Hi Freesurfer experts,
A newbie question regarding working with QDEC. When I try to upload the qdec.table.dat file (attached) an error messages pops up "Error loading the data table". To the best of my knowledge I've followed the guidelines on the tutorial in terms of formatting. What would be your suggestions to troubleshoot this?
Thanks!
Fidel
The last line does not end in a new line. Open it in your text editor, go to the last line, hit return, save it, and try again. doug
On 05/15/2012 05:15 PM, Fidel Vila wrote:
Hi Freesurfer experts,
A newbie question regarding working with QDEC. When I try to upload the qdec.table.dat file (attached) an error messages pops up "Error loading the data table". To the best of my knowledge I've followed the guidelines on the tutorial in terms of formatting. What would be your suggestions to troubleshoot this?
Thanks!
Fidel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Freesurfer experts,
I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all.
Advice on how to troubleshoot this would be appreciate.
Thanks,
Fidel
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote:
Hi Freesurfer experts,
I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all.
Advice on how to troubleshoot this would be appreciate.
Thanks,
Fidel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for your prompt reply, Doug.
I've been checking and following the wiki instructions with regards to setting up proper paths, and I could not find an obvious (to me) problem there.
I attach a file with things I have tried and issues I have found.
Further advice will be greatly appreciate it.
Many thanks,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote:
Hi Freesurfer experts,
I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all.
Advice on how to troubleshoot this would be appreciate.
Thanks,
Fidel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Are the missing files in $FREESURFER_HOME/bin and is that path in your system PATH variable?
On 07/26/2012 01:29 PM, Fidel Vila wrote:
Thanks for your prompt reply, Doug.
I've been checking and following the wiki instructions with regards to setting up proper paths, and I could not find an obvious (to me) problem there.
I attach a file with things I have tried and issues I have found.
Further advice will be greatly appreciate it.
Many thanks,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote:
Hi Freesurfer experts,
I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all.
Advice on how to troubleshoot this would be appreciate.
Thanks,
Fidel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.
Shall I report this as a bug?
Regards,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote:
Hi Freesurfer experts,
I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all.
Advice on how to troubleshoot this would be appreciate.
Thanks,
Fidel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
And there is nothing in /Applications/freesurfer/bin? Are there any files in the other directories? Do you have permission to install it in that location? If nothing is in the bin dir, then there is no need to try recon-all, it will always fail. doug
On 07/31/2012 04:05 PM, Fidel Vila wrote:
Hi Doug,
I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.
Shall I report this as a bug?
Regards,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote:
Hi Freesurfer experts,
I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all.
Advice on how to troubleshoot this would be appreciate.
Thanks,
Fidel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
And there is nothing in /Applications/freesurfer/bin?
There are 357 items in /Applications/freesurfer/bin
Are there any files in the other directories?
Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in /Applications/ freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
Do you have permission to install it in that location?
I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
And there is nothing in /Applications/freesurfer/bin? Are there any files in the other directories? Do you have permission to install it in that location? If nothing is in the bin dir, then there is no need to try recon-all, it will always fail. doug
On 07/31/2012 04:05 PM, Fidel Vila wrote:
Hi Doug,
I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.
Shall I report this as a bug?
Regards,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote:
Hi Freesurfer experts,
I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all.
Advice on how to troubleshoot this would be appreciate.
Thanks,
Fidel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
This is strange, it must be something that is specific to the PPC Mac distribution. Nick is going to have to deal with this, but he won't be back until Mon. Can you wait that long? doug
On 07/31/2012 06:01 PM, Fidel Vila wrote:
And there is nothing in /Applications/freesurfer/bin?
There are 357 items in /Applications/freesurfer/bin
Are there any files in the other directories?
Indeed, from /Application/freesurfer/average (50 items in here) to /Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in /Applications/freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
Do you have permission to install it in that location?
I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
And there is nothing in /Applications/freesurfer/bin? Are there any files in the other directories? Do you have permission to install it in that location? If nothing is in the bin dir, then there is no need to try recon-all, it will always fail. doug
On 07/31/2012 04:05 PM, Fidel Vila wrote:
Hi Doug,
I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.
