[Freesurfer] reconstruction stop
hi i am new in freesurfer (even if i used it many times doing reonstructions using the script reconn-all in the past and on another machine), i launched a reconstruction of one patient using the reconn-all script and i gave before this the path to the SUBJECTS_dir. and one or two minutes later it stopped and prompted recon-all finished without error at Mon Nov 14 13:44:11 CET 2011 done and all the directories in the SUBJECTS_DIR were created with the mgz file created. thank you ___ 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] Freesurfer on Windows!
Hello Friends, I am a newcomer to freesurfer and wanted to use it in windows. I downloaded as instructed the freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi-for windows the virtual box version is 4.1.6 and installed with the required settings as mentioned in your website. I tried it in two systems one with a windows xp, 4 GB RAM, Intel Core Quad CPU, 2,40 GhZ, 64 bit system and the other system Windows 7, Intel Xeon 2.53 Ghz(2 processors), 24 Gb RAM, 64 bit system In both the sytems i was able to configure the virtual box for the xubuntu linux but it starts and progress bar in the middle and then the application closes without any errors. Is this a known problem? Am i missing something? Thanking you With regards Dr.-Ing M.Muthuraman Klinik für Neurology Schittenhelmstrasse 10 Kiel-24105 Germany. ___ 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] error with mri_glmfit and question about registering rh to lh
Hi all, I receive the error: ERROR: MRISread: cannot read surface data from file ./long/surf/lh.thickness.fsaverage.S1-S3.mgh! when I run mri_glmfit with the command: mri_glmfit --glmdir long/g1v0 --surf long lh thickness.fsaverage.S1-S3.mgh --fsgd long/S1-S3.fsgd --osgm I am working on mri_glmfit for a one sample ttest of the thickness of multiple patients, all qcached to fsaverage. I ran the reconstruction and then ran -qcache for each subject. I then used mri_calc to find the difference in thicknesses of Session 1 and 3 for each patient (in fsaverage) and concatenated with mri_concat for the glm. But when I run the glm, it gives me the above error. How would I fix this? Also, I am wondering if there is a way to register the right hemisphere to the left hemisphere, since we are working with stroke patients and would like to compare all the contralesional hemispheres. Thank you! Kelsi ___ 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] DTI Group Analysis Study
Dear Anastasia, Thank you very much for your help. I have done a TBSS group analysis in FSL and I would like to do a similar study using Freesurfer. I understood I can use TRACULA for a similar TBSS study. Is this right? Or I should better use the dt_recon? I would like to compare my results from FSl with th eone from Freesurfer: TRACULA or dt_recon method. Please advise. Many thanks, Antonella From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Friday, November 11, 2011 4:45 PM Subject: Re: [Freesurfer] DTI Group Analysis Study 1. Currently trac-all uses only the MNI template, not CVS. So yes, all steps apply. 2. See the tracula tutorial, section outputs from tracula, to see where to find the MNI-space outputs. 3. What clusters are you talking about? Do you want to do a voxel-based analysis? If so, why are you using tracula? Go through the tracula tutorial and read the tracula paper below to understand what tracula does: http://frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract On Fri, 11 Nov 2011, Antonella Kis wrote: Hi, I am trying to do a DTI Group Analysis study using a MNI152 standard space for registration. 1). I wonder in case I want to use MNI 152 and not CVS space using TRACULA if I have to follow all the steps starting Setting Up a Configuration File to run Tracula and then to continue with the following three steps in the TRACULA processing stream (which is called by the command trac-all): * Pre-processing * FSL's bedpostX * Reconstructing white-matter (WM) pathways 2). Can I check the registration for individual subjects to see if it worked well or not on the MNI 152 template? 3) How can I see if there are clusters that survives to multiple comparison in group 1 (controls) versus group 2 (patients) without and covariant (not gender, not age). Can I get a txt file as output for this clusters? Thank you. Antonella ___ 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 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] CVS template for registration
Dear all: Based on the DTI Basic Tutorial I understood that MRI data can be resampled registered in CVS space (by running mri_cvs_register), but alternatively can be normalized in any other (for example, MNI or Talairach). Can you please let me know how this can be done in MNI152 space? Should I run mri_mni152_register? Is CVS a good template for younger subjects (children age 6-13)? Many thanks, Antonella ___ 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] DTI Group Analysis Study
