[Freesurfer] FreeSurfer 6
Hey Guys, Sorry if this is a frequently asked question. Do we have an updated ETA for version 6 of Freesurfer? We are planning on upgrading our 1024-node cluster and version 6 is a big deal for us. Best Pedro Paulo Jr. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] Head motion during MRI acquisition reduces gray matter volume and thickness estimates
The paper Martin Reuter and the FS group wrote was featured in an article of Discover Magazine by Neuroskeptic. http://blogs.discovermagazine.com/neuroskeptic/2014/12/19/head-motion-structural-scans/#.VJhYkBSACk Reuter M, Tisdall MD, Qureshi A, Buckner RL, van der Kouwe AJ, Fischl B (2014). Head motion during MRI acquisition reduces gray matter volume and thickness estimates. NeuroImage, 107C, 107-115 PMID: 25498430 http://www.ncbi.nlm.nih.gov/pubmed/25498430 ___ 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] Generating T1 + Aseg views without Tkmedit and Freeview
This server cannot run any X11 for security reasons. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Nov 5, 2014 at 8:11 PM, Chris Watson christopher.wat...@childrens.harvard.edu wrote: Have you tried installing 'xauth' on the server and connecting via 'ssh -X'? That should show all graphical output on the local machine. On 11/05/2014 05:03 PM, Bruce Fischl wrote: Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work, and maybe still does, but I don't think we ever implemented it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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 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] Generating T1 + Aseg views without Tkmedit and Freeview
Hi Bruce. I believe Tksurfer, even with renderoffscreen, requires X11. I suppose I could export one slice of T1 data and the same Slice of Aseg data and make a script to superimpose both. Not sure which of the cmd line tools to use for this slice export. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Nov 5, 2014 at 8:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work, and maybe still does, but I don't think we ever implemented it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] Generating T1 + Aseg views without Tkmedit and Freeview
I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] Freesurfer course 2015 Brazil
We don't have a date yet. An estimate would be March/April - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Fri, Oct 24, 2014 at 3:00 PM, Andrea Horváth andrhorv...@gmail.com wrote: Dear Freesurfers, Does anyone know the exact date of the upcoming Freesurfer course in Sao Paolo, Brazil? I know that it is too early, but we need the date for a travel grant application. Thank you for your help in advance! Cheers, Andrea -- *Andrea Horvath M.D.* PhD Fellow Diagnostic Centre of Pécs horvath.andr...@pte.hu ___ 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] recon-all subject folder size
300mb is fine. - 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, Feb 24, 2014 at 3:01 PM, Durai Arasan dura...@gmail.com wrote: Hi Freesurfer experts, I am successfully running recon-all on my cluster. However I find that the subject folders have sizes ranging from 300mb to 900mb. I grepped all recon-all.log files for finished without error and that seemed fine for all subjects. But I would like to know what is the expected subject folder size when you run recon-all (with -all option) starting from a standard MPRAGE T1 image. This might be useful since I have limited control over the cluster nodes where the processing takes place. Thank you Durai On Mon, Feb 17, 2014 at 2:55 AM, Durai Arasan dura...@gmail.com wrote: Hi Freesurfer experts, so I got this error when I ran recon-all on my cluster. I am really hoping this is just a case of missing GCC libraries and nothing is wrong with the Freesurfer installation on the nodes. Kindly confirm this. Thank you ** Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /** Actual FREESURFER_HOME /** Linux * SMP Fri Mar 22 05:41:51 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_convert) mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_convert) mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_convert) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by tkregister2_cmdl) tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by tkregister2_cmdl) tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by tkregister2_cmdl) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_make_uchar) mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_make_uchar) mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_make_uchar) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_normalize) mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_normalize) mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_normalize) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_watershed) mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_watershed) mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_watershed) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_gcut) mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_gcut) mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_gcut) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_segment) mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_segment) mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_segment) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_label2label) mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_label2label) mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_label2label) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_em_register) mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_em_register) mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by mri_em_register) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by mri_ca_normalize) mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by mri_ca_normalize) mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7
Re: [Freesurfer] longer run time on 5.3 versus 5.2 ?
I saw this issue too. The total running time went from an average of 16.3h to 20.4h - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Tue, Jun 4, 2013 at 2:54 PM, Mehul Sampat mpsam...@gmail.com wrote: Hi Bruce, Okay. It went from ~4 hours in 5.2 to ~9 hours in 5.3; we thought it was a big change to and are trying to isolate the root cause We are running 75 cases run with 5.3 that have been run with 5.2 before; once they are done, will let you all know if this issue is seen in other cases too. Mehul ps: the cases were run on different machines but the specs of the two machines are quite similar; we are also trying to see if it is hard-ware related.. On Tue, Jun 4, 2013 at 10:37 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Mehul no, that's definitely not expected for it to go from 20 min to almost 5 hours! We'll investigate as that shouldn't be the case. Bruce On Tue, 4 Jun 2013, Mehul Sampat wrote: In some cases, we are seeing that, for the same subject, the run time is slower for 5.3 versus 5.2; A quick check on recon-all-status.log shows that the CA Reg Inv step is taking longer with 5.3. recon-all-status.log from data processed with 5.2: #@# CA Reg Thu Jan 17 16:03:53 PST 2013 #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013 recon-all-status.log from data processed with 5.3 #@# CA Reg Mon Jun 3 19:46:37 PDT 2013 #@# CA Reg Inv Tue Jun 4 04:52:57 PDT 2013 Is this expected ? Or in your own testing are the recon-all processing times similar for 5.2 versus 5.3 ? The recon-all.log file for both cases are attached; Thanks Mehul 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/**compliancelinehttp://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 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] [Release] - iSurf BrainView 4.1.0
Today it was released the version 4.1.0 of iSurf BrainView for iPad, iPhone and iPod Touch. Major changes: - Color scheme has been changed to match Windows 8 Version. - Icon has been redesigned as suggested by many users. - Now it supports the new resolution. 1136x640 - 3D engine has been redesigned to take advantage of new iOS device GPU - Aseg from FreeSurfer 5.2 As usual suggestions and feedback are welcome. The link for download is: http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8 - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] Very different results between 5.1.0 and 5.2.0
