Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
/MNI/MincUtilities/volume_min.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MincUtilities/get_dimension_order.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MincUtilities/compute_resample_args.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MincUtilities/compute_reshape_args.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MincUtilities/volume_minmax.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MincUtilities/auto_threshold.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/PathUtilities/ freesurfer/mni/lib/perl5/5.8.5/auto/MNI/PathUtilities/split_path.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/PathUtilities/autosplit.ix freesurfer/mni/lib/perl5/5.8.5/auto/MNI/PathUtilities/replace_dir.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/PathUtilities/expand_path.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/PathUtilities/merge_paths.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/PathUtilities/replace_ext.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/PathUtilities/normalize_dirs.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/NumericUtilities/ freesurfer/mni/lib/perl5/5.8.5/auto/MNI/NumericUtilities/autosplit.ix freesurfer/mni/lib/perl5/5.8.5/auto/MNI/NumericUtilities/labs.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/NumericUtilities/in_range.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/NumericUtilities/round.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/ freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/statfs.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/search_directories.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/check_output_dirs.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/autosplit.ix freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/generate_numbered_filename.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/find_program.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/find_programs.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/check_files.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/check_input_dirs.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/test_file.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/FileUtilities/check_output_path.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MiscUtilities/ freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MiscUtilities/timestamp.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MiscUtilities/nlist_equal.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MiscUtilities/make_banner.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MiscUtilities/autosplit.ix freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MiscUtilities/userstamp.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MiscUtilities/shellquote.al freesurfer/mni/lib/perl5/5.8.5/auto/MNI/MiscUtilities/lcompare.al freesurfer/mni/bin/ freesurfer/mni/bin/mincmath freesurfer/mni/bin/mincinfo freesurfer/mni/bin/nu_correct freesurfer/mni/bin/mincresample freesurfer/mni/bin/evaluate_field freesurfer/mni/bin/volume_stats freesurfer/mni/bin/minc_modify_header freesurfer/mni/bin/make_template freesurfer/mni/bin/sharpen_volume freesurfer/mni/bin/minclookup freesurfer/mni/bin/resample_labels freesurfer/mni/bin/spline_smooth freesurfer/mni/bin/volume_hist freesurfer/mni/bin/nu_evaluate freesurfer/mni/bin/sharpen_hist freesurfer/mni/bin/nu_estimate_np_and_em freesurfer/mni/share/ freesurfer/mni/share/N3/ freesurfer/mni/share/N3/average_305_mask_1mm.mnc.gz Regards, Christoph Gesendet: Mittwoch, 19. November 2014 um 23:49 Uhr Von: Satrajit Ghosh sa...@mit.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch hi jens, here is the post - the links were all broken, but i've updated them below. note that this run was from nov 2013. i would recommend doing a run with all the current patches installed. an update on the files needed for a vanilla recon-all run (evaluation done using cde:http://www.pgbovine.net/cde.html): freesurfer files: https://www.dropbox.com/s/ei3m9dcvq8zemps/fslist.txt?dl=0[https://www.dropbox.com/s/ei3m9dcvq8zemps/fslist.txt?dl=0] all files (fs + system+ output): https://www.dropbox.com/s/1rjk7s0qyzn2hm5/allfiles.txt?dl=0[https://www.dropbox.com/s/1rjk7s0qyzn2hm5/allfiles.txt?dl=0] size of fs components (641M): https://www.dropbox.com/s/mmcadnp63ao4dv8/size.txt?dl=0[https://www.dropbox.com/s/mmcadnp63ao4dv8/size.txt?dl=0] one thing that surprised me a bit was that no component of fsaverage appeared to be used (other than the directory being touched). this could be something the program missed, or is actually true. cheers, satra On Wed, Nov 19, 2014 at 5:03 PM, Jens Offenbach wolle5...@gmx.de[wolle5...@gmx.de] wrote:Hi satra, I have tried to find some posts about the minimum files required to run recon-all, but I cannot find anything. Could you please try to find the post in the archives and provide me the link? Thank you very much! Gesendet: Mittwoch, 19. November 2014 um 15:23 Uhr Von: Satrajit Ghosh sa...@mit.edu[sa...@mit.edu] An: Freesurfer support list freesurfer
[Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me: I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family? On the FTP server I have found a patch for 5.3.0, but I am not sure how to apply it or if I must apply it? The Readme says to replace “mri_segstats”. What about the other files “recon-all, fsfast, tksurferfv, …”? I want to reduce the archive to its bare minimum, otherwise the automated deployment process takes too long. It should contain only those files which are necessary to execute the pipeline without any viewer or examples. Which files and folders can be deleted safely? The most important issue is to monitor the FreeSurfer pipeline execution. I know that the scripts folder contains some status files which offer important data helping me to monitor the pipeline execution progress of “recon-all”. Unfortunately, that is not enough… If one step takes e.g. approximately 20 hours, I have to say something about the progress within this current step. Is there any possibility to monitor the progress of a single step. We need something that allows us to say e.g. that Step “CA Reg” has 34 % of its work done so far which means that the overall pipeline progress is e.g. 63 %. Is it possible to say that a specific step takes a specific portion of the overall pipeline execution time. What influences this portion (format or quality of input, platform, …)? Thank you very much for your help! Regards Jens ___ 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] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
Dear Jens, I can offer just a bit of information and I also have a question. We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos 6 compiles work. The package appears to be self-contained as I have seen no faults on failures to find shared libraries. We simply untar freesurfer to a convenient location and set the PATH and FREESURFERHOME environment variables accordingly. I see no reason why that shouldn't work in a cloud solution except that I do not know what you have in mind as a use for your solution. Will there be a group of users who are provided access so that they can run freesurfer on an image data set through a portal to your cloud? Are you using the cloud to distribute the calculation to many machines? If so, what is the granularity of this, e.g. does one freesurfer run get one machine? Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- boun...@nmr.mgh.harvard.edu] On Behalf Of Jens Offenbach Sent: Wednesday, November 19, 2014 5:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0- patch We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me: I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family? On the FTP server I have found a patch for 5.3.0, but I am not sure how to apply it or if I must apply it? The Readme says to replace “mri_segstats”. What about the other files “recon-all, fsfast, tksurferfv, …”? I want to reduce the archive to its bare minimum, otherwise the automated deployment process takes too long. It should contain only those files which are necessary to execute the pipeline without any viewer or examples. Which files and folders can be deleted safely? The most important issue is to monitor the FreeSurfer pipeline execution. I know that the scripts folder contains some status files which offer important data helping me to monitor the pipeline execution progress of “recon-all”. Unfortunately, that is not enough… If one step takes e.g. approximately 20 hours, I have to say something about the progress within this current step. Is there any possibility to monitor the progress of a single step. We need something that allows us to say e.g. that Step “CA Reg” has 34 % of its work done so far which means that the overall pipeline progress is e.g. 63 %. Is it possible to say that a specific step takes a specific portion of the overall pipeline execution time. What influences this portion (format or quality of input, platform, …)? Thank you very much for your help! Regards Jens ___ 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
Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
Hi Jens you could estimate it, but it might not be exactly right. There's no way to know how long it will take to converge as it depends on the details of the anatomy. If the current output is not verbose enough for you, you can turn on more output by: setenv DIAG 0x04040 if you run some recons with this on you'll be able to get an idea of how many integration steps each pipeline step takes cheers Bruce On Wed, 19 Nov 2014, Jens Offenbach wrote: We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me: I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family? On the FTP server I have found a patch for 5.3.0, but I am not sure how to apply it or if I must apply it? The Readme says to replace “mri_segstats”. What about the other files “recon-all, fsfast, tksurferfv, …”? I want to reduce the archive to its bare minimum, otherwise the automated deployment process takes too long. It should contain only those files which are necessary to execute the pipeline without any viewer or examples. Which files and folders can be deleted safely? The most important issue is to monitor the FreeSurfer pipeline execution. I know that the scripts folder contains some status files which offer important data helping me to monitor the pipeline execution progress of “recon-all”. Unfortunately, that is not enough… If one step takes e.g. approximately 20 hours, I have to say something about the progress within this current step. Is there any possibility to monitor the progress of a single step. We need something that allows us to say e.g. that Step “CA Reg” has 34 % of its work done so far which means that the overall pipeline progress is e.g. 63 %. Is it possible to say that a specific step takes a specific portion of the overall pipeline execution time. What influences this portion (format or quality of input, platform, …)? Thank you very much for your help! Regards Jens ___ 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.
Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
I have corresponding setup modules for auto-deployment and configuration in the cloud, but it still takes some time (even in the local cloud network) to transfer the archive from the fileserver to the virtual machine and especially to untar that archive. A manual untar took nearly 20 minutes, that's too slow for on-demand provisioning. I think the subjects folder can be removed. It seems to contain only example mri data, but I want to make sure not to remove anything that is actually required for analysis purposes. I need a minimum archive file which is able to perform the pipeline execution. Yes, we have a cloud portal, where different consumers can request the freesurfer service after uploading their mri raw files. The virtual machines are created and configured on the fly starting from a raw OS image. When the freesurfer run terminates the virtual machines are destroyed and the whole procedures starts again if someone requests a new freesurfer service (Create and start a virtual machine, transfer freesurfer archive, untar that archive, set environmement variables ...). We only want to parallelize different freesurfer jobs and not the freesurfer pipeline itself. We do not have a medical background. Regards, Jens Gesendet: Mittwoch, 19. November 2014 um 13:14 Uhr Von: Krieger, Donald N. krieg...@upmc.edu An: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch Dear Jens, I can offer just a bit of information and I also have a question. We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos 6 compiles work. The package appears to be self-contained as I have seen no faults on failures to find shared libraries. We simply untar freesurfer to a convenient location and set the PATH and FREESURFERHOME environment variables accordingly. I see no reason why that shouldn't work in a cloud solution except that I do not know what you have in mind as a use for your solution. Will there be a group of users who are provided access so that they can run freesurfer on an image data set through a portal to your cloud? Are you using the cloud to distribute the calculation to many machines? If so, what is the granularity of this, e.g. does one freesurfer run get one machine? Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- boun...@nmr.mgh.harvard.edu] On Behalf Of Jens Offenbach Sent: Wednesday, November 19, 2014 5:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0- patch We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me: I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family? On the FTP server I have found a patch for 5.3.0, but I am not sure how to apply it or if I must apply it? The Readme says to replace “mri_segstats”. What about the other files “recon-all, fsfast, tksurferfv, …”? I want to reduce the archive to its bare minimum, otherwise the automated deployment process takes too long. It should contain only those files which are necessary to execute the pipeline without any viewer or examples. Which files and folders can be deleted safely? The most important issue is to monitor the FreeSurfer pipeline execution. I know that the scripts folder contains some status files which offer important data helping me to monitor the pipeline execution progress of “recon-all”. Unfortunately, that is not enough… If one step takes e.g. approximately 20 hours, I have to say something about the progress within this current step. Is there any possibility to monitor the progress of a single step. We need something that allows us to say e.g. that Step “CA Reg” has 34 % of its work done so far which means that the overall pipeline progress is e.g. 63 %. Is it possible to say that a specific step takes a specific portion of the overall pipeline execution time. What influences this portion (format or quality of input, platform, …)? Thank you very much for your help! Regards Jens ___ 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[http://www.partners.org/complianceline] . If the e-mail was sent to you in error
Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
hi jens, if you search the archives, there is a post that lists the minimal set of files needed for running recon-all. i used a tool called cde to create it: http://www.pgbovine.net/cde.html this reduces the archive down to about 650MB comprising binaries and atlases. this wouldn't be for general purpose freesurfer processing, just for running recon-all. cheers, satra On Wed, Nov 19, 2014 at 8:40 AM, Jens Offenbach wolle5...@gmx.de wrote: I have corresponding setup modules for auto-deployment and configuration in the cloud, but it still takes some time (even in the local cloud network) to transfer the archive from the fileserver to the virtual machine and especially to untar that archive. A manual untar took nearly 20 minutes, that's too slow for on-demand provisioning. I think the subjects folder can be removed. It seems to contain only example mri data, but I want to make sure not to remove anything that is actually required for analysis purposes. I need a minimum archive file which is able to perform the pipeline execution. Yes, we have a cloud portal, where different consumers can request the freesurfer service after uploading their mri raw files. The virtual machines are created and configured on the fly starting from a raw OS image. When the freesurfer run terminates the virtual machines are destroyed and the whole procedures starts again if someone requests a new freesurfer service (Create and start a virtual machine, transfer freesurfer archive, untar that archive, set environmement variables ...). We only want to parallelize different freesurfer jobs and not the freesurfer pipeline itself. We do not have a medical background. Regards, Jens Gesendet: Mittwoch, 19. November 2014 um 13:14 Uhr Von: Krieger, Donald N. krieg...