Shall I report this as a bug?
Regards,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote:
Hi Freesurfer experts,
I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all.
Advice on how to troubleshoot this would be appreciate.
Thanks,
Fidel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Hi,
I'm reposting this, hoping Nick has returned and can provide some guidance.
Thanks,
Fidel
On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:
This is strange, it must be something that is specific to the PPC Mac distribution. Nick is going to have to deal with this, but he won't be back until Mon. Can you wait that long? doug
On 07/31/2012 06:01 PM, Fidel Vila wrote:
And there is nothing in /Applications/freesurfer/bin?
There are 357 items in /Applications/freesurfer/bin
Are there any files in the other directories?
Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in / Applications/freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
Do you have permission to install it in that location?
I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
And there is nothing in /Applications/freesurfer/bin? Are there any files in the other directories? Do you have permission to install it in that location? If nothing is in the bin dir, then there is no need to try recon-all, it will always fail. doug
On 07/31/2012 04:05 PM, Fidel Vila wrote:
Hi Doug,
I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.
Shall I report this as a bug?
Regards,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote:
Hi Freesurfer experts,
I recently installed FS (PowerPC architecture version available on FS website) on a Mac OS X 10.4.11 and I get the attached output error when running recon-all.
Advice on how to troubleshoot this would be appreciate.
Thanks,
Fidel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Fidel,
I don't know why those files are missing from the Tiger ppc distribution, but i confirmed that indeed they are. Here is a tarball of the distribution which contains everything:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
save it to your /Applications directory, and then from the Terminal type:
cd /Applications sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
you dont need to remove your existing install.
Nick
Hi,
I'm reposting this, hoping Nick has returned and can provide some guidance.
Thanks,
Fidel
On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:
This is strange, it must be something that is specific to the PPC Mac distribution. Nick is going to have to deal with this, but he won't be back until Mon. Can you wait that long? doug
On 07/31/2012 06:01 PM, Fidel Vila wrote:
And there is nothing in /Applications/freesurfer/bin?
There are 357 items in /Applications/freesurfer/bin
Are there any files in the other directories?
Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in / Applications/freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
Do you have permission to install it in that location?
I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
And there is nothing in /Applications/freesurfer/bin? Are there any files in the other directories? Do you have permission to install it in that location? If nothing is in the bin dir, then there is no need to try recon-all, it will always fail. doug
On 07/31/2012 04:05 PM, Fidel Vila wrote:
Hi Doug,
I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.
Shall I report this as a bug?
Regards,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote: > Hi Freesurfer experts, > > I recently installed FS (PowerPC architecture version available > on FS website) on a Mac OS X 10.4.11 and I get the attached > output error when running recon-all. > > Advice on how to troubleshoot this would be appreciate. > > Thanks, > > Fidel > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks a lot Nick.
It worked like a charm:
"recon-all -s struct_FS finished without error at Thu Aug 23 03:52:39 PDT 2012 done"
For other users whose OS automatically unzips the .gz,
the command to type is:
sudo tar xvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar
Thanks!
Fidel
On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote:
Fidel,
I don't know why those files are missing from the Tiger ppc distribution, but i confirmed that indeed they are. Here is a tarball of the distribution which contains everything:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
save it to your /Applications directory, and then from the Terminal type:
cd /Applications sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
you dont need to remove your existing install.
Nick
Hi,
I'm reposting this, hoping Nick has returned and can provide some guidance.
Thanks,
Fidel
On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:
This is strange, it must be something that is specific to the PPC Mac distribution. Nick is going to have to deal with this, but he won't be back until Mon. Can you wait that long? doug
On 07/31/2012 06:01 PM, Fidel Vila wrote:
And there is nothing in /Applications/freesurfer/bin?
There are 357 items in /Applications/freesurfer/bin
Are there any files in the other directories?
Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in / Applications/freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
Do you have permission to install it in that location?