Daniel, Unfortunately, since I run all the individuals again with FreeSurfer 5.2, I just saved from the 5.1 the info I was using for comparison between version - the aseg stats. I don't have cortical thickness information for 5.1 unless we run all the cases again in 5.1 - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Apr 11, 2013 at 2:47 PM, Yang, Daniel yung-jui.y...@yale.eduwrote: Hi PPJ and all, I found that the 5.2 – 5.1 difference is primarily seen in the cortical thickness, and much less so in the aseg.volume. Here, I picked right-amygdala volume as an example of aseg.volume and rh_bankssts_thickness as an example of rh.aparc.thickness. While the correlation between the two versions of right-amygdala is r = .92 (n = 161), that of the rh_bankssts_thickness is r = .45. Presumably I believe the correlation should be .90 for a strong continuity between the two versions? Do you have anything in the cortical thickness? Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 From: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Date: Wednesday, April 10, 2013 11:07 AM To: Daniel Yang yung-jui.y...@yale.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Ok, I'll try to put together a stat from aparc too. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel yung-jui.y...@yale.eduwrote: Hi PPJ, Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any chance you could also provide the cortical thickness of the 2009 atlas (e.g., rh)? I will take a look into the aseg.volume in my data too. Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 From: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Date: Wednesday, April 10, 2013 10:49 AM To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: Daniel Yang yung-jui.y...@yale.edu, freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 You'll find attached some preliminary data of the comparison we did among versions. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi PPJ That's exactly what we are doing. Good to hear its stable for you Bruce On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br wrote: I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing between version 5.2.0 and 5.1, besides the obvious new features, is processing time. Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. Besides that there's no visible difference in terms of cortical thickness, volumes, etc. If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel yung-jui.y...@yale.eduwrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing between version 5.2.0 and 5.1, besides the obvious new features, is processing time. Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. Besides that there's no visible difference in terms of cortical thickness, volumes, etc. If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel yung-jui.y...@yale.eduwrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the region I examined with my samples, it's not a systematic predictable bias. Any solution? -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/18/13 6:27 PM, Matt Glasser m...@ma-tea.com wrote: Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more correct, 5.1 or 5.2. Peace, Matt. On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University of Pennsylvania School of Medicine 3rd Floor, Room 312 3710 Hamilton Walk (Goddard Laboratories) Philadelphia, PA 19104-6241 email - rida...@mail.med.upenn.edu - Original Message - From: Daniel Yang yung-jui.y...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in particular. Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0. They are significantly different, t(160) = 56.71. The correlation between the two versions is r = .33 Is this something possible?? I can't see what went wrong in my procedures. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ 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 ___ 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
Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
Ok, I'll try to put together a stat from aparc too. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel yung-jui.y...@yale.eduwrote: Hi PPJ, Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any chance you could also provide the cortical thickness of the 2009 atlas (e.g., rh)? I will take a look into the aseg.volume in my data too. Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 From: Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Date: Wednesday, April 10, 2013 10:49 AM To: Bruce Fischl fis...@nmr.mgh.harvard.edu Cc: Daniel Yang yung-jui.y...@yale.edu, freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0 You'll find attached some preliminary data of the comparison we did among versions. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi PPJ That's exactly what we are doing. Good to hear its stable for you Bruce On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br wrote: I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing between version 5.2.0 and 5.1, besides the obvious new features, is processing time. Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance. Besides that there's no visible difference in terms of cortical thickness, volumes, etc. If you have access to computer resources to spare you can run recon-all of both versions in some well known database of images and do a more formal test. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel yung-jui.y...@yale.eduwrote: Dear FreeSurfer Experts and Users, Did anyone find similar things using FS 5.2 (please see my previous post below)? That is, FS 5.2 is including more non-cortical black spaces within pial surfaces, compared to FS 5.1? I'm not interested in nitpicking but I feel this is a rather serious issue, so I would like to raise it again before it's completely forgotten. At the meantime I keep receiving Emails from people asking me this issue. Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/19/13 7:07 AM, Yang, Daniel yung-jui.y...@yale.edu wrote: Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more black spaces in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the region I examined with my samples, it's not a systematic predictable bias. Any solution? -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 3/18/13 6:27 PM, Matt Glasser m...@ma-tea.com wrote: Do the surfaces look correct in these regions? You might post some screenshots of subjects who have a big difference between 5.1 and 5.2 with the 5.1 and 5.2 white and pial surfaces on volume slices that highlight the difference. Without this kind of info, its hard to know which was more correct, 5.1 or 5.2. Peace, Matt. On 3/18/13 5:13 PM, Ritobrato Datta rida...@mail.med.upenn.edu wrote: I concur. I have seen similar results in primary visual cortex from ~40 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3. Ritobrato Datta, Ph.D. Post Doctoral Researcher Department of Neurology University of Pennsylvania School of Medicine 3rd Floor, Room 312 3710 Hamilton Walk (Goddard Laboratories) Philadelphia, PA 19104-6241 email - rida...@mail.med.upenn.edu - Original Message - From: Daniel Yang yung-jui.y...@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT) Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0 Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer
[Freesurfer] iSurf BrainView now available for Windows 8 {Disarmed}
Today Microsoft approved iSurf BrainView version for Windows 8 Tablets and computers. It's a free App. http://apps.microsoft.com/windows/en-us/app/brainview/be2623f5-c5e3-4295-a28e-d3f64dc19266 BrainView is a Brain MRI tutor based on the MRI automatic segmentation produced by FreeSurfer. FreeSurfer is a software package developed by investigators at the Athinoula A. Martinos Center for Biomedical Imaging. This App uses its automatic segmentation to produce an automatic atlas of neuroimaging based on T1 MRI Images. It also displays 3D accurate models of brain cortex with automatic structure labeling. A great tool for teaching brain MRI and for learning neuroanatomy. For more reference on the educational use of iSurf BrainView: Oliveira Jr, PPM; Fischl, Bruce; Amaro, Edson Teaching neuroanatomy using Iphone and IPad. In: Human Brain Mapping, 2011, Quebec, CA. Proc. Human Brain Mapping 2011, 2011. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com http://www.netfilter.com.br ___ 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 in Talairach transform version 5.2
