Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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 gr...@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 gr...@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
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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 gr...@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 gr...@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
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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 gr...@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 gr...@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
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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 gr...@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 gr...@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
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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 Last login: Tue Jul 31 12:51:32 on ttyp2 Welcome to Darwin! a3128u:~ FVila$ export FREESURFER_HOME=/Applications/freesurfer a3128u:~ FVila$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /Applications//fsl a3128u:~ FVila$ recon-all -i /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid struct_FS Subject Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc tcsh: talairach_avi: Command not found. tcsh: mri_watershed: Command not found. tcsh: mri_segment: Command not found. tcsh: mri_tessellate: Command not found. tcsh: mri_concatenate_lta: Command not found. tcsh: mri_normalize_tp2: Command not found. tcsh: mris_smooth: Command not found. tcsh: mris_inflate: Command not found. tcsh: mris_curvature: Command not found. tcsh: mris_sphere: Command not found. tcsh: mris_fix_topology: Command not found. tcsh: mris_topo_fixer: Command not found. tcsh: mris_ca_label: Command not found. tcsh: mris_euler_number: Command not found. tcsh: mris_make_surfaces: Command not found. tcsh: mris_register: Command not found. tcsh: mris_volmask: Command not found. tcsh: mris_anatomical_stats: Command not found. tcsh: mrisp_paint: Command not found. tcsh: mris_curvature_stats: Command not found. tcsh: mris_calc: Command not found. tcsh: mri_robust_register: Command not found. tcsh: mri_robust_template: Command not found. tcsh: mri_segstats: Command not found. /Applications/freesurfer/subjects/struct_FS \n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/struct_FS/mri/orig/001.mgz \n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/struct_FS/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/struct_FS/mri/orig/001.mgz... #-- recon-all -s struct_FS finished without error at Tue Jul 31 12:54:59 PDT 2012 done a3128u:~ FVila$ On 25-Jul-12, at 8:22 PM, Douglas Greve wrote: did you set up your environment so that your path environmentvariable has all the proper paths in it? Look at the wiki forinstructions.dougOn 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/freesurferThe 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 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.
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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 gr...@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
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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 gr...@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
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
Try re-installing. Make sure you have enough disk space. doug On 07/30/2012 12:43 AM, Fidel Vila wrote: Hi Doug. The missing files are NOT in $FREESURFER_HOME/bin; So, I guess that's why they are not found even though the path is set up in the system PATH variable. Suggestions? Fidel 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 mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Fidel Vila-Rodriguez, MD, FRCPC Clinical Assistant Professor, Faculty of Medicine, Dpt. of Psychiatry, University of British Columbia UBC Clinician Investigator Fellow UBC Graduate Program in Neuroscience Ph.D Candidate BC Mental Health and Addiction Research Institute A3-128-4, 938 West 28th Ave Vancouver, BC V5Z 4H4 Tel: 604-875-2000 Ext. 4732 Fax: 604-875-3871 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
Hi Doug. The missing files are NOT in $FREESURFER_HOME/bin; So, I guess that's why they are not found even though the path is set up in the system PATH variable. Suggestions? Fidel 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 Vila-Rodriguez, MD, FRCPC Clinical Assistant Professor, Faculty of Medicine, Dpt. of Psychiatry, University of British Columbia UBC Clinician Investigator Fellow UBC Graduate Program in Neuroscience Ph.D Candidate BC Mental Health and Addiction Research Institute A3-128-4, 938 West 28th Ave Vancouver, BC V5Z 4H4 Tel: 604-875-2000 Ext. 4732 Fax: 604-875-3871 ___ 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.