I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
And there is nothing in /Applications/freesurfer/bin? Are there any files in the other directories? Do you have permission to install it in that location? If nothing is in the bin dir, then there is no need to try recon-all, it will always fail. doug
On 07/31/2012 04:05 PM, Fidel Vila wrote:
Hi Doug,
I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.
Shall I report this as a bug?
Regards,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote: > Hi Freesurfer experts, > > I recently installed FS (PowerPC architecture version available > on FS website) on a Mac OS X 10.4.11 and I get the attached > output error when running recon-all. > > Advice on how to troubleshoot this would be appreciate. > > Thanks, > > Fidel > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
I run recon-all and worked well, but then I added the hippo-subfields flag and quitted with errors. The hippo-subfields.log says "kvlSegmentHippocamlSubfields.sh: Command not found".
I went into the bin folder and all the kvl files are missing.
Advice will be appreciate it.
Thanks,
Fidel
On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote:
Fidel,
I don't know why those files are missing from the Tiger ppc distribution, but i confirmed that indeed they are. Here is a tarball of the distribution which contains everything:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
save it to your /Applications directory, and then from the Terminal type:
cd /Applications sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
you dont need to remove your existing install.
Nick
Hi,
I'm reposting this, hoping Nick has returned and can provide some guidance.
Thanks,
Fidel
On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:
This is strange, it must be something that is specific to the PPC Mac distribution. Nick is going to have to deal with this, but he won't be back until Mon. Can you wait that long? doug
On 07/31/2012 06:01 PM, Fidel Vila wrote:
And there is nothing in /Applications/freesurfer/bin?
There are 357 items in /Applications/freesurfer/bin
Are there any files in the other directories?
Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in / Applications/freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
Do you have permission to install it in that location?
I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
And there is nothing in /Applications/freesurfer/bin? Are there any files in the other directories? Do you have permission to install it in that location? If nothing is in the bin dir, then there is no need to try recon-all, it will always fail. doug
On 07/31/2012 04:05 PM, Fidel Vila wrote:
Hi Doug,
I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.
Shall I report this as a bug?
Regards,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
did you set up your environment so that your path environment variable has all the proper paths in it? Look at the wiki for instructions. doug
On 7/25/12 7:57 PM, Fidel Vila wrote: > Hi Freesurfer experts, > > I recently installed FS (PowerPC architecture version available > on FS website) on a Mac OS X 10.4.11 and I get the attached > output error when running recon-all. > > Advice on how to troubleshoot this would be appreciate. > > Thanks, > > Fidel > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Fidel,
Sorry, but the GEMS tools are not built for our mac powerpc distribution. we no longer support that platform (or at least we dont make an effort to build the entire freesurfer toolset on it). Our focus is now on getting a 64b Mac (Mountain) Lion build working.
Nick
Hi Nick,
I run recon-all and worked well, but then I added the hippo-subfields flag and quitted with errors. The hippo-subfields.log says "kvlSegmentHippocamlSubfields.sh: Command not found".
I went into the bin folder and all the kvl files are missing.
Advice will be appreciate it.
Thanks,
Fidel
On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote:
Fidel,
I don't know why those files are missing from the Tiger ppc distribution, but i confirmed that indeed they are. Here is a tarball of the distribution which contains everything:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
save it to your /Applications directory, and then from the Terminal type:
cd /Applications sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
you dont need to remove your existing install.
Nick
Hi,
I'm reposting this, hoping Nick has returned and can provide some guidance.
Thanks,
Fidel
On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:
This is strange, it must be something that is specific to the PPC Mac distribution. Nick is going to have to deal with this, but he won't be back until Mon. Can you wait that long? doug
On 07/31/2012 06:01 PM, Fidel Vila wrote:
And there is nothing in /Applications/freesurfer/bin?
There are 357 items in /Applications/freesurfer/bin
Are there any files in the other directories?
Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in / Applications/freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
Do you have permission to install it in that location?