I'm having some recon-all errors like this: mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.3505/src.mnc transforms/talairach.auto.xfm Use of uninitialized value $path in join or string at /usr/local/freesurfer/mni/bin/mritotal line 462. mritotal: Couldn't find configuration file mritotal.cfg anywhere in :/usr/local/freesurfer/mni/bin/../etc/mni_autoreg ERROR: mritotal failed, see transforms/talairach.log Linux ip-10-147-137-177 3.2.39-6.88.amzn1.i686 #1 SMP Sat Mar 2 05:13:38 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s caso765 exited with ERRORS at Mon Mar 25 19:24:29 UTC 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Is this file /usr/local/freesurfer/mni/bin/../etc/mni_autoreg really missing in the distribution? ___ 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] FS 5.2-beta run-times on Amazon Web services (AWS)
In the http://cerebralvol.com service we are having 23.5 hours average with 5.1 and 23.8 hours average with 5.2-Beta Notice that in order to minimize the cost to the user we are running it in m1.medium We have achieved a full recon-all in less than 4 hours (3.83 hours) with cg1.4xlarge But for a large amount of data I believe our 1024-core m1.medium is the best cost benefit. - 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, Feb 2, 2013 at 2:11 AM, Mehul Sampat mpsam...@gmail.com wrote: Hi Bruce, No I did not specify the # of open mp threads on the recon-all cmd line. These run times were obtained by running one subject per core. for example cc2.8xlarge has 8 cores and so we ran 8 subjects at once; Thanks for the info about the # of open mp threads options; I will look into it. One other note: Bruce, Nick did you improve the memory management in 5.2 ? On our local machine we noticed we can run 6 subjects simultaneously even though we only have 12gb of ram. I thought some of the them might crash since we only have 2gb per subject but no crashes so far over 30 subjects.. Mehul On Fri, Feb 1, 2013 at 7:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Mehul did you specify the # of open mp threads on the recon-all cmd line? cheers Bruce On Fri, 1 Feb 2013, Mehul Sampat wrote: Hi Folks, Just wanted to share our experience with running FS 5.2-beta on Amazon Web Services (AWS). Basically, AWS has multiple instance types (http://aws.amazon.com/ec2/**instance-types/http://aws.amazon.com/ec2/instance-types/) and we were trying to figure out the most cost-effective approach. We ran two subjects through FS 5.2-beta on M1 Large Instance (m1.large) and Cluster Compute Eight Extra Large Instance (cc2.8xlarge). (same subjects run on both instance). We expected cc2.8xlarge to be faster (but it is also more expensive: $2.4 per hour; 8 cores); The run-times we got: instance-type subject start-time end-time run-time m1.large subject-1 01:05:44 UTC 2013 15:40:45 UTC 2013 ~14hr-35mins m1.large subject-2 01:06:06 UTC 2013 15:08:45 UTC 2013 ~14hr-02mins cc2.8xlarge subject-1 01:26:38 UTC 2013 12:30:23 UTC 2013 ~11hr-04mins cc2.8xlarge subject-2 01:27:28 UTC 2013 12:19:08 UTC 2013 ~10hr-52mins Although m1.large is a few hours slower, it seems to be the more cost effective option since it is $0.24 per hour (2 cores). If you have run Freesurfer on AWS, do you have a similar experience ? Any suggestions to speed up the run-times on AWS would be very helpful. Thanks Mehul 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/**compliancelinehttp://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 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] FreeSurfer problem on VirtualBox Linux
Unfortunately Windows XP SP3 is no longer Tier-1 supported for VirtualBox. I suggest you to try it on Windows 7 or Windows 8. cheers PPJ - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Jan 9, 2013 at 7:49 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: Carissa, Unfortunately I dont think we can help with this problem, as we currently do not have the resources to support the Windows VM instance. However, an alternative that has worked for others is to do the following: install the FSL Windows VM, described here: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Windows once that is up-and-running, then within that linux instance, just download and install our linux centos 4 freesurfer build. this also means you can update to v5.2 when that is released in a couple weeks. Nick On Wed, 2013-01-09 at 08:34 +, Carissa Nadia Kuswanto (IMH) wrote: Hi there, My operating system is Windows XP SP3 and it has been loaded with VirtualBox 4.2.6 for Windows hosts and we would like to run freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi. But when we attempt to launch FreeSurfer, the terminal seems to hang with the following message: GRUB loading stage 1.5 GRUB loading, please wait... Would you kindly help us on how to overcome this problem? I thank you in advance for your kind attention. Best regards, Carissa __ The information contained in this e-mail and the attachments (if any) may be privileged and confidential and is intended solely for the named addressee. If you are not the intended recipient, please do not print, retain copy, disseminate, distribute, or use this e-mail or any part thereof. Please notify the sender immediately by replying to this e-mail and delete all copies of this e-mail and the attachments. ___ 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 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] mri_cc segfault
Bruce found that the data had the direction cosine wrong. I have fixed the direction and I'm running it again. I've put the data in the ftp - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Tue, Dec 18, 2012 at 8:41 PM, Nick Schmansky ni...@nmr.mgh.harvard.eduwrote: PPJ, Hi, if you want, you can send me the input files (the two aseg's and the lta) and i can try to replicate the segfault in a debugger. also, if you want, there is a beta of the upcoming v5.2 which is posted here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/ which you could try. hopefully that mri_cc doesnt segfault. Nick On Tue, 2012-12-18 at 12:46 -0200, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm having a segfault with mri_cc it's happening sometimes using FreeSurfer 5.1 Searching the mailing list I saw a similar problem in 2008 but with no answers. The relevant portion of recon-all.log: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta c70eb728-c505-46c2-a2a1-1ed409c36ea1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/norm.mgz 2358 voxels in left wm, 13846 in right wm, xrange [122, 136] searching rotation angles z=[-10 4], y=[-31 -17] ^Msearching scale 1 Z rot -9.8 ^Msearching scale 1 Z rot -9.5 ^Msearching scale 1 Z rot -9.3 ^Msearching scale 1 Z rot -9.0 ^Msearching scale 1 Z rot -8.8 ^Msearching scale 1 Z rot -8.5 ^Msearching scale 1 Z rot -8.3 ^Msearching scale 1 Z rot -8.0 ^Msearching scale 1 Z rot -7.8 ^Msearching scale 1 Z rot -7.5 ^Msearching scale 1 Z rot -7.3 ^Msearching scale 1 Z rot -7.0 ^Msearching scale 1 Z rot -6.8 ^Msearching scale 1 Z rot -6.5 ^Msearching scale 1 Z rot -6.3 ^Msearching scale 1 Z rot -6.0 ^Msearching scale 1 Z rot -5.8 ^Msearching scale 1 Z rot -5.5 ^Msearching scale 1 Z rot -5.3 ^Msearching scale 1 Z rot -5.0 ^Msearching scale 1 Z rot -4.8 ^Msearching scale 1 Z rot -4.5 ^Msearching scale 1 Z rot -4.3 ^Msearching scale 1 Z rot -4.0 ^Msearching scale 1 Z rot -3.8 ^Msearching scale 1 Z rot -3.5 ^Msearching scale 1 Z rot -3.3 ^Msearching scale 1 Z rot -3.0 ^Msearching scale 1 Z rot -2.8 ^Msearching scale 1 Z rot -2.5 ^Msearching scale 1 Z rot -2.3 ^Msearching scale 1 Z rot -2.0 ^Msearching scale 1 Z rot -1.8 ^Msearching scale 1 Z rot -1.5 ^Msearching scale 1 Z rot -1.3 ^Msearching scale 1 Z rot -1.0 ^Msearching scale 1 Z rot -0.8 ^Msearching scale 1 Z rot -0.5 ^Msearching scale 1 Z rot -0.3 ^Msearching scale 1 Z rot -0.0 ^Msearching scale 1 Z rot 0.2 ^Msearching scale 1 Z rot 0.5 ^Msearching scale 1 Z rot 0.7 ^Msearching scale 1 Z rot 1.0 ^Msearching scale 1 Z rot 1.2 ^Msearching scale 1 Z rot 1.5 ^Msearching scale 1 Z rot 1.7 ^Msearching scale 1 Z rot 2.0 ^Msearching scale 1 Z rot 2.2 ^Msearching scale 1 Z rot 2.5 ^Msearching scale 1 Z rot 2.7 ^Msearching scale 1 Z rot 3.0 ^Msearching scale 1 Z rot 3.2 ^Msearching scale 1 Z rot 3.5 ^Msearching scale 1 Z rot 3.7 global minimum found at slice 129.0, rotations (-2.52, -3.27) final transformation (x=129.0, yr=-2.521, zr=-3.273): 0.997 0.057 -0.044 -2.975; -0.057 0.998 0.003 -6.742; 0.044 -0.000 0.999 -9.547; 0.000 0.000 0.000 1.000; Segmentation fault Thanks PPJ - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] mri_cc segfault
