Re: [Freesurfer] parellizing Freesurfer
Hi Pedro and everyone, Thanks so much for pointing me there. I seems like the only way to parallelize is to run several recon-all simultanously intstead of wating for one to finshe and then run the following. I wonder if you (of someone else) managed to achieve some further decrease in running times, making a single recon-all run faster or something like that. Was it any different in the Amazon EC2? It would seem that the analysis fo functional data (at least parts of it) could run in parallel, since the analysis of one voxel is independent of the rest. I would love to know if this is something people do. An ugly implementation could be to split the volumes into several small volume files and run the analysis separately and then merge back the output volumes. Has anyone done something like that or nicer? Thanks! Pablo 2011/2/26 Pedro Paulo de Magalhães Oliveira Junior > Yes. Take a look at: > http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIreducethetimeofrecon-allinagroupofpatients.3F > > Also I have successfully executed it at Amazon EC2 instances. > > PPJ > - > Pedro Paulo de Magalhães Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br > -- For mobile: http://www.netfilter.com.br/mobile > > > > > On Sat, Feb 26, 2011 at 19:59, Pablo Polosecki < > ppolose...@mail.rockefeller.edu> wrote: > >> Hi all, >> >> I was wondering if someone out there has any experience trying to >> parallelize their analysis streams in clusters or multiprocessor machines. I >> was thinking also about the cloud computing services offered by Google, >> Amazon or other. Has anyone tried or has any plans of implementing something >> along those lines? >> >> Best wishes, >> >> Pablo >> >> >> >> >> ___ >> 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] installation problem
Do I need to run the SetupFreeSurferEnv.csh every time before I start the Freesurfer? I thought it is only for initial intallation? PS: even after I run the SetupFreeSurferEnv.csh when i installed Freesurfer the other day, it showed freesurfer-Linux-centos4-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/jie/Documents/freesurfer/ FSFAST_HOME /home/jie/Documents/freesurfer//fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects MNI_DIR /ho me/jie/Documents/freesurfer//mni But it did not work for the test "tkmedit bert orig.mgz"; it reponded“Illegal instruction” Any suggestion for the problem? Thanks Jie > From: ni...@nmr.mgh.harvard.edu > To: remembe...@hotmail.com > Date: Sat, 26 Feb 2011 18:30:31 -0500 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] installation problem > > the SetupFreeSurferEnv.csh file needs to be run. see installation > instructions: > > http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration > > n. > > On Fri, 2011-02-25 at 08:25 +0800, Liukarl wrote: > > Hello, Nick > > > > I tried mri_convert work, glxgears,tksurfer, qdec,freeview. It all > > respond as "Command not found" > > > > two questions: > > > > 1) How should I initiate freesufter evey time i turn on the computer? > > > > 2) The other day when I installed freesurfer,i typed “tkmedit bert > > orig.mgz”, it reponded “Illegal instruction”. If I typed in > > “recon-all”, it showed > > “ Required Arguments: > > -subjid > > -…... ” > > > > and the other arguments. > > > > But when i tried the “recon-all” today, it said "Command not found". > > > > Another thing is i installed the freesurfer in my Document folder, > > instead of the local folder. Although i am the administrator, Ubuntu > > would not allow me to move any file to the local folder.. > > > > Any idea of the problem of freesurfer in my computer? > > > > thanks > > > > Jie > > > > > > > > > > > > > From: ni...@nmr.mgh.harvard.edu > > > To: remembe...@hotmail.com > > > Date: Wed, 23 Feb 2011 18:32:58 -0500 > > > CC: freesurfer@nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] installation problem > > > > > > does mri_convert work? > > > > > > glxgears? > > > > > > tksurfer? > > > > > > qdec? > > > > > > freeview? > > > > > > your installation should work on ubuntu, as it has for other people, > > so > > > i'm a bit at a loss. > > > > > > n. > > > > > > On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote: > > > > Hello, Nick > > > > > > > > the output of uname -a is > > > > > > > > "Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21 > > > > 17:40:48 UTC 2011 i686 GNU/Linux" > > > > > > > > thanks > > > > > > > > Jie > > > > > > > > > > > > > > > > > > > > > Subject: Re: [Freesurfer] installation problem > > > > > From: ni...