I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
And there is nothing in /Applications/freesurfer/bin? Are there any files in the other directories? Do you have permission to install it in that location? If nothing is in the bin dir, then there is no need to try recon-all, it will always fail. doug
On 07/31/2012 04:05 PM, Fidel Vila wrote:
Hi Doug,
I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.
Shall I report this as a bug?
Regards,
Fidel
On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:
> did you set up your environment so that your path environment > variable has all the proper paths in it? Look at the wiki for > instructions. > doug > > On 7/25/12 7:57 PM, Fidel Vila wrote: >> Hi Freesurfer experts, >> >> I recently installed FS (PowerPC architecture version available >> on FS website) on a Mac OS X 10.4.11 and I get the attached >> output error when running recon-all. >> >> Advice on how to troubleshoot this would be appreciate. >> >> Thanks, >> >> Fidel >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello--was just thinking about upgrading to Mountain Lion. Am I to assume freesurfer will not work if I do this?
Anthony
On 9/10/12 11:58 AM, Nick Schmansky wrote:
Fidel,
Sorry, but the GEMS tools are not built for our mac powerpc distribution. we no longer support that platform (or at least we dont make an effort to build the entire freesurfer toolset on it). Our focus is now on getting a 64b Mac (Mountain) Lion build working.
Nick
Hi Nick,
I run recon-all and worked well, but then I added the hippo-subfields flag and quitted with errors. The hippo-subfields.log says "kvlSegmentHippocamlSubfields.sh: Command not found".
I went into the bin folder and all the kvl files are missing.
Advice will be appreciate it.
Thanks,
Fidel
On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote:
Fidel,
I don't know why those files are missing from the Tiger ppc distribution, but i confirmed that indeed they are. Here is a tarball of the distribution which contains everything:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
save it to your /Applications directory, and then from the Terminal type:
cd /Applications sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
you dont need to remove your existing install.
Nick
Hi,
I'm reposting this, hoping Nick has returned and can provide some guidance.
Thanks,
Fidel
On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:
This is strange, it must be something that is specific to the PPC Mac distribution. Nick is going to have to deal with this, but he won't be back until Mon. Can you wait that long? doug
On 07/31/2012 06:01 PM, Fidel Vila wrote:
And there is nothing in /Applications/freesurfer/bin?
There are 357 items in /Applications/freesurfer/bin
Are there any files in the other directories?
Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in / Applications/freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
Do you have permission to install it in that location?
I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
And there is nothing in /Applications/freesurfer/bin? Are there any files in the other directories? Do you have permission to install it in that location? If nothing is in the bin dir, then there is no need to try recon-all, it will always fail. doug
On 07/31/2012 04:05 PM, Fidel Vila wrote: > Hi Doug, > > I re-installed freesurfer, and I still get the same error message > (terminal output attached); bin files are still missing from bin > folder. > > Shall I report this as a bug? > > Regards, > > Fidel > > > > > On 25-Jul-12, at 8:22 PM, Douglas Greve wrote: > >> did you set up your environment so that your path environment >> variable has all the proper paths in it? Look at the wiki for >> instructions. >> doug >> >> On 7/25/12 7:57 PM, Fidel Vila wrote: >>> Hi Freesurfer experts, >>> >>> I recently installed FS (PowerPC architecture version available >>> on FS website) on a Mac OS X 10.4.11 and I get the attached >>> output error when running recon-all. >>> >>> Advice on how to troubleshoot this would be appreciate. >>> >>> Thanks, >>> >>> Fidel >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> The information in this e-mail is intended only for the person >> to whom it is >> addressed. If you believe this e-mail was sent to you in error >> and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent >> to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail.
>>
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
Anthony,
Our Leopard build should work on Mountain Lion, although I havent confirmed this. It works on Lion.
The Leopard build is 32b, so some stuff which can use >4GB of memory (like mri_cvs_register) will fail due to inability to alloc memory.
Nick
On Mon, 2012-09-10 at 12:04 -0400, Anthony Dick wrote:
Hello--was just thinking about upgrading to Mountain Lion. Am I to assume freesurfer will not work if I do this?