I'm having a segfault with mri_cc it's happening sometimes using FreeSurfer 5.1 Searching the mailing list I saw a similar problem in 2008 but with no answers. The relevant portion of recon-all.log: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta c70eb728-c505-46c2-a2a1-1ed409c36ea1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/transforms/cc_up.lta reading aseg from /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/aseg.auto_noCCseg.mgz reading norm from /usr/local/freesurfer/subjects/c70eb728-c505-46c2-a2a1-1ed409c36ea1/mri/norm.mgz 2358 voxels in left wm, 13846 in right wm, xrange [122, 136] searching rotation angles z=[-10 4], y=[-31 -17] ^Msearching scale 1 Z rot -9.8 ^Msearching scale 1 Z rot -9.5 ^Msearching scale 1 Z rot -9.3 ^Msearching scale 1 Z rot -9.0 ^Msearching scale 1 Z rot -8.8 ^Msearching scale 1 Z rot -8.5 ^Msearching scale 1 Z rot -8.3 ^Msearching scale 1 Z rot -8.0 ^Msearching scale 1 Z rot -7.8 ^Msearching scale 1 Z rot -7.5 ^Msearching scale 1 Z rot -7.3 ^Msearching scale 1 Z rot -7.0 ^Msearching scale 1 Z rot -6.8 ^Msearching scale 1 Z rot -6.5 ^Msearching scale 1 Z rot -6.3 ^Msearching scale 1 Z rot -6.0 ^Msearching scale 1 Z rot -5.8 ^Msearching scale 1 Z rot -5.5 ^Msearching scale 1 Z rot -5.3 ^Msearching scale 1 Z rot -5.0 ^Msearching scale 1 Z rot -4.8 ^Msearching scale 1 Z rot -4.5 ^Msearching scale 1 Z rot -4.3 ^Msearching scale 1 Z rot -4.0 ^Msearching scale 1 Z rot -3.8 ^Msearching scale 1 Z rot -3.5 ^Msearching scale 1 Z rot -3.3 ^Msearching scale 1 Z rot -3.0 ^Msearching scale 1 Z rot -2.8 ^Msearching scale 1 Z rot -2.5 ^Msearching scale 1 Z rot -2.3 ^Msearching scale 1 Z rot -2.0 ^Msearching scale 1 Z rot -1.8 ^Msearching scale 1 Z rot -1.5 ^Msearching scale 1 Z rot -1.3 ^Msearching scale 1 Z rot -1.0 ^Msearching scale 1 Z rot -0.8 ^Msearching scale 1 Z rot -0.5 ^Msearching scale 1 Z rot -0.3 ^Msearching scale 1 Z rot -0.0 ^Msearching scale 1 Z rot 0.2 ^Msearching scale 1 Z rot 0.5 ^Msearching scale 1 Z rot 0.7 ^Msearching scale 1 Z rot 1.0 ^Msearching scale 1 Z rot 1.2 ^Msearching scale 1 Z rot 1.5 ^Msearching scale 1 Z rot 1.7 ^Msearching scale 1 Z rot 2.0 ^Msearching scale 1 Z rot 2.2 ^Msearching scale 1 Z rot 2.5 ^Msearching scale 1 Z rot 2.7 ^Msearching scale 1 Z rot 3.0 ^Msearching scale 1 Z rot 3.2 ^Msearching scale 1 Z rot 3.5 ^Msearching scale 1 Z rot 3.7 global minimum found at slice 129.0, rotations (-2.52, -3.27) final transformation (x=129.0, yr=-2.521, zr=-3.273): 0.997 0.057 -0.044 -2.975; -0.057 0.998 0.003 -6.742; 0.044 -0.000 0.999 -9.547; 0.000 0.000 0.000 1.000; Segmentation fault Thanks PPJ - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] Public Supercomputing service to process FreeSurfer data
We are announcing today the release of the Public Beta of CerebralVol.comhttp://cerebralvol.com/, a public cloud based supercomputer service to process FreeSurfer data. CerebralVol.com users can process large amount of data using recon-all in a single day without the hassle of dealing with Unix commands, scripts, etc. Users can upload input data (NifTI and MGZ) through the web and download the results of the recon-all from the web interface. It's also possible to separate your cases in Groups and have Studies associated with the Groups. This week we are shipping the service with 20 CPUs and we are growing it to 1024 CPUs by the end of next week. The system will be fully operational by January with 4096 nodes available to process more than 4000 recon-all per day. Those of you who want to know more about the technical details of the project can find more information at https://www.cerebralvol.com/about.html also you can find information regarding HIPAA at https://www.cerebralvol.com/hipaa.html Signup for free at: https://www.cerebralvol.com We strongly appreciate any suggestions and feedback. Pedro Paulo Oliveira Jr. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] slanted
No! Do you have a dropbox account? Copy there and send the link to them. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Jul 11, 2012 at 3:39 PM, Borzello, Mia mborze...@partners.orgwrote: can i just send it to freesurfer@nmr.mgh.harvard.edu? thanks From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:58 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted when you say ftp doesn't work, what do you mean? It works for me: ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:fischl): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp cd /space/incoming 250 Directory successfully changed. ftp ls 227 Entering Passive Mode (132,183,202,158,147,239) 150 Here comes the directory listing. 226 Transfer done (but failed to open directory). ftp put test.mgz local: test.mgz remote: test.mgz 227 Entering Passive Mode (132,183,202,158,147,226) 150 Ok to send data. 226 File receive OK. 1696595 bytes sent in 0.209 secs (7.9e+03 Kbytes/sec) On Wed, 11 Jul 2012, Borzello, Mia wrote: i saw the instructions, but it doesn't give an e-mail specifically for that and ftp surfer.nmr.mgh.harvard.edu doesn't work. From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [ fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:24 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: Hi, I'm not exactly sure what the problem is, but for some reason, this brain is kind of sheered. I'm not sure if it's because of the CT, but on the right side of the picture i attached, it kind of wider on one side. It's alignment isn't right, and using rotate does help. How should I correct this? Thanks, Mia ___ 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 ___ 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
Re: [Freesurfer] TkSurfer and new color table. Mislabelling
Thanks Douglas. It did work using the color table with just the included labels (I had to renumber the labels in the table) For left: 1 ctx-lh-bankssts 255 42 0 0 2 ctx-lh-caudalmiddlefrontal 255 14 0 0 3 ctx-lh-entorhinal 255 17 0 0 4 ctx-lh-paracentral 255 43 0 0 5 ctx-lh-parstriangularis 255 15 0 0 6 ctx-lh-postcentral 255 14 0 0 7 ctx-lh-superiorfrontal 255 79 0 0 8 ctx-lh-frontalpole 255 17 0 0 9 ctx-lh-temporalpole 255 14 0 0 For right: 1 ctx-rh-bankssts 255 18 0 0 2 ctx-rh-isthmuscingulate 255 39 0 0 3 ctx-rh-medialorbitofrontal 255 60 0 0 4 ctx-rh-parstriangularis 255 13 0 0 5 ctx-rh-rostralanteriorcingulate 255 40 0 0 6 ctx-rh-superiorparietal 255 48 0 0 7 ctx-rh-frontalpole 255 106 0 0 On Thu, Jul 5, 2012 at 7:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Pedro Paulo, it is not quite the right procedure, but I'm surprised that it gave unknown for all labels. Try modifying the colortable.txt such that the first entry is the name and color for your first label, etc. doug On 07/05/2012 03:44 PM, Pedro Paulo de Magalhães Oliveira Junior wrote: Doug, I did mri_annotation2label --subject bert --hemi lh --outdir $SUBJECTS_DIR/bert/label mri_annotation2label --subject bert --hemi rh --outdir $SUBJECTS_DIR/bert/label And then mris_label2annot --s bert --hemi lh --ctab $FREESURFER_HOME/**FreeSurferColorLUT.txt --l lh.bankssts.label --l lh.caudalmiddlefrontal.label --l lh.entorhinal.label --l lh.paracentral.label --l lh.parstriangularis.label --l lh.postcentral.label --l lh.superiorfrontal.label --l lh.frontalpole.label --l lh.temporalpole.label --a myannot and mris_label2annot --s bert --hemi rh --ctab $FREESURFER_HOME/**FreeSurferColorLUT.txt --l rh.bankssts.label --l rh.isthmuscingulate.label --l rh.medialorbitofrontal.label --l rh.parstriangularis.label --l rh.rostralanteriorcingulate.**label --l rh.superiorparietal.label --l rh.frontalpole.label --a myannot If this is the right procedure I guess I'll have to modify the existing annot in matlab because all the surface is being labelled as Unknown. Thanks PPJ On Thu, Jul 5, 2012 at 4:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: You can also break up the annot into labels ( mri_annotation2label) then recombine them with a new color table with mris_label2annot. doug On 07/05/2012 02:57 PM, Bruce Fischl wrote: Hi PPJ, I think the color lut is embedded in the aparc.annot. If you want to change it you have to change the one that's in the .annot. I would do it in matlab. cheers Bruce On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm trying to generate an image to a paper and I have to colorize some areas of the cortex with specific colors. I have edited the FreeSurferColorLUT.txt changing the following lines: 1001 ctx-lh-bankssts 255 42 0 0 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0 1006 ctx-lh-entorhinal 255 17 0 0 1017 ctx-lh-paracentral 255 43 0 0 1020 ctx-lh-parstriangularis 255 15 0 0 1022 ctx-lh-postcentral 255 14 0 0 1028 ctx-lh-superiorfrontal 255 79 0 0 1032 ctx-lh-frontalpole 255 17 0 0 1033 ctx-lh-temporalpole 255 14 0 0 2001 ctx-rh-bankssts 255 18 0 0 2010 ctx-rh-isthmuscingulate 255 39 0 0 2014 ctx-rh-medialorbitofrontal 255 60 0 0 2020 ctx-rh-parstriangularis 255 13 0 0 2026 ctx-rh-**rostralanteriorcingulate 255 40 0 0 2029 ctx-rh-superiorparietal 255 48 0 0 2032 ctx-rh-frontalpole 255 106 0 0 all other regions are 127 127 127 0 When I load the surface for some case with: tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt I get the usual coloring scheme with the labels correct. TkSurfer seems to be ignoring FreeSurferColorLUT.txt, but the labels are placed in the right spots. When I try to manually force the FreeSurferColorLUT.txt I'm visualizing an all grey image. And the surface is completely mislabeled, there is a 4th ventricle in the surface, putamen in the surface, etc. What am I doing wrong? --**--** - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br http://www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/**artist/netfilter/id365306441http://itunes.apple.com/br/artist/netfilter/id365306441 __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo
[Freesurfer] TkSurfer and new color table. Mislabelling
I'm trying to generate an image to a paper and I have to colorize some areas of the cortex with specific colors. I have edited the FreeSurferColorLUT.txt changing the following lines: 1001 ctx-lh-bankssts 255 42 0 0 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0 1006 ctx-lh-entorhinal 255 17 0 0 1017 ctx-lh-paracentral 255 43 0 0 1020 ctx-lh-parstriangularis 255 15 0 0 1022 ctx-lh-postcentral 255 14 0 0 1028 ctx-lh-superiorfrontal 255 79 0 0 1032 ctx-lh-frontalpole 255 17 0 0 1033 ctx-lh-temporalpole 255 14 0 0 2001 ctx-rh-bankssts 255 18 0 0 2010 ctx-rh-isthmuscingulate 255 39 0 0 2014 ctx-rh-medialorbitofrontal 255 60 0 0 2020 ctx-rh-parstriangularis 255 13 0 0 2026 ctx-rh-rostralanteriorcingulate 255 40 0 0 2029 ctx-rh-superiorparietal 255 48 0 0 2032 ctx-rh-frontalpole 255 106 0 0 all other regions are 127 127 127 0 When I load the surface for some case with: tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt I get the usual coloring scheme with the labels correct. TkSurfer seems to be ignoring FreeSurferColorLUT.txt, but the labels are placed in the right spots. When I try to manually force the FreeSurferColorLUT.txt I'm visualizing an all grey image. And the surface is completely mislabeled, there is a 4th ventricle in the surface, putamen in the surface, etc. What am I doing wrong? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] TkSurfer and new color table. Mislabelling
Doug, I did mri_annotation2label --subject bert --hemi lh --outdir $SUBJECTS_DIR/bert/label mri_annotation2label --subject bert --hemi rh --outdir $SUBJECTS_DIR /bert/label And then mris_label2annot --s bert --hemi lh --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l lh.bankssts.label --l lh.caudalmiddlefrontal.label --l lh.entorhinal.label --l lh.paracentral.label --l lh.parstriangularis.label --l lh.postcentral.label --l lh.superiorfrontal.label --l lh.frontalpole.label --l lh.temporalpole.label --a myannot and mris_label2annot --s bert --hemi rh --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --l rh.bankssts.label --l rh.isthmuscingulate.label --l rh.medialorbitofrontal.label --l rh.parstriangularis.label --l rh.rostralanteriorcingulate.label --l rh.superiorparietal.label --l rh.frontalpole.label --a myannot If this is the right procedure I guess I'll have to modify the existing annot in matlab because all the surface is being labelled as Unknown. Thanks PPJ On Thu, Jul 5, 2012 at 4:01 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: You can also break up the annot into labels ( mri_annotation2label) then recombine them with a new color table with mris_label2annot. doug On 07/05/2012 02:57 PM, Bruce Fischl wrote: Hi PPJ, I think the color lut is embedded in the aparc.annot. If you want to change it you have to change the one that's in the .annot. I would do it in matlab. cheers Bruce On Thu, 5 Jul 2012, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm trying to generate an image to a paper and I have to colorize some areas of the cortex with specific colors. I have edited the FreeSurferColorLUT.txt changing the following lines: 1001 ctx-lh-bankssts 255 42 0 0 1003 ctx-lh-caudalmiddlefrontal 255 14 0 0 1006 ctx-lh-entorhinal 255 17 0 0 1017 ctx-lh-paracentral 255 43 0 0 1020 ctx-lh-parstriangularis 255 15 0 0 1022 ctx-lh-postcentral 255 14 0 0 1028 ctx-lh-superiorfrontal 255 79 0 0 1032 ctx-lh-frontalpole 255 17 0 0 1033 ctx-lh-temporalpole 255 14 0 0 2001 ctx-rh-bankssts 255 18 0 0 2010 ctx-rh-isthmuscingulate 255 39 0 0 2014 ctx-rh-medialorbitofrontal 255 60 0 0 2020 ctx-rh-parstriangularis 255 13 0 0 2026 ctx-rh-rostralanteriorcingulate 255 40 0 0 2029 ctx-rh-superiorparietal 255 48 0 0 2032 ctx-rh-frontalpole 255 106 0 0 all other regions are 127 127 127 0 When I load the surface for some case with: tksurfer bert lh pial -annot aparc -ctab FreeSurferColorLUT.txt I get the usual coloring scheme with the labels correct. TkSurfer seems to be ignoring FreeSurferColorLUT.txt, but the labels are placed in the right spots. When I try to manually force the FreeSurferColorLUT.txt I'm visualizing an all grey image. And the surface is completely mislabeled, there is a 4th ventricle in the surface, putamen in the surface, etc. What am I doing wrong? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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. ___ 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] .license file
If FreeSurfer on Mac has been installed on /Applications you may need to type sudo cat $FREESURFER_HOME/.license and enter your account password when asked - 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, Jun 18, 2012 at 10:57 AM, Paul Raines rai...@nmr.mgh.harvard.eduwrote: I am assuming you are on a OSX box which has that stupid protection. Just open a Terminal and run cat $FREESURFER_HOME/.license then type in the 3 lines and Enter and then do a Control-D to exit -- Paul Raines (http://help.nmr.mgh.harvard.**eduhttp://help.nmr.mgh.harvard.edu ) On Sun, 17 Jun 2012 1:45am, Monica Giraldo wrote: Hello, I created a file with this data, but when I'm going to save it as .license doesnt let me because a message appears and says that files starting with . are of the system and that i have to choose another name. What can I do? Thanks. Mónica Giraldo Chica PhD. Candidate Biomedicine Sherman Health Science Research Centre www.monicagiraldochica.com __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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 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] [Release] - iSurf BrainView 4.0.5
Today it was released the version 4.0.5 of iSurf Brainview, it's a major redesign version release for IPad, IPhone and IPod Touch. The UI has been redesigned to be more compliant to the Apple Human Interface Guidelines. As usual suggestions and feedback are welcome. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423mt=8 Note: A version for Windows Phone 7.5 (Nokia Lumia 900, 800, 710, etc) is under development. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] OBJ conversion
There's a how-to in the FreeSurfer website: http://surfer.nmr.mgh.harvard.edu/fswiki/HowTo/HowTo Pedro Paulo Jr. On Mon, Feb 20, 2012 at 23:32, Manfred G Kitzbichler manfr...@nmr.mgh.harvard.edu wrote: Hi Darshan, as Bruce suggested, you can use mris_convert to get an STL file which you can import into Blender or MeshLab. Both write Wavefront OBJ files. - Manfred On 02/20/2012 07:24 PM, Darshan P wrote: Hello all, I was wondering if I can convert the surface outputs to an OBJ mesh file format . Since most of the applications are in windows I was hoping if there is conversion tool to do this . Regards Darshan ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Manfred G. Kitzbichlerhttps://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=1377, Research Fellow Harvard Medical School Mass General Hospital Martinos Center for Biomedical Imaging 149 Thirteenth Street, Rm 10.018 Charlestown, MA 02129, USA ___ 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] iSurf Brainview now ported to Mac
Today Apple released in the Mac Store, for free, the version of iSurf BrainView for Mac. It's yet not as complete as the iPad and iPhone version but it has some nice features to help you or your students to learn neuroanatomy using FreeSurfer automated parcellation and subcortical segmentation. You can download it at: http://itunes.apple.com/us/app/isurf-brainview-desktop/id491367143?ls=1mt=12 As usual, suggestions are welcome. Happy 2012 for everyone. PPJ - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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