@nmr.mgh.harvard.edu > > > > > To: remembe...@hotmail.com > > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > > Date: Wed, 23 Feb 2011 11:59:16 -0500 > > > > > > > > > > what is the output of > > > > > > > > > > uname -a > > > > > > > > > > > > > > > On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote: > > > > > > Hello, Freesurfer experts: > > > > > > > > > > > > > > > > > > > > > > > > I emailed some installation problems a couple days ago, but > > > > haven’t > > > > > > answered yet. I am new to freesurfer and try to install the > > newest > > > > > > version of freesurfer in Ubuntu system. I closely followed the > > > > > > instructions, and the only difference is that I installed it > > in my > > > > > > Documents, instead of local folder. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Below is the output after “source > > > > $FREESURFER_HOME/SetUpFreeSurfer.sh” > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > freesurfer-Linux-centos4-stable-pub-v5.0.0 > > > > > > > > > > > > > > > > > > > > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > > > > > > > > > > > > > > > > > > > > > FREESURFER_HOME /home/jie/Documents/freesurfer/ > > > > > > > > > > > > > > > > > > > > > > > > FSFAST_HOME /home/jie/Documents/freesurfer//fsfast > > > > > > > > > > > > > > > > > > > > > > > > FSF_OUTPUT_FORMAT nii > > > > > > > > > > > > > > > > > > > > > > > > SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects > > > > > > > > > > > > > > > > > > > > > > > > MNI_DIR /ho me/jie/Documents/freesurfer//mni > > > > > > > > > > > > > > > > > > > > > > > > Everything seems fine and I also added the .license file to > > the< > > > > br>> > freesurfer folder. But when I test it by “tkmedit bert > > > > orig.mgz”, it > > > > > > reponds “Illegal instruction” > > > > > > > > > > > > > > > > > > > > > > > > If I type in “recon-all”, it will show > > > > > > > > > > > > > > > > > > > > > > > > “ Required Arguments: > > > > > > > > > > > >
Re: [Freesurfer] parellizing Freesurfer
Yes. Take a look at: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowcanIreducethetimeofrecon-allinagroupofpatients.3F Also I have successfully executed it at Amazon EC2 instances. PPJ - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Sat, Feb 26, 2011 at 19:59, Pablo Polosecki < ppolose...@mail.rockefeller.edu> wrote: > Hi all, > > I was wondering if someone out there has any experience trying to > parallelize their analysis streams in clusters or multiprocessor machines. I > was thinking also about the cloud computing services offered by Google, > Amazon or other. Has anyone tried or has any plans of implementing something > along those lines? > > Best wishes, > > Pablo > > > > > ___ > 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] installation problem
the SetupFreeSurferEnv.csh file needs to be run. see installation instructions: http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration n. On Fri, 2011-02-25 at 08:25 +0800, Liukarl wrote: > Hello, Nick > > I tried mri_convert work, glxgears,tksurfer, qdec,freeview. It all > respond as "Command not found" > > two questions: > > 1) How should I initiate freesufter evey time i turn on the computer? > > 2) The other day when I installed freesurfer,i typed “tkmedit bert > orig.mgz”, it reponded “Illegal instruction”. If I typed in > “recon-all”, it showed > “ Required Arguments: > -subjid > -…... ” > > and the other arguments. > > But when i tried the “recon-all” today, it said "Command not found". > > Another thing is i installed the freesurfer in my Document folder, > instead of the local folder. Although i am the administrator, Ubuntu > would not allow me to move any file to the local folder.. > > Any idea of the problem of freesurfer in my computer? > > thanks > > Jie > > > > > > > From: ni...@nmr.mgh.harvard.edu > > To: remembe...