Dear Anastasia, Thank you very much for your help. I have done a TBSS group analysis in FSL and I would like to do a similar study using Freesurfer. I understood I can use TRACULA for a similar TBSS study. Is this right? Or I should better use the dt_recon? I would like to compare my results from FSl with th eone from Freesurfer: TRACULA or dt_recon method. Please advise. Many thanks, Antonella From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Antonella Kis ator...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Friday, November 11, 2011 4:45 PM Subject: Re: [Freesurfer] DTI Group Analysis Study 1. Currently trac-all uses only the MNI template, not CVS. So yes, all steps apply. 2. See the tracula tutorial, section outputs from tracula, to see where to find the MNI-space outputs. 3. What clusters are you talking about? Do you want to do a voxel-based analysis? If so, why are you using tracula? Go through the tracula tutorial and read the tracula paper below to understand what tracula does: http://frontiersin.org/neuroinformatics/10.3389/fninf.2011.00023/abstract On Fri, 11 Nov 2011, Antonella Kis wrote: Hi, I am trying to do a DTI Group Analysis study using a MNI152 standard space for registration. 1). I wonder in case I want to use MNI 152 and not CVS space using TRACULA if I have to follow all the steps starting Setting Up a Configuration File to run Tracula and then to continue with the following three steps in the TRACULA processing stream (which is called by the command trac-all): * Pre-processing * FSL's bedpostX * Reconstructing white-matter (WM) pathways 2). Can I check the registration for individual subjects to see if it worked well or not on the MNI 152 template? 3) How can I see if there are clusters that survives to multiple comparison in group 1 (controls) versus group 2 (patients) without and covariant (not gender, not age). Can I get a txt file as output for this clusters? Thank you. Antonella ___ 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 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] CVS template for registration
Hi Antonella we have had good results with surface-based registration that is the heart of CVS down to below age 5. See: Evaluating the validity of volume-based and surface-based brain image registration for developmental cognitive neuroscience studies in children 4 to 11 years of age., Satrajit S. Ghosh, Sita Kakunoori, Jean Augustinack, Alfonso Nieto-Castanon, Ioulia Kovelman, Nadine Gaab, Joanna A. Christodoulou, Christina Triantafyllou, John D.E. Gabrieli, Bruce Fischl (2010). NeuroImage 53 (2010) 85 https://surfer.nmr.mgh.harvard.edu/ftp/articles/Ghosh_2010_KidRegistration.pdf cheers Bruce On Mon, 14 Nov 2011, Antonella Kis wrote: Dear all: Based on the DTI Basic Tutorial I understood that MRI data can be resampled registered in CVS space (by running mri_cvs_register), but alternatively can be normalized in any other (for example, MNI or Talairach). Can you please let me know how this can be done in MNI152 space? Should I run mri_mni152_register? Is CVS a good template for younger subjects (children age 6-13)? Many thanks, Antonella ___ 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] CVS template for registration
Dear all: Based on the DTI Basic Tutorial I understood that MRI data can be resampled registered in CVS space (by running mri_cvs_register), but alternatively can be normalized in any other (for example, MNI or Talairach). Can you please let me know how this can be done in MNI152 space? Should I run mri_mni152_register? Is CVS a good template for younger subjects (children age 6-13)? Many thanks, Antonella___ 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] flipping surface data
Try these instructions. You won't actually need to do the download and install in you're local, but you will need to use the dev env. doug Download these files ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz # Copy surfreg and xhemireg into $FREESURFER_HOME/bin # Copy mris_preproc into $FREESURFER_HOME/bin after making a backup # Untar fsaverage_sym.tar.gz into your $SUBJECTS_DIR cd $SUBJECTS_DIR tar xvfz fsaverage_sym.tar.gz - To apply an existing atlas (eg, fsaverage_sym) to an anatomical analysis # Reg to atlas (1-2 hours per subject) # Creates $subject/xhemi # Creates lh.fsaverage_sym.sphere.reg in $subject and $subject/xhemi foreach subject (subjectlist) surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi end # Create a stack of subjects mris_preproc --target fsaverage_sym --hemi lh --xhemi --paired-diff \ --srcsurfreg fsaverage_sym.sphere.reg \ --meas thickness \ --out lh.lh-rh.thickness.sm00.mgh \ --s subj1 --s subj2 ... # Smooth mris_fwhm --s fsaverage_sym --hemi lh --cortex --smooth-only --fwhm 5\ --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm05.mgh # Analyze mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 \ --osgm --surf fsaverage_sym lh # View tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh kelsi wrote: Hi Freesurfers, Is there a tool to flip the orientation of surface data to the opposite hemisphere? We are working with stroke patients, and I would like to do analysis of the contralesional hemisphere of all the patients. However, this requires putting them on the same hemisphere for ttests, etc. I saw an earlier thread online about a program for flipping in the works, I was just wondering if this is now possible? Thank you! Kelsi ___ 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 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] dt_recon registration