As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/15 Joshua Lee jki...@ucdavis.edu It would be great if Freesurfer maintained an official AMI. One important reason to do so is security. If the AMI is maintained by the organization, then people can feel reassured that their data is not being downloaded to a compromised instance, not that any on this board would have such malicious intent. Moreover, it could contain such scripts as makes the analysis process easier. - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 2011/11/14 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br 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. ___ 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
I have restored the image: 060244368407/FREESURFER51 I'll create a web service that can log the number of instances spawned. Is that ok with you? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi PPJ, I would rather people use FS without licenses than find themselves unable to use it, so why not leave it for now. Can you put a request that they first download a license or register on your website? Alternatively, can you just remove the .license file from the AMI forcing the users to get one? thanks for making this available Bruce On Fri, 18 Nov 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: As requested I removed the AMI image because that image contains a .license file. I can republish the image when we find a solution for the licensing issue. --**--**- Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.**com/br/artist/netfilter/** id365306441 http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/15 Joshua Lee jki...@ucdavis.edu It would be great if Freesurfer maintained an official AMI. One important reason to do so is security. If the AMI is maintained by the organization, then people can feel reassured that their data is not being downloaded to a compromised instance, not that any on this board would have such malicious intent. Moreover, it could contain such scripts as makes the analysis process easier. - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 2011/11/14 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br 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 http://itunes.apple.com/br/artist/netfilter/id365306441 On Mon, Nov 14, 2011 at 21:07, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: 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. 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/**compliancelinehttp://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
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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
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.eduwrote: 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 cluster and your license to each instance. A few details: Ubuntu 10.04 x86 built from StarClusters ami-8cf913e5 us-east-1 region See the StarCluster details at http://web.mit.edu/stardev/cluster/ Customizing StarCluster ( http://web.mit.edu/stardev/cluster/docs/latest/manual/create_new_ami.html ) s3fs (http://code.google.com/p/s3fs/) Freesurfer 5.1 32-bit NeuroDebian ready (so you can apt-get install mricron, fsl, nipype, etc.) Thanks again for starting this thread, and let me know if I can help in any way. It would be great to see cloud resources be readily accessibly to the community with minimal effort to get a cluster with freesurfer and tools available via neurodebian up and running. Cheers, Nolan ___ 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
Re: [Freesurfer] Amazon EC2 Version of FreeSurfer 5.1 Available
I've put together the basic tutorial on getting started using Amazon AWS system: It's in the same place Nick pointed out: https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/9 Nick Schmansky ni...@nmr.mgh.harvard.edu Pedro Paulo, thanks for posting the info. i've added this to the Download wiki page, and created a stub page for the Amazon Cloud: https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud i've never set one up so i have no idea how to do it. maybe someone can flesh-out this page as using the ec2 seems like a great alternative to a cluster. n. On Wed, 2011-11-09 at 22:44 -0200, Pedro Paulo de Magalhães Oliveira Junior wrote: No. This is for non GPU instances -- iOS 5.0 Em 09/11/2011, às 22:28, Satrajit Ghosh sa...@mit.edu escreveu: hi pedro, will this work with gpu instances as well? cheers, satra 2011/11/9 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Some weeks ago I was asked about a public image (AMI) to run in the Amazon EC2 infrastructure If you want to use FreeSurfer in the EC2 infrastructure you can use this public AMI: 060244368407/FREESURFER51 Just for your information this AMI can run a recon-all in 23 hours in an Amazon AWS Small Instance. So with the current Amazon cost per Small Instance/Hour you'll have a recon-all for USD 2.04 Amazon request a credit card in order to create an account in http://aws.amazon.com Hope it helps, Pedro Paulo Jr. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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 ___ 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] Amazon EC2 Version of FreeSurfer 5.1 Available
Some weeks ago I was asked about a public image (AMI) to run in the Amazon EC2 infrastructure If you want to use FreeSurfer in the EC2 infrastructure you can use this public AMI: *060244368407/FREESURFER51* Just for your information this AMI can run a recon-all in 23 hours in an Amazon AWS Small Instance. So with the current Amazon cost per Small Instance/Hour you'll have a recon-all for USD 2.04 Amazon request a credit card in order to create an account in http://aws.amazon.com Hope it helps, Pedro Paulo Jr. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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
No. This is for non GPU instances -- iOS 5.0 Em 09/11/2011, às 22:28, Satrajit Ghosh sa...@mit.edu escreveu: hi pedro, will this work with gpu instances as well? cheers, satra 2011/11/9 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Some weeks ago I was asked about a public image (AMI) to run in the Amazon EC2 infrastructure If you want to use FreeSurfer in the EC2 infrastructure you can use this public AMI: *060244368407/FREESURFER51* Just for your information this AMI can run a recon-all in 23 hours in an Amazon AWS Small Instance. So with the current Amazon cost per Small Instance/Hour you'll have a recon-all for USD 2.04 Amazon request a credit card in order to create an account in http://aws.amazon.com Hope it helps, Pedro Paulo Jr. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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
Tomorrow I'll post a tutorial. It's quite simple - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 2011/11/9 Nick Schmansky ni...@nmr.mgh.harvard.edu Pedro Paulo, thanks for posting the info. i've added this to the Download wiki page, and created a stub page for the Amazon Cloud: https://surfer.nmr.mgh.harvard.edu/fswiki/AmazonCloud i've never set one up so i have no idea how to do it. maybe someone can flesh-out this page as using the ec2 seems like a great alternative to a cluster. n. On Wed, 2011-11-09 at 22:44 -0200, Pedro Paulo de Magalhães Oliveira Junior wrote: No. This is for non GPU instances -- iOS 5.0 Em 09/11/2011, às 22:28, Satrajit Ghosh sa...@mit.edu escreveu: hi pedro, will this work with gpu instances as well? cheers, satra 2011/11/9 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Some weeks ago I was asked about a public image (AMI) to run in the Amazon EC2 infrastructure If you want to use FreeSurfer in the EC2 infrastructure you can use this public AMI: 060244368407/FREESURFER51 Just for your information this AMI can run a recon-all in 23 hours in an Amazon AWS Small Instance. So with the current Amazon cost per Small Instance/Hour you'll have a recon-all for USD 2.04 Amazon request a credit card in order to create an account in http://aws.amazon.com Hope it helps, Pedro Paulo Jr. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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 ___ 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] Recon-all step estimate
Is there any script that I can use to estimate which step recon-all are in? My idea is to have a progress indicator for recon-all and this script would be very useful. thanks Pedro Paulo Jr ___ 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] Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?