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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{\rtf1\ansi\ansicpg1252\cocoartf949\cocoasubrtf540
{\fonttbl\f0\fswiss\fcharset0 Helvetica;}
{\colortbl;\red255\green255\blue255;}
\margl1440\margr1440\vieww25400\viewh16080\viewkind0
\pard\tx566\tx1133\tx1700\tx2267\tx2834\tx3401\tx3968\tx4535\tx5102\tx5669\tx6236\tx6803\ql\qnatural\pardirnatural
\f0\fs24 \cf0 \
\b #Checked paths on SetUpFreesurfer.sh to make sure they direct to the right spot\
#Run commands to setup FS environment
\b0 \
\
a3128u:/Applications FVila$ export FREESURFER_HOME=/Applications/freesurfer\
a3128u:/Applications FVila$ source $FREESURFER_HOME/SetUpFreeSurfer.sh\
freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 \
Setting up environment for FreeSurfer/FS-FAST (and FSL)\
FREESURFER_HOME /Applications/freesurfer\
FSFAST_HOME /Applications/freesurfer/fsfast\
FSF_OUTPUT_FORMAT nii.gz\
SUBJECTS_DIR /Applications/freesurfer/subjects\
MNI_DIR /Applications/freesurfer/mni\
FSL_DIR /users/FVila/fsl\
\
\b #Paths point to the right place in terms of HOME, FSFAST, SUBJECTS_DIR, etc \
#Try to run a recon-all -i command
\b0 \
\
a3128u:/Applications FVila$ recon-all -i /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid FS_struct.nii.gz \
\
Subject Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0\
Current Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0\
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects\
Actual FREESURFER_HOME /Applications/freesurfer\
\
\b #I get a list of commands not found
\b0 \
\
Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc\
tcsh: talairach_avi: Command not found.\
tcsh: mri_watershed: Command not found.\
tcsh: mri_segment: Command not found.\
tcsh: mri_tessellate: Command not found.\
tcsh: mri_concatenate_lta: Command not found.\
tcsh: mri_normalize_tp2: Command not found.\
tcsh: mris_smooth: Command not found.\
tcsh: mris_inflate: Command not found.\
tcsh: mris_curvature: Command not found.\
tcsh: mris_sphere: Command not found.\
tcsh: mris_fix_topology: Command not found.\
tcsh: mris_topo_fixer: Command not found.\
tcsh: mris_ca_label: Command not found.\
tcsh: mris_euler_number: Command not found.\
tcsh: mris_make_surfaces: Command not found.\
tcsh: mris_register: Command not found.\
tcsh: mris_volmask: Command not found.\
tcsh: mris_anatomical_stats: Command not found.\
tcsh: mrisp_paint: Command not found.\
tcsh: mris_curvature_stats: Command not found.\
tcsh: mris_calc: Command not found.\
tcsh: mri_robust_register: Command not found.\
tcsh: mri_robust_template: Command not found.\
tcsh: mri_segstats: Command not found.\
/Applications/freesurfer/subjects/FS_struct.nii.gz\
\\n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz \\n\
mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz \
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $\
reading from /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz...\
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00\
i_ras = (-1, 0, 0)\
j_ras = (0, 1, 0)\
k_ras = (0, 0, 1)\
writing to /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz...\
\
#--\
\
\b #But the recon-all is reported as finished without error.
\b0 \
\
recon-all -s FS_struct.nii.gz finished without error at Wed Jul 25 16:46:00 PDT 2012\
done\
\
\
\b #I go into the /freesurfer/bin folder to check whether the commands listed above as not found are actually there... they are missing (??)\
\b0 \
a3128u:/Applications/freesurfer/bin FVila$ ls\
LongQdecTable.pyminc2seqinfomri_motion_correct2\
UpdateNeededmisc.py mri_ms_fitparms\
aparc2feat mkfsdistmri_multispectral_segment\
aparcstats2tablemkheadsurf mri_nl_align\
aparcstatsdiff mkima_index.tcl mri_nl_align_binary\
aseg2feat mkmnc_index.tcl mri_nlfilter\
asegstats2table mksubjdirs mri_normalize\
asegstatsdiff mksurfatlas mri_nu_correct.mni\
avi2talxfm mkxsubjreg mri_or\
batchjobs
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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] tcsh: tailarach_avi: Command not found
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 a3128u:/Applications FVila$ export FREESURFER_HOME=/Applications/freesurfer a3128u:/Applications FVila$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /users/FVila/fsl a3128u:/Applications FVila$ recon-all -i /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid FS_struct.nii.gz ERROR: You are trying to re-run an existing subject with (possibly) new input data (-i). If this is truly new input data, you should delete the subject folder and re-run, or specify a different subject name. If you are just continuing an analysis of an existing subject, then omit all -i flags. a3128u:/Applications FVila$ recon-all -i /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid FS_struct.nii.gz Subject Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc tcsh: talairach_avi: Command not found. tcsh: mri_watershed: Command not found. tcsh: mri_segment: Command not found. tcsh: mri_tessellate: Command not found. tcsh: mri_concatenate_lta: Command not found. tcsh: mri_normalize_tp2: Command not found. tcsh: mris_smooth: Command not found. tcsh: mris_inflate: Command not found. tcsh: mris_curvature: Command not found. tcsh: mris_sphere: Command not found. tcsh: mris_fix_topology: Command not found. tcsh: mris_topo_fixer: Command not found. tcsh: mris_ca_label: Command not found. tcsh: mris_euler_number: Command not found. tcsh: mris_make_surfaces: Command not found. tcsh: mris_register: Command not found. tcsh: mris_volmask: Command not found. tcsh: mris_anatomical_stats: Command not found. tcsh: mrisp_paint: Command not found. tcsh: mris_curvature_stats: Command not found. tcsh: mris_calc: Command not found. tcsh: mri_robust_register: Command not found. tcsh: mri_robust_template: Command not found. tcsh: mri_segstats: Command not found. /Applications/freesurfer/subjects/FS_struct.nii.gz \n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz \n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz... #-- recon-all -s FS_struct.nii.gz finished without error at Wed Jul 25 16:46:00 PDT 2012 done ___ 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.
Re: [Freesurfer] tcsh: tailarach_avi: Command not found
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 ___ 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.