@upmc.edu An: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch Dear Jens, I can offer just a bit of information and I also have a question. We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos 6 compiles work. The package appears to be self-contained as I have seen no faults on failures to find shared libraries. We simply untar freesurfer to a convenient location and set the PATH and FREESURFERHOME environment variables accordingly. I see no reason why that shouldn't work in a cloud solution except that I do not know what you have in mind as a use for your solution. Will there be a group of users who are provided access so that they can run freesurfer on an image data set through a portal to your cloud? Are you using the cloud to distribute the calculation to many machines? If so, what is the granularity of this, e.g. does one freesurfer run get one machine? Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- boun...@nmr.mgh.harvard.edu] On Behalf Of Jens Offenbach Sent: Wednesday, November 19, 2014 5:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0- patch We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me: I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family? On the FTP server I have found a patch for 5.3.0, but I am not sure how to apply it or if I must apply it? The Readme says to replace “mri_segstats”. What about the other files “recon-all, fsfast, tksurferfv, …”? I want to reduce the archive to its bare minimum, otherwise the automated deployment process takes too long. It should contain only those files which are necessary to execute the pipeline without any viewer or examples. Which files and folders can be deleted safely? The most important issue is to monitor the FreeSurfer pipeline execution. I know that the scripts folder contains some status files which offer important data helping me to monitor the pipeline execution progress of “recon-all”. Unfortunately, that is not enough… If one step takes e.g. approximately 20 hours, I have to say something about the progress within this current step. Is there any possibility to monitor the progress of a single step. We need something that allows us to say e.g. that Step “CA Reg” has 34 % of its work done so far which means that the overall pipeline progress is e.g. 63 %. Is it possible to say that a specific step takes a specific portion of the overall pipeline execution time. What influences this portion (format or quality of input, platform, …)? Thank you very much for your help! Regards Jens
Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
Hi satra, I have tried to find some posts about the minimum files required to run recon-all, but I cannot find anything. Could you please try to find the post in the archives and provide me the link? Thank you very much! Gesendet: Mittwoch, 19. November 2014 um 15:23 Uhr Von: Satrajit Ghosh sa...@mit.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch hi jens, if you search the archives, there is a post that lists the minimal set of files needed for running recon-all. i used a tool called cde to create it: http://www.pgbovine.net/cde.html this reduces the archive down to about 650MB comprising binaries and atlases. this wouldn't be for general purpose freesurfer processing, just for running recon-all. cheers, satra On Wed, Nov 19, 2014 at 8:40 AM, Jens Offenbach wolle5...@gmx.de[wolle5...@gmx.de] wrote:I have corresponding setup modules for auto-deployment and configuration in the cloud, but it still takes some time (even in the local cloud network) to transfer the archive from the fileserver to the virtual machine and especially to untar that archive. A manual untar took nearly 20 minutes, that's too slow for on-demand provisioning. I think the subjects folder can be removed. It seems to contain only example mri data, but I want to make sure not to remove anything that is actually required for analysis purposes. I need a minimum archive file which is able to perform the pipeline execution. Yes, we have a cloud portal, where different consumers can request the freesurfer service after uploading their mri raw files. The virtual machines are created and configured on the fly starting from a raw OS image. When the freesurfer run terminates the virtual machines are destroyed and the whole procedures starts again if someone requests a new freesurfer service (Create and start a virtual machine, transfer freesurfer archive, untar that archive, set environmement variables ...). We only want to parallelize different freesurfer jobs and not the freesurfer pipeline itself. We do not have a medical background. Regards, Jens Gesendet: Mittwoch, 19. November 2014 um 13:14 Uhr Von: Krieger, Donald N. krieg...@upmc.edu[krieg...@upmc.edu] An: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu[freesurfer@nmr.mgh.harvard.edu] Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch Dear Jens, I can offer just a bit of information and I also have a question. We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos 6 compiles work. The package appears to be self-contained as I have seen no faults on failures to find shared libraries. We simply untar freesurfer to a convenient location and set the PATH and FREESURFERHOME environment variables accordingly. I see no reason why that shouldn't work in a cloud solution except that I do not know what you have in mind as a use for your solution. Will there be a group of users who are provided access so that they can run freesurfer on an image data set through a portal to your cloud? Are you using the cloud to distribute the calculation to many machines? If so, what is the granularity of this, e.g. does one freesurfer run get one machine? Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu[freesurfer-boun...@nmr.mgh.harvard.edu] [mailto:freesurfer-[freesurfer-] boun...