made available).
However, if you need to re-install, then at the point where the error is displayed, before closing that box, click on the upper-bar menu item 'Window->Installer Log', which will show the error in more detail.
This Mac installation is a bit in-flux as we prepare for an official release in a couple weeks, so I apologize for the troubles. Linux distributions with decent install instructions will also be forthcoming (in the upcoming release).
Any suggestions are appreciated.
Nick Schmansky, Engineer email: nicks at nmr.mgh.harvard.edu MGH/MIT/HMS Martinos Center for Biomedical Imaging 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 USA
On Wed, 2005-07-27 at 07:52 -0500, Hans Johnson wrote:
Hello Freesurfer Developers,
We are attempting to install freesurfer as one of our standard image processing packages at the Mental Health Clinical Research Center Image Processing Lab at The University of Iowa. Our environment consists of Redhat EL3WS, Redhat EL4WS, and MacOSX 10.4 operating systems.
I could only find a matching MacOSX version of the software. Will the Redhat series of OS be supported?
Additionally, I am attempting to install freesurfer on Mac OS X 10.4, but after the installer spends several minutes installing, it reports "There were errors installing the software" "Please try installing again".
Your help and advise is greatly appreciated.
Thanks, Hans J. Johnson, PhD Director of Image Processing The Department of Psychiatry, The University of Iowa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hans,
Hello, from your comments, I think I spoke too soon in stating that your installation completed successfully. In a successful installation, the freesurfer/bin directory is placed in the path. Also, the MINC tools, which are included in the Mac OS X Tiger 'full' distribution, are installed (in the freesurfer/lib/mni directory) and setup automatically by the SetUpFreeSurfer.csh script (via the call to the FreeSurferEnv.csh script).
I suspect that the original install failed for reasons other than failing to write the /Library/Receipts directory (as I had earlier suspected). If you would like to try a re-install, then when it reaches the failure point, before closing the Installer application, click on the menu item 'Windows->Installer Log', and it should display the reason for installation failure. I am a bit curious as to the reason for the failure.
I believe a bash version of SetUpFreeSurfer will be included in the next release.
I appreciate your comments, and hope this install can be made to work for you.
Nick
On Wed, 2005-07-27 at 12:54 -0500, Hans Johnson wrote:
Nick,
It does seem that the freesurfer files are installed on my Mac.
Just some minor notes:
- Bash/POSIX shell is not supported.
'source /Users/Shared/freesurfer/SetUpFreeSurfer.csh' 2) After changing to tcsh and resourcing 'source /Users/Shared/freesurfer/SetUpFreeSurfer.csh' the PATH does not include /Users/Shared/freesurfer/bin. 3) During sourcing, warnings are presented about MINC_BIN_DIR and MINC_LIB_DIR not being defined. If they are included with freesurfer, they should be set automatically, if not, the warning message should indicate where to get the package.
I have not actually ran any data yet.
Thank you for your help.
Hans
On 7/27/05 8:32 AM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Hans,
Hello, Does your Mac OS X Tiger freesurfer installation work despite the reported error? I suspect that the problem is that it failed to write the 'receipt' to the /Library/Receipt directory, which requires Administrator privileges.
This is the only part of the install (as currently implemented) that necessitates Admin privileges, but does not (currently) prompt for it.
If, following the running of the command: 'source /Users/Shared/freesurfer/SetUpFreeSurfer.csh' you are able to run freesurfer commands (such as recon-all --help), then the installation proceeded correctly. BTW, 'recon-all --help' is the epicenter of freesurfer, and the best place to begin working with the tools (although an updated tutorial is soon to be made available).
However, if you need to re-install, then at the point where the error is displayed, before closing that box, click on the upper-bar menu item 'Window->Installer Log', which will show the error in more detail.
This Mac installation is a bit in-flux as we prepare for an official release in a couple weeks, so I apologize for the troubles. Linux distributions with decent install instructions will also be forthcoming (in the upcoming release).
Any suggestions are appreciated.
Nick Schmansky, Engineer email: nicks at nmr.mgh.harvard.edu MGH/MIT/HMS Martinos Center for Biomedical Imaging 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 USA
On Wed, 2005-07-27 at 07:52 -0500, Hans Johnson wrote:
Hello Freesurfer Developers,
We are attempting to install freesurfer as one of our standard image processing packages at the Mental Health Clinical Research Center Image Processing Lab at The University of Iowa. Our environment consists of Redhat EL3WS, Redhat EL4WS, and MacOSX 10.4 operating systems.
I could only find a matching MacOSX version of the software. Will the Redhat series of OS be supported?
Additionally, I am attempting to install freesurfer on Mac OS X 10.4, but after the installer spends several minutes installing, it reports "There were errors installing the software" "Please try installing again".
Your help and advise is greatly appreciated.
Thanks, Hans J. Johnson, PhD Director of Image Processing The Department of Psychiatry, The University of Iowa
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Hans Johnson -
Nick Schmansky