Anthony
On 9/10/12 11:58 AM, Nick Schmansky wrote:
Fidel,
Sorry, but the GEMS tools are not built for our mac powerpc distribution. we no longer support that platform (or at least we dont make an effort to build the entire freesurfer toolset on it). Our focus is now on getting a 64b Mac (Mountain) Lion build working.
Nick
Hi Nick,
I run recon-all and worked well, but then I added the hippo-subfields flag and quitted with errors. The hippo-subfields.log says "kvlSegmentHippocamlSubfields.sh: Command not found".
I went into the bin folder and all the kvl files are missing.
Advice will be appreciate it.
Thanks,
Fidel
On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote:
Fidel,
I don't know why those files are missing from the Tiger ppc distribution, but i confirmed that indeed they are. Here is a tarball of the distribution which contains everything:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
save it to your /Applications directory, and then from the Terminal type:
cd /Applications sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
you dont need to remove your existing install.
Nick
Hi,
I'm reposting this, hoping Nick has returned and can provide some guidance.
Thanks,
Fidel
On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:
This is strange, it must be something that is specific to the PPC Mac distribution. Nick is going to have to deal with this, but he won't be back until Mon. Can you wait that long? doug
On 07/31/2012 06:01 PM, Fidel Vila wrote:
> And there is nothing in /Applications/freesurfer/bin? There are 357 items in /Applications/freesurfer/bin
> Are there any files in the other directories? Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in / Applications/freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
> Do you have permission to install it in that location? I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
> And there is nothing in /Applications/freesurfer/bin? Are there > any files in the other directories? Do you have permission to > install it in that location? If nothing is in the bin dir, then > there is no need to try recon-all, it will always fail. > doug > > > > On 07/31/2012 04:05 PM, Fidel Vila wrote: >> Hi Doug, >> >> I re-installed freesurfer, and I still get the same error message >> (terminal output attached); bin files are still missing from bin >> folder. >> >> Shall I report this as a bug? >> >> Regards, >> >> Fidel >> >> >> >> >> On 25-Jul-12, at 8:22 PM, Douglas Greve wrote: >> >>> did you set up your environment so that your path environment >>> variable has all the proper paths in it? Look at the wiki for >>> instructions. >>> doug >>> >>> On 7/25/12 7:57 PM, Fidel Vila wrote: >>>> Hi Freesurfer experts, >>>> >>>> I recently installed FS (PowerPC architecture version available >>>> on FS website) on a Mac OS X 10.4.11 and I get the attached >>>> output error when running recon-all. >>>> >>>> Advice on how to troubleshoot this would be appreciate. >>>> >>>> Thanks, >>>> >>>> Fidel >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> The information in this e-mail is intended only for the person >>> to whom it is >>> addressed. If you believe this e-mail was sent to you in error >>> and the e-mail >>> contains patient information, please contact the Partners >>> Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent >>> to you in error >>> but does not contain patient information, please contact the >>> sender and properly >>> dispose of the e-mail. >>> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
FSv5.1 seems to run fine on 64-bit Mountain Lion, as far as I can tell, but I have not tried GEMS or TRACULA just yet... (I upgraded before installing, in case that matters.)
I use XQuartz for tkmedit, freeview, fslview, etc.
So far so good!
~ShannonB
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Monday, September 10, 2012 1:46 PM To: Anthony Dick Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] kvl binaries missing from ppc 5.1 stable release
Anthony,
Our Leopard build should work on Mountain Lion, although I havent confirmed this. It works on Lion.
The Leopard build is 32b, so some stuff which can use >4GB of memory (like mri_cvs_register) will fail due to inability to alloc memory.
Nick
On Mon, 2012-09-10 at 12:04 -0400, Anthony Dick wrote:
Hello--was just thinking about upgrading to Mountain Lion. Am I to assume freesurfer will not work if I do this?