Hi Antonella, 1) I will be very grateful if you can confirm if my coding is write. First can you please let me know if by default dt_recon is re-sample FA to talairch space? In this case because I want to register on CVS should I add the --no-tal flag? I am asking this question because after I ran the following command I see in my output directory called P07_dti a file called fa_tal.nii as well as fa_tal.nii.reg. The talairach registration and resampling does take place by default, but that should not affect your further processing as the fa.nii file (in the native space) is not deleted from the directory. So you can either leave the default settings or you can also use --no-tal. 2) Do I need this files if I want to do a group study for my FA and mean diffusivity, similar to TBSS in FSL? Are you referring to the tal registration files? If you want to do the group study in the CVS spacem then you will not need the tal registration files. 3) Can I use the talairch registration or should I use the CVS? Depends on where you want to do your analysis. 4) Should I add the flag --no-tal? You can. If you don't you just end up with two additional files. This is what I was running: setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/DTI_FS/dtrecon dt_recon --i P07_dti.nii.gz -- b P07.bvals P07.bvects --s P07 --o P07_dti where P07_dti.nii.gz is my DTI volume P07.bvals P07.bvects are the bvals and bvects for my subject P07 is my structural recons data for my P07 subject 5) From the dt_recon --help I understand that dt_recon is doing the registration of lowb to same-subject anatomical using FSLs flirt (creates mask.nii and register.dat). mri_vol2vol --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/lowb.nii \ --targ $SUBJECTS_DIR/P07/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/P07/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/register.dat --no-save-reg Actually dt-recon now uses bbregister, but the output of this step is still register.dat. With the above you move the wmparc into the diffusion space. 6) Should I run mri_vol2vol to re-sample the structural volume in the diffusion space and register in the CVS space: mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.mgz \ --o /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.ANAT+CVS-to-avg35.mgz \ --interp trilin --no-save-reg With the above you are going to move your diffusion file (fa) into the CVS space (by implicitely combining a moprh moving the diffusion file to the structural space and then to the CVS space) and not resampling the structural volume in the diffusion space. 7) I found online that the default CVS template is cvs_avg35 which is supplied with my FreeSurfer distribution. Can you please tell me in which directory is located or how I can obtain the cvs_avg35? It should be in $FREESURFER_HOME/subjects (as indicated above in your command --targ). --Lilla___ 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] Amazon EC2 Version of FreeSurfer 5.1 Available
Thanks again Pedro. I just ran 220 brains through in day or two using the cloud. Fantastic. The script people have been talking about would have been useful. One thing I didn't realize was that I should have moved the freesurfer subject directory from /usr/local/freesurfer/subjects to the larger disk that comes with the instance. I had disk-write errors because the the main partition ran out of space. Anyway, ec2 rocks with Freesurfer. - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 2011/11/12 Nolan Nichols bnn...@uw.edu If only running a small number of instances, I think it is reasonable to leave the ami w/o a .license file since it is easy enough to scp it up to the cloud. For running a cluster it would be nice to have a script, perhaps using Fabric, to upload a .license file to each instance in a cluster. As it stands, the starcluster FS AMI does not have a .license file and requires one to be uploaded manually. Nolan 2011/11/12 Thomas Ballinger thomasballin...@gmail.com: Perhaps the AMI image could be without a licence file and uploading one (acquired though normal means) would be required? (I suppose that's the basic solution we're looking for a clean way around) 2011/11/12 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Maybe we can set up a web server in the Martinos center and the AMI Image can authenticate in it. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Sat, Nov 12, 2011 at 15:28, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: I'm happy to see the work getting the cloud to be feasible. I still need to catch up on this thread but one issue that I'd like to sort out is tracking the license count. Its fine for a new user to use an existing image, but I think there will need to be a way to remind people to request our .license file even if they don't actually use the file so that cloud usages get counted (license count is critical for us for grant renewal purposes). Ideas on a clean way to do this? N. On Nov 12, 2011, at 11:10 AM, Thomas Ballinger thomasballin...@gmail.com wrote: Satra, the ipython example looks great. The scripts I posted also use fabric for running Freesurfer, but don't download Freesurfer due to it already being installed on Pedro's image. I agree with Satra that individually administered instances might work better for those wishing to run a few cases with Freesurfer, particularly due to the predictable long running time (lessening the benefits of job distribution) and ability of a recon-all job to efficiently use all of a ec2 small instance's cpu. I think starcluster is pretty awesome, and I would love to push people in that direction, but it won't be quite as push-button, and the benefits may be minimal for small use cases. That's not to say there aren't plenty of folks who would rather use Nolan's solution (me for one :)) Tom On Sat, Nov 12, 2011 at 9:14 AM, Nolan Nichols bnn...