@hotmail.com > > Date: Wed, 23 Feb 2011 18:32:58 -0500 > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] installation problem > > > > does mri_convert work? > > > > glxgears? > > > > tksurfer? > > > > qdec? > > > > freeview? > > > > your installation should work on ubuntu, as it has for other people, > so > > i'm a bit at a loss. > > > > n. > > > > On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote: > > > Hello, Nick > > > > > > the output of uname -a is > > > > > > "Linux Jie-Liu-Linux 2.6.35-25-generic #44-Ubuntu SMP Fri Jan 21 > > > 17:40:48 UTC 2011 i686 GNU/Linux" > > > > > > thanks > > > > > > Jie > > > > > > > > > > > > > > > > Subject: Re: [Freesurfer] installation problem > > > > From: ni...@nmr.mgh.harvard.edu > > > > To: remembe...@hotmail.com > > > > CC: freesurfer@nmr.mgh.harvard.edu > > > > Date: Wed, 23 Feb 2011 11:59:16 -0500 > > > > > > > > what is the output of > > > > > > > > uname -a > > > > > > > > > > > > On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote: > > > > > Hello, Freesurfer experts: > > > > > > > > > > > > > > > > > > > > I emailed some installation problems a couple days ago, but > > > haven’t > > > > > answered yet. I am new to freesurfer and try to install the > newest > > > > > version of freesurfer in Ubuntu system. I closely followed the > > > > > instructions, and the only difference is that I installed it > in my > > > > > Documents, instead of local folder. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Below is the output after “source > > > $FREESURFER_HOME/SetUpFreeSurfer.sh” > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > freesurfer-Linux-centos4-stable-pub-v5.0.0 > > > > > > > > > > > > > > > > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > > > > > > > > > > > > > > > > > FREESURFER_HOME /home/jie/Documents/freesurfer/ > > > > > > > > > > > > > > > > > > > > FSFAST_HOME /home/jie/Documents/freesurfer//fsfast > > > > > > > > > > > > > > > > > > > > FSF_OUTPUT_FORMAT nii > > > > > > > > > > > > > > > > > > > > SUBJECTS_DIR /home/jie/Documents/freesurfer//subjects > > > > > > > > > > > > > > > > > > > > MNI_DIR /ho me/jie/Documents/freesurfer//mni > > > > > > > > > > > > > > > > > > > > Everything seems fine and I also added the .license file to > the< > > > br>> > freesurfer folder. But when I test it by “tkmedit bert > > > orig.mgz”, it > > > > > reponds “Illegal instruction” > > > > > > > > > > > > > > > > > > > > If I type in “recon-all”, it will show > > > > > > > > > > > > > > > > > > > > “ Required Arguments: > > > > > > > > > > > > > > > > > > > > -subjid > > > > > > > > > > > > > > > > > > > > -…... ” and the other arguments. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > How to fix the problem and make Fressurfer run? Any help is > > > > > appreciated. Thanks a lot! > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > PS: my Ubuntu is 32-bit and choose the 32-bit version > Freesurfer. > > > > > > > > > > > > > > > > > > > > Jie > > > > > > > > > > ___ > > > > > 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 i nformation, 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] Qdec - ROI - different thickness results
the easiest way to determine X from Y and blue from red (ie, which group is getting thicker or thinner) is to Ctrl-right click on a vertex within the region of interest on the cortex result display. a plot will appear showing the raw thickness values for your groups, and which-is-which should obvious. n. On Fri, 2011-02-25 at 15:33 +, Alex Hanganu wrote: > Dear Freesurfer Experts, > > In qdec for question: > "Does the average thickness differ between X and Y" > we received blue colored regions, meaning that thickness for group Y > is lower then X ? > > We created ROIs for each region, and extracted cortical thickness for > each ROI for each subject using mris_anatomical_stats. > > in results: for each ROI, mean cortical thickness of Y group are > higher then X. > > is it a mistake, or the question was misunderstood ? > > Sincerely, > Alex. > > ___ > 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] qdec problems