I have one. I'll give you the link -- iOS 5.0 Em 28/10/2011, às 20:52, Joshua Lee jki...@ucdavis.edu escreveu: Are there any existing Amazon EC2 AMI registered publicly that can be used? I want to analyze a lot of data fast. Thanks, - Joshua Lee ___ 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] cortical thickness asymmetries
We have mentioned this in: Use of SVM Methods with Surface-Based Cortical and Volumetric Subcortical Measurements to Detect Alzheimer's Disease You can find the PDF in the FreeSurfer page: http://surfer.nmr.mgh.harvard.edu/ftp/articles/Oliveira_JAD2010.pdf I don't have a good explanation though. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Oct 27, 2011 at 10:03, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: not that I know of Bruce On Thu, 27 Oct 2011, Irene Altarelli wrote: Dear Freesurfer experts, have cortical thickness asymmetries ever been looked at using Destrieux parcellation scheme, either in adults or (even better) in children? Thanks! Irene ___ 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] implementation on Neurodebian
No. Cuda only runs in NVidia hardware. - 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, Oct 24, 2011 at 13:01, Cartik Sharma cartik.sha...@childmind.orgwrote: Bruce, http://surfer.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide#Benchmarks Found this link..clearly impressive, are these benchmarks for GPU enabled cards with CUDA or also with ATI Radeon GPU enabled cards? Best, Cartik On Oct 24, 2011, at 10:30 AM, Bruce Fischl wrote: not yet, although it is something we are working on. cheers Bruce On Mon, 24 Oct 2011, Cartik Sharma wrote: Hi Knut, Good to know we can speed things up with CUDA. I have a multicore CPU and was wondering if there is a parallelized version of Freesurfer on the CPU. Thanks for the speedup! Best regards, Cartik On Oct 24, 2011, at 4:41 AM, Knut J Bjuland wrote: Hi Cartik You use -use-gpu to offload rendering to the GPU using cuda. Knut J From: cartik.sha...@childmind.org To: knut...@hotmail.com Subject: Re: [Freesurfer] implementation on Neurodebian Date: Thu, 20 Oct 2011 15:48:10 + Hi Knut: Cool..is this speeding up things by rendering on the GPU. Is there a way to offload computation to the GPU. Best regards, Cartik On Oct 20, 2011, at 10:57 AM, Knut J Bjuland wrote: Hi Cartik If you enable cuda with -use-gpu the recon-all will run faster. Knut J Den 17.10.2011 16:41, skrev Cartik Sharma: Dear Freesurfer developer(s), Is there a way to get Freesurfer run faster on Neurodebian. While the package produces some truly out of the world segmentations and labels for the cortical surface, it seems to take time. For eg: Defect correction and retesellation takes an hour, other steps take longer..I'm not sure if it's the original dataset, the OS platform (i.e Virtual Machine, Neurodebian) or original computational engine itself. Would be happy in efforts and hints to make this run faster. Best regards, Cartik Sharma ___ 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 ___ 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] [Major Upgrade] - iSurf Brainview 4.0.0
Today it was released the version 4.0.0 of iSurf Brainview, it's a majorversion release for IPad, IPhone and IPod Touch. It's also a landmark release. Major New Features - 3D Visualization of Cortical structure - 3D Model is fully touchable and displays the name of touched structure using aparc.annot Minor Changes - iOS5 compliance - Memory usage improvement - Versioning As usual suggestions and feedbacks are welcome. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423mt=8 A personal note: This App is being used in the Radiology course. All med students in São Paulo University now have basic MRI neuroanatomy training using iSurf - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] mris_convert exporting parcellation per vertex
Yes, but --seg in mri_annotation2label --subject bert --hemi lh --seg saida.mgz produces a volume and not a surface. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Tue, Oct 11, 2011 at 13:12, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Have you tried using mri_annotation2label with the --seg output option? doug Michael Waskom wrote: If you know Python, you can likely do this pretty easily with tools from the PySurfer package: http://pysurfer.github.com/ (Check out surfer.io.read_annotation). If you're just using the io routines, you won't need the somewhat heavy Mayavi visualization dependencies. You should be able to read in and manipulate surfaces/annotations just with numpy. Best, Michael 2011/10/8 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto: fis...@nmr.mgh.**harvard.edu fis...@nmr.mgh.harvard.edu it wouldn't be that hard to put something together if you want to avoid matlab. Spec out what you need and send me a sample, maybe on Bert Bruce On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: Thanks. I suppose I can't do this without matlab. Right? -- iOS 5.0 Em 08/10/2011, às 19:29, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.**harvard.edu fis...@nmr.mgh.harvard.edu escreveu: there is a write_annotation.m file you can use On Sat, 8 Oct 2011, Anderson Winkler wrote: ops, it seems the comments inside the dpxwrite.m no longer reflect what it does. You probably don't need this, but anyway, the version attached is more up-to-date. Anderson On 08/10/11 17:28, Anderson Winkler wrote: Hi Pedro, There is probably a way to do that using FS tools from the command line, but the attached script should do the same. The result is a data-per-vertex file, which is the same as the .asc files from mris_convert. There is no geometry input, hence the vertex coordinates are all set to (0,0,0). Hope it helps! All the best, Anderson On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior wrote: I need to create a file where I have the parcellation value (structure name) per vertex. I've tried�mris_convert --annot /Applications/freesurfer/ subjects/bert/label/lh.aparc. annot /Applications/freesurfer/ subjects/bert/surf/lh.pial parc.asc But I get the error:�ERROR: unknown file annot file type specified for output: saida.asc Has someone done this before? Thanks -- -- - Pedro Paulo de Magalh�es Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br http://www.netfilter.com.br -- For mobile:�http://itunes.apple. com/br/artist/netfilter/ id365306441 http://itunes.apple.com/br/**artist/netfilter/id365306441http://itunes.apple.com/br/artist/netfilter/id365306441 __ _ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard. edu/mailman/listinfo/ freesurfer https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer 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/**compliancelinehttp://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
Re: [Freesurfer] mris_convert exporting parcellation per vertex
Michael,
Thanks for the hint.
Here's a program that converts the surface + annotation in a Stanford PLY
Object file
# Create ply
# Stanford Object format
from surfer import io as io_
surface = io_.read_geometry
('/Applications/freesurfer/subjects/bert/surf/lh.pial')
labels = io_.read_annot
('/Applications/freesurfer/subjects/bert/label/lh.aparc.annot')
facenum = len(surface[1])
vertnum = len(surface[0])
print ply
print format ascii 1.0
print comment VCGLIB generated
print element vertex %d%vertnum
print property float x
print property float y
print property float z
#print property int flags
print property uchar red
print property uchar green
print property uchar blue
print property uchar alpha
print element face %d%facenum
print property list uchar int vertex_indices
print end_header
for i in xrange(vertnum):
vert = surface[0][i];
color = labels[1][labels[0][i]]
print %f %f %f %d %d %d
%d%(vert[0],vert[1],vert[2],color[0],color[1],color[2],color[3])
for i in xrange(facenum):
face = surface[1][i]
print 3 %d %d %d%(face[0],face[1],face[2])
2011/10/9 Michael Waskom mwas...@stanford.edu
If you know Python, you can likely do this pretty easily with tools from
the PySurfer package: http://pysurfer.github.com/
(Check out surfer.io.read_annotation).
If you're just using the io routines, you won't need the somewhat heavy
Mayavi visualization dependencies. You should be able to read in and
manipulate surfaces/annotations just with numpy.
Best,
Michael
2011/10/8 Bruce Fischl fis...@nmr.mgh.harvard.edu
it wouldn't be that hard to put something together if you want to avoid
matlab. Spec out what you need and send me a sample, maybe on Bert
Bruce
On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
Thanks.
I suppose I can't do this without matlab. Right?
-- iOS 5.0
Em 08/10/2011, às 19:29, Bruce Fischl fis...@nmr.mgh.harvard.edu
escreveu:
there is a write_annotation.m file you can use
On Sat, 8 Oct 2011, Anderson Winkler wrote:
ops, it seems the comments inside the dpxwrite.m no longer reflect what
it does. You probably don't need this, but anyway, the version attached is
more up-to-date.
Anderson
On 08/10/11 17:28, Anderson Winkler wrote:
Hi Pedro,
There is probably a way to do that using FS tools from the command
line, but the attached script should do the same. The result is a
data-per-vertex file, which
is the same as the .asc files from mris_convert. There is no
geometry input, hence the vertex coordinates are all set to (0,0,0).
Hope it helps!
All the best,
Anderson
On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior
wrote:
I need to create a file where I have the parcellation value
(structure name) per vertex.
I've tried�mris_convert --annot /Applications/freesurfer/**
subjects/bert/label/lh.aparc.**annot
/Applications/freesurfer/**subjects/bert/surf/lh.pial
parc.asc
But I get the error:�ERROR: unknown file annot file type specified
for output: saida.asc
Has someone done this before?
Thanks
--**--**
-
Pedro Paulo de Magalh�es Oliveira Junior
Netfilter SpeedComm Telecom -- www.netfilter.com.br
-- For mobile:�http://itunes.apple.**com/br/artist/netfilter/**
id365306441 http://itunes.apple.com/br/artist/netfilter/id365306441
__**_
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Re: [Freesurfer] mris_convert exporting parcellation per vertex
Thanks.
It works as I wished.
from surfer import io as sIo
a = sIo.read_annot('label/lh.aparc.annot')
b = sIo.read_geometry('surf/lh.pial')
And now I can have each vertex labeled
-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
2011/10/9 Michael Waskom mwas...@stanford.edu
If you know Python, you can likely do this pretty easily with tools from
the PySurfer package: http://pysurfer.github.com/
(Check out surfer.io.read_annotation).
If you're just using the io routines, you won't need the somewhat heavy
Mayavi visualization dependencies. You should be able to read in and
manipulate surfaces/annotations just with numpy.
Best,
Michael
2011/10/8 Bruce Fischl fis...@nmr.mgh.harvard.edu
it wouldn't be that hard to put something together if you want to avoid
matlab. Spec out what you need and send me a sample, maybe on Bert
Bruce
On Sat, 8 Oct 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
Thanks.