@uw.edu wrote: Hi Satra, Fabric does look nice, thanks for pointing it out and for a link to the ipython_in_a_box example. That framework might work for what I had in mind for freesurfer and starcluster, which uses the same idea to keep the initial AMI footprint smaller/flexible. Cheers, Nolan On Nov 12, 2011 7:32 AM, Satrajit Ghosh sa...@mit.edu wrote: hi nolan, i think starcluster is a great way to create a cluster on aws. but for those wanting to create a single instance and install things on an ami without actually having a large ami, fabric might be a good option. fabric: http://docs.fabfile.org/en/1.3.2/index.html example: (another neurodebian ami) https://github.com/wholeslide/ipython_in_a_box/blob/master/fabfile.py cheers, satra On Sat, Nov 12, 2011 at 6:11 AM, Nolan Nichols bnn...@uw.edu wrote: Thanks, Pedro! I am glad to see that you posted a public AMI for freesurfer. And thanks to Thomas for producin documentation on how to use it. This thread inspired me share a StarCluster AMI (ami-27f1384e in the us-east-1 region) that I built for batch FS jobs, which includes the initial setup for installing tools from the NeuroDebian repository. I've also been playing around with using s3fs, which allows Amazon's S3 to be mounted as a drive and accessed directly as the subjects_dir. The AMI can be launched here: https://console.aws.amazon.com/ec2/home?region=us-east-1#launchAmi=ami-27f1384e I did not include the .license for FS as I wasn't sure about licensing issues, but I would be happy to publish an AMI with a built-in license if I get the go ahead. For now you will need to start a
Re: [Freesurfer] Freesurfer on Windows!
I'd try reinstalling virtualbox. Then I'd make sure that you adjust the vm with enough ram, videocard memory, etc. It should work fine. I run the same setup all the time, and I don't believe that this is a 'known issue'. Joshua On Mon, Nov 14, 2011 at 8:25 AM, m.muthura...@neurologie.uni-kiel.dewrote: Hello Friends, I am a newcomer to freesurfer and wanted to use it in windows. I downloaded as instructed the freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi-for windows the virtual box version is 4.1.6 and installed with the required settings as mentioned in your website. I tried it in two systems one with a windows xp, 4 GB RAM, Intel Core Quad CPU, 2,40 GhZ, 64 bit system and the other system Windows 7, Intel Xeon 2.53 Ghz(2 processors), 24 Gb RAM, 64 bit system In both the sytems i was able to configure the virtual box for the xubuntu linux but it starts and progress bar in the middle and then the application closes without any errors. Is this a known problem? Am i missing something? Thanking you With regards Dr.-Ing M.Muthuraman Klinik für Neurology Schittenhelmstrasse 10 Kiel-24105 Germany. ___ 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 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] Amazon EC2 Version of FreeSurfer 5.1 Available
Glad to hear it works well. To revisit the issue of the license (in the form of the .license file which needs to be in the $FREESURFER_HOME directory and the request of which is used for usage tracking), I think the convention to follow for any publicly available AMI freesurfer instances should be to not include a .license file with it, so as to force the download of this file (so that freesurfer usage will be tracked). A user need only do this once for however many times they use the cloud instance. N. On Mon, 2011-11-14 at 17:16 -0500, Joshua Lee wrote: Thanks again Pedro. I just ran 220 brains through in day or two using the cloud. Fantastic. The script people have been talking about would have been useful. One thing I didn't realize was that I should have moved the freesurfer subject directory from /usr/local/freesurfer/subjects to the larger disk that comes with the instance. I had disk-write errors because the the main partition ran out of space. Anyway, ec2 rocks with Freesurfer. - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 2011/11/12 Nolan Nichols bnn...@uw.edu If only running a small number of instances, I think it is reasonable to leave the ami w/o a .license file since it is easy enough to scp it up to the cloud. For running a cluster it would be nice to have a script, perhaps using Fabric, to upload a .license file to each instance in a cluster. As it stands, the starcluster FS AMI does not have a .license file and requires one to be uploaded manually. Nolan 2011/11/12 Thomas Ballinger thomasballin...@gmail.com: Perhaps the AMI image could be without a licence file and uploading one (acquired though normal means) would be required? (I suppose that's the basic solution we're looking for a clean way around) 2011/11/12 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Maybe we can set up a web server in the Martinos center and the AMI Image can authenticate in it. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Sat, Nov 12, 2011 at 15:28, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: I'm happy to see the work getting the cloud to be feasible. I still need to catch up on this thread but one issue that I'd like to sort out is tracking the license count. Its fine for a new user to use an existing image, but I think there will need to be a way to remind people to request our .license file even if they don't actually use the file so that cloud usages get counted (license count is critical for us for grant renewal purposes). Ideas on a clean way to do this? N. On Nov 12, 2011, at 11:10 AM, Thomas Ballinger thomasballin...@gmail.com wrote: Satra, the ipython example looks great. The scripts I posted also use fabric for running Freesurfer, but don't download Freesurfer due to it already being installed on Pedro's image. I agree with Satra that individually administered instances might work better for those wishing to run a few cases with Freesurfer, particularly due to the predictable long running time (lessening the benefits of job distribution) and ability of a recon-all job to efficiently use all of a ec2 small instance's cpu. I think starcluster is pretty awesome, and I would love to push people in that direction, but it won't be quite as push-button, and the benefits may be minimal for small use cases. That's not to say there aren't plenty of folks who would rather use Nolan's solution (me for one :)) Tom On Sat, Nov 12, 2011 at 9:14 AM, Nolan Nichols bnn...@uw.edu wrote: Hi Satra, Fabric does look nice, thanks for pointing it out and for a link to the ipython_in_a_box example. That framework might work for what I had in mind for freesurfer and starcluster, which uses the same idea to keep the initial AMI footprint smaller/flexible.
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
Ok. I'll label as private this AMI that has .license file. Maybe we can make a tutorial on how to create an AMI instead. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Mon, Nov 14, 2011 at 21:07, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Glad to hear it works well. To revisit the issue of the license (in the form of the .license file which needs to be in the $FREESURFER_HOME directory and the request of which is used for usage tracking), I think the convention to follow for any publicly available AMI freesurfer instances should be to not include a .license file with it, so as to force the download of this file (so that freesurfer usage will be tracked). A user need only do this once for however many times they use the cloud instance. N. On Mon, 2011-11-14 at 17:16 -0500, Joshua Lee wrote: Thanks again Pedro. I just ran 220 brains through in day or two using the cloud. Fantastic. The script people have been talking about would have been useful. One thing I didn't realize was that I should have moved the freesurfer subject directory from /usr/local/freesurfer/subjects to the larger disk that comes with the instance. I had disk-write errors because the the main partition ran out of space. Anyway, ec2 rocks with Freesurfer. - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 2011/11/12 Nolan Nichols bnn...@uw.edu If only running a small number of instances, I think it is reasonable to leave the ami w/o a .license file since it is easy enough to scp it up to the cloud. For running a cluster it would be nice to have a script, perhaps using Fabric, to upload a .license file to each instance in a cluster. As it stands, the starcluster FS AMI does not have a .license file and requires one to be uploaded manually. Nolan 2011/11/12 Thomas Ballinger thomasballin...@gmail.com: Perhaps the AMI image could be without a licence file and uploading one (acquired though normal means) would be required? (I suppose that's the basic solution we're looking for a clean way around) 2011/11/12 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Maybe we can set up a web server in the Martinos center and the AMI Image can authenticate in it. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Sat, Nov 12, 2011 at 15:28, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: I'm happy to see the work getting the cloud to be feasible. I still need to catch up on this thread but one issue that I'd like to sort out is tracking the license count. Its fine for a new user to use an existing image, but I think there will need to be a way to remind people to request our .license file even if they don't actually use the file so that cloud usages get counted (license count is critical for us for grant renewal purposes). Ideas on a clean way to do this? N. On Nov 12, 2011, at 11:10 AM, Thomas Ballinger thomasballin...@gmail.com wrote: Satra, the ipython example looks great. The scripts I posted also use fabric for running Freesurfer, but don't download Freesurfer due to it already being installed on Pedro's image. I agree with Satra that individually administered instances might work better for those wishing to run a few cases with Freesurfer, particularly due to the predictable long running time (lessening the benefits of job distribution) and ability of a recon-all job to efficiently use all of a ec2 small instance's cpu. I think starcluster is pretty awesome, and I would love to push people in that direction, but it won't be quite as push-button, and the benefits may be minimal for small use cases. That's not to say there aren't plenty of folks who would rather use Nolan's solution (me for one :))