i think part of the confusion results from the option in qdec to import the ROI thickness values into qdec for selection as factors in an analysis. if what you want to do is simply look for cortex-wide (ie vertex-wide) differences in thickness between two groups (patients vs. controls), then you dont need to import thickness stats as factors. if you wanted to do an ROI analysis of patients vs controls, then you wouldnt use qdec, but any old stats package, importing the data from the freesurfer stats tables. so try running a sraightforward analysis in qdec, with a qdec.table.dat like this for example fsidgroup subj1 patient subj2 patient subj3 control subj4 control and look in the area of banksts for changes if you expect them there. there is a multiple comparison correction option as well. n. On Sat, 2011-02-26 at 16:38 +0800, 汪贵宏 wrote: > Hi all, > > > > I want to analyse the thickness difference between patients and > normals,but I can not understand the results that I got from > qdec-analysis .I hope someone can help me. > > Firstly,as the papers says, the Cortical (surface-based) > Analysis measures the Distance between white and pial surfaces , get > One value per vertex in result.And also,there are 33 areas when we > choose to analyses,and we can only get the thickness of these 33 areas > per hemisphere,so,my question is why it has just one thickness value > in such a large area on the hemisphere? > > Secondly,in my opinion,there will be red or green in a large scale if > it does exist thickness differences between the patients and normals > in one areas,such as "lh_bankssts_thickness",but,the results seems not > in that way,why? > > Do I explain my questions clearly? > > Thanks, > > wang > > > > > ___ > 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.
[Freesurfer] parellizing Freesurfer
Hi all, I was wondering if someone out there has any experience trying to parallelize their analysis streams in clusters or multiprocessor machines. I was thinking also about the cloud computing services offered by Google, Amazon or other. Has anyone tried or has any plans of implementing something along those lines? Best wishes, Pablo ___ 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] qdec problems
Hi Wang, you can do different types of analysis. You can do a vertex-wise comparison, in which case you'll have about 150,000 tests/hemisphere. This makes the multiple comparison problem pretty bad, so people frequently collapse into regions of interest (ROIs). We provide anatomical ROIs which you can use for this purpose. does that clarify things? I don't understand the red-green part of your question. cheers Bruce On Sat, 26 Feb 2011, [GBK] Íô¹óºê wrote: Hi all, I want to analyse the thickness difference between patients and normals,but I can not understand the results that I got from qdec-analysis .I hope someone can help me. Firstly,as the papers says, the Cortical (surface-based) Analysis measures the Distance between white and pial surfaces , get One value per vertex in result.And also,there are 33 areas when we choose to analyses,and we can only get the thickness of these 33 areas per hemisphere,so,my question is why it has just one thickness value in such a large area on the hemisphere? Secondly,in my opinion,there will be red or green in a large scale if it does exist thickness differences between the patients and normals in one areas,such as "lh_bankssts_thickness",but,the results seems not in that way,why? Do I explain my questions clearly? Thanks, wang___ 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] qdec problems
Hi all, I want to analyse the thickness difference between patients and normals,but I can not understand the results that I got from qdec-analysis .I hope someone can help me. Firstly,as the papers says, the Cortical (surface-based) Analysis measures the Distance between white and pial surfaces , get One value per vertex in result.And also,there are 33 areas when we choose to analyses,and we can only get the thickness of these 33 areas per hemisphere,so,my question is why it has just one thickness value in such a large area on the hemisphere? Secondly,in my opinion,there will be red or green in a large scale if it does exist thickness differences between the patients and normals in one areas,such as "lh_bankssts_thickness",but,the results seems not in that way,why? Do I explain my questions clearly? Thanks, wang___ 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.