@nmr.mgh.harvard.edu[boun...@nmr.mgh.harvard.edu]] On Behalf Of Jens Offenbach Sent: Wednesday, November 19, 2014 5:47 AM To: freesurfer@nmr.mgh.harvard.edu[freesurfer@nmr.mgh.harvard.edu] Subject: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0- patch We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me: I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to download (CentOS 4 x86_64 (64b))? Does it work anyway on the Ubuntu family? On the FTP server I have found a patch for 5.3.0, but I am not sure how to apply it or if I must apply it? The Readme says to replace “mri_segstats”. What about the other files “recon-all, fsfast, tksurferfv, …”? I want to reduce the archive to its bare minimum, otherwise the automated deployment process takes too long. It should contain only those files which are necessary to execute the pipeline without any viewer or examples. Which files and folders can be deleted safely? The most important issue is to monitor the FreeSurfer pipeline execution. I know that the scripts folder contains some status files which offer important data helping me to monitor the pipeline execution progress of “recon-all”. Unfortunately, that is not enough… If one
Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch
hi jens, here is the post - the links were all broken, but i've updated them below. note that this run was from nov 2013. i would recommend doing a run with all the current patches installed. an update on the files needed for a vanilla recon-all run (evaluation done using cde:http://www.pgbovine.net/cde.html): freesurfer files: https://www.dropbox.com/s/ei3m9dcvq8zemps/fslist.txt?dl=0 all files (fs + system+ output): https://www.dropbox.com/s/1rjk7s0qyzn2hm5/allfiles.txt?dl=0 size of fs components (641M): https://www.dropbox.com/s/mmcadnp63ao4dv8/size.txt?dl=0 one thing that surprised me a bit was that no component of fsaverage appeared to be used (other than the directory being touched). this could be something the program missed, or is actually true. cheers, satra On Wed, Nov 19, 2014 at 5:03 PM, Jens Offenbach wolle5...@gmx.de wrote: Hi satra, I have tried to find some posts about the minimum files required to run recon-all, but I cannot find anything. Could you please try to find the post in the archives and provide me the link? Thank you very much! Gesendet: Mittwoch, 19. November 2014 um 15:23 Uhr Von: Satrajit Ghosh sa...@mit.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch hi jens, if you search the archives, there is a post that lists the minimal set of files needed for running recon-all. i used a tool called cde to create it: http://www.pgbovine.net/cde.html this reduces the archive down to about 650MB comprising binaries and atlases. this wouldn't be for general purpose freesurfer processing, just for running recon-all. cheers, satra On Wed, Nov 19, 2014 at 8:40 AM, Jens Offenbach wolle5...@gmx.de[ wolle5...@gmx.de] wrote:I have corresponding setup modules for auto-deployment and configuration in the cloud, but it still takes some time (even in the local cloud network) to transfer the archive from the fileserver to the virtual machine and especially to untar that archive. A manual untar took nearly 20 minutes, that's too slow for on-demand provisioning. I think the subjects folder can be removed. It seems to contain only example mri data, but I want to make sure not to remove anything that is actually required for analysis purposes. I need a minimum archive file which is able to perform the pipeline execution. Yes, we have a cloud portal, where different consumers can request the freesurfer service after uploading their mri raw files. The virtual machines are created and configured on the fly starting from a raw OS image. When the freesurfer run terminates the virtual machines are destroyed and the whole procedures starts again if someone requests a new freesurfer service (Create and start a virtual machine, transfer freesurfer archive, untar that archive, set environmement variables ...). We only want to parallelize different freesurfer jobs and not the freesurfer pipeline itself. We do not have a medical background. Regards, Jens Gesendet: Mittwoch, 19. November 2014 um 13:14 Uhr Von: Krieger, Donald N. krieg...@upmc.edu[krieg...@upmc.edu] An: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu[ freesurfer@nmr.mgh.harvard.edu] Betreff: Re: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0-patch Dear Jens, I can offer just a bit of information and I also have a question. We are using Fedora 11.0 on an x86_64 box and both the Centos 4 and Centos 6 compiles work. The package appears to be self-contained as I have seen no faults on failures to find shared libraries. We simply untar freesurfer to a convenient location and set the PATH and FREESURFERHOME environment variables accordingly. I see no reason why that shouldn't work in a cloud solution except that I do not know what you have in mind as a use for your solution. Will there be a group of users who are provided access so that they can run freesurfer on an image data set through a portal to your cloud? Are you using the cloud to distribute the calculation to many machines? If so, what is the granularity of this, e.g. does one freesurfer run get one machine? Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu[ freesurfer-boun...@nmr.mgh.harvard.edu] [mailto:freesurfer-[freesurfer-] boun...@nmr.mgh.harvard.edu[boun...@nmr.mgh.harvard.edu]] On Behalf Of Jens Offenbach Sent: Wednesday, November 19, 2014 5:47 AM To: freesurfer@nmr.mgh.harvard.edu[freesurfer@nmr.mgh.harvard.edu] Subject: [Freesurfer] Pipeline/Step Progress Monitoring, Packaging and 5.3.0- patch We are currently working on a solution that brings FreeSurfer in the cloud. Unfortunately, we are facing a lot of problems. Hopefully, someone can help me: I want to run