Anthony
On 9/10/12 11:58 AM, Nick Schmansky wrote:
Fidel,
Sorry, but the GEMS tools are not built for our mac powerpc
distribution.
we no longer support that platform (or at least we dont make an effort to build the entire freesurfer toolset on it). Our focus is now on getting a 64b Mac (Mountain) Lion build working.
Nick
Hi Nick,
I run recon-all and worked well, but then I added the hippo-subfields flag and quitted with errors. The hippo-subfields.log says "kvlSegmentHippocamlSubfields.sh: Command not found".
I went into the bin folder and all the kvl files are missing.
Advice will be appreciate it.
Thanks,
Fidel
On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote:
Fidel,
I don't know why those files are missing from the Tiger ppc distribution, but i confirmed that indeed they are. Here is a tarball of the distribution which contains everything:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurf er-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
save it to your /Applications directory, and then from the Terminal type:
cd /Applications sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz
you dont need to remove your existing install.
Nick
Hi,
I'm reposting this, hoping Nick has returned and can provide some guidance.
Thanks,
Fidel
On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:
This is strange, it must be something that is specific to the PPC Mac distribution. Nick is going to have to deal with this, but he won't be back until Mon. Can you wait that long? doug
On 07/31/2012 06:01 PM, Fidel Vila wrote:
> And there is nothing in /Applications/freesurfer/bin? There are 357 items in /Applications/freesurfer/bin
> Are there any files in the other directories? Indeed, from /Application/freesurfer/average (50 items in here) to / Applications/freesurfer/trctrain (35 items) as well as
'LICENSE'
file, 'README' file, etc. Not to forget my user license file (i.e. .license)
The executable files missing in /Applications/freesurfer/bin seem to be:
talairach_avi ;mri_watershed ; ;mri_segment ;mri_tessellate ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate ;mris_curvature ;mris_sphere ;mris_fix_topology ;mris_topo_fixer ;mris_ca_label ;mris_euler_number ;mris_make_surfaces ;mris_register ;mris_volmask ;mris_anatomical_stats ;mrisp_paint ;mris_curvature_stats ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats
Also, running grep -f /CommandsNotFound.txt (file listing the commands listed above) /Files_in_Bin.txt (list of 357 items in / Applications/freesurfer/bin folder) retrieves no matching pattern.
The list of commands above matches the list of warning errors (i.e. command not found) when I run recon-all.
> Do you have permission to install it in that location? I do.
Could this be related to compillation of files for the May 2011 5.1. stable release for ppc?
Appreciate your advice and support as I understand ppc machines might not be one of the highest priorities...
Regards,
Fidel
On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:
> And there is nothing in /Applications/freesurfer/bin? Are there > any files in the other directories? Do you have permission to > install it in that location? If nothing is in the bin dir, then > there is no need to try recon-all, it will always fail. > doug > > > > On 07/31/2012 04:05 PM, Fidel Vila wrote: >> Hi Doug, >> >> I re-installed freesurfer, and I still get the same error >> message (terminal output attached); bin files are still >> missing from bin folder. >> >> Shall I report this as a bug? >> >> Regards, >> >> Fidel >> >> >> >> >> On 25-Jul-12, at 8:22 PM, Douglas Greve wrote: >> >>> did you set up your environment so that your path environment >>> variable has all the proper paths in it? Look at the wiki for >>> instructions. >>> doug >>> >>> On 7/25/12 7:57 PM, Fidel Vila wrote: >>>> Hi Freesurfer experts, >>>> >>>> I recently installed FS (PowerPC architecture version >>>> available on FS website) on a Mac OS X 10.4.11 and I get the >>>> attached output error when running recon-all. >>>> >>>> Advice on how to troubleshoot this would be appreciate. >>>> >>>> Thanks, >>>> >>>> Fidel >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> The information in this e-mail is intended only for the >>> person to whom it is addressed. If you believe this e-mail >>> was sent to you in error and the e-mail contains patient >>> information, please contact the Partners Compliance HelpLine >>> at http://www.partners.org/complianceline . If the e-mail was >>> sent to you in error but does not contain patient >>> information, please contact the sender and properly dispose >>> of the e-mail. >>> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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