I suppose I can't do this without matlab. Right?
-- iOS 5.0
Em 08/10/2011, às 19:29, Bruce Fischl fis...@nmr.mgh.harvard.edu
escreveu:
there is a write_annotation.m file you can use
On Sat, 8 Oct 2011, Anderson Winkler wrote:
ops, it seems the comments inside the dpxwrite.m no longer reflect what
it does. You probably don't need this, but anyway, the version attached is
more up-to-date.
Anderson
On 08/10/11 17:28, Anderson Winkler wrote:
Hi Pedro,
There is probably a way to do that using FS tools from the command
line, but the attached script should do the same. The result is a
data-per-vertex file, which
is the same as the .asc files from mris_convert. There is no
geometry input, hence the vertex coordinates are all set to (0,0,0).
Hope it helps!
All the best,
Anderson
On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior
wrote:
I need to create a file where I have the parcellation value
(structure name) per vertex.
I've tried�mris_convert --annot /Applications/freesurfer/**
subjects/bert/label/lh.aparc.**annot
/Applications/freesurfer/**subjects/bert/surf/lh.pial
parc.asc
But I get the error:�ERROR: unknown file annot file type specified
for output: saida.asc
Has someone done this before?
Thanks
--**--**
-
Pedro Paulo de Magalh�es Oliveira Junior
Netfilter SpeedComm Telecom -- www.netfilter.com.br
-- For mobile:�http://itunes.apple.**com/br/artist/netfilter/**
id365306441 http://itunes.apple.com/br/artist/netfilter/id365306441
__**_
Freesurfer mailing list
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it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
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HelpLine at
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properly
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[Freesurfer] mris_convert exporting parcellation per vertex
I need to create a file where I have the parcellation value (structure name) per vertex. I've tried mris_convert --annot /Applications/freesurfer/subjects/bert/label/lh.aparc.annot /Applications/freesurfer/subjects/bert/surf/lh.pial parc.asc But I get the error: ERROR: unknown file annot file type specified for output: saida.asc Has someone done this before? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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] mris_convert exporting parcellation per vertex
Thanks. I suppose I can't do this without matlab. Right? -- iOS 5.0 Em 08/10/2011, às 19:29, Bruce Fischl fis...@nmr.mgh.harvard.edu escreveu: there is a write_annotation.m file you can use On Sat, 8 Oct 2011, Anderson Winkler wrote: ops, it seems the comments inside the dpxwrite.m no longer reflect what it does. You probably don't need this, but anyway, the version attached is more up-to-date. Anderson On 08/10/11 17:28, Anderson Winkler wrote: Hi Pedro, There is probably a way to do that using FS tools from the command line, but the attached script should do the same. The result is a data-per-vertex file, which is the same as the .asc files from mris_convert. There is no geometry input, hence the vertex coordinates are all set to (0,0,0). Hope it helps! All the best, Anderson On 08/10/11 17:17, Pedro Paulo de Magalh�es Oliveira Junior wrote: I need to create a file where I have the parcellation value (structure name) per vertex. I've tried�mris_convert --annot /Applications/freesurfer/subjects/bert/label/lh.aparc.annot /Applications/freesurfer/subjects/bert/surf/lh.pial parc.asc But I get the error:�ERROR: unknown file annot file type specified for output: saida.asc Has someone done this before? Thanks - Pedro Paulo de Magalh�es Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile:�http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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 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
[Freesurfer] Process monkey data
I have data from 100 monkeys and I need to compare cortical thickness among two groups. In the wiki page there is an entry MonkeyData that has a set of scripts which break-down the steps needed, unfortunately I'm having trouble with this scripts and FS 5.1 Are there an updated version of those procedures? Thanks PPJ -- iOS 5.0 ___ 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] tksurfer display
Can you describe the hardware / video card you are using? - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Sep 22, 2011 at 12:12, Peter Glynn pgl...@bu.edu wrote: Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn ___ 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] tksurfer display
I have added this answer to the FAQ: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Thu, Sep 22, 2011 at 14:33, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: I found this site for the type of problem we are having with tksurfer http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems Jim -- *From:* Peter Glynn [mailto:pgl...@bu.edu] *Sent:* Thu 9/22/2011 11:21 AM *To:* Alexopoulos, Dimitrios *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] tksurfer display attached find the output image. It looks very similar to Jim's, just rotated 180 degrees. On Thu, Sep 22, 2011 at 11:37 AM, Alexopoulos, Dimitrios alexopoulo...@kids.wustl.edu wrote: Interesting. I've had this problem trying to view the data on my dual boot Windows PC by remotely login with SSH to the linux server while running Xming or Hummingbird Exceed on the PC side. (Output image attached). Could it be some 3D rendering issue? I have no problem viewing the surfaces from my local ubuntu linux running freesurfer. tkmedit displays volumes properly. Jim -- *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Peter Glynn *Sent:* Thu 9/22/2011 10:12 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] tksurfer display Hello, I'm new to freesurfer and just downloaded and installed it on my dual boot windows/linux (centos release 5.5). I went through the instructions to check if everything is properly installed. Everything seemed to be fine except for tksurfer. When I enter the tksurfer bert rh pial command, tksurfer does launch but it only displays a very small sliver of a brain surface. Is this a common problem? Is something wrong with my installation? Any suggestions would be great. Thanks! Peter Glynn The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. ___ 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] Renaming a processed subject
You can just rename the directory ABC1234 to Case1 *mv ABC1234 Case1* On Thu, Sep 1, 2011 at 12:01, Irwin, William wir...@memory.ucsf.edu wrote: Hi ** ** For purposes of de-identification, is there an easy way to “rename” all the contents of data for a processed subject? ** ** For example, If I want to do share data or do reliability training on an existing subject (e.g., “ABC1234”), I want to rename everything associated with this case to “Case1”. ** ** Thanks Wil ** ** William Irwin | Imaging Core Supervisor UCSF | Memory and Aging Center 350 Parnassus Avenue, Suite 905 San Francisco CA 94143-1207 wir...@memory.ucsf.edu | memory.ucsf.edu p: 415.476.1680 | f: 415.476.1816 ** ** ** ** ___ 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] FreeSurfer on AWS
I'll try to write a tutorial this weekend -- iOS 5 Em 18/08/2011, às 20:01, Nolan Nichols bnn...@uw.edu escreveu: Hi Pedro, I came across your post on the FreeSurfer mailing list and am trying to find the AMI you created ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018272.html). I have tried a few times now to install FreeSurfer 5.1 on an AMI with EBS, but it is not working. Is there any chance you could help me out? Thanks! Nolan ___ 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] Nvidia upgrade considerations
I would go for a complete new PC. You won't benefit much of a GTX590 in an old PC PPJ - Pedro Paulo de Magalhães Oliveira Junior -- check our new iOS app: Cargohttp://itunes.apple.com/app/cargo/id444529879?ls=1mt=8 2011/8/5 Andries R. Van Der Leij a.r.vanderl...@gmail.com Hi pedro and Richard, Thank you for the responses! The T7400 has just one gpu slot, so I'll probably just buy the single 590, which itself is a dual card. The 2050 doesn't seem to be worth it on these older systems (ddr2, etc). For my supervisor, what kind of performance increase should I expect if we buy a newer nehalem system? Regards, Andries van der leij Sent from my iPhone On Aug 5, 2011, at 20:21, R Edgar freesurfer@gmail.com wrote: 2011/8/5 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.b r: In my experience you'll have the benefit of using two cards simultaneously. That means you can run two recon-all with gpu acceleration simultaneously. The SLI is more important for graphics (cad, gaming) than for CUDA. So, I'd go for 2 GTX580 CUDA doesn't use SLI at all - you don't want it. So long as each card has enough RAM to handle one recon job, having more cards and using the environment variable to select the GPU is certainly the way to go. I don't think that Freesurfer is particularly heavy on the PCIe bus, so you should even be able to get one of the dual GPU cards and get good performance. However, Nehalem does help the data reorganisation required for the GPU. Richard ___ 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] Re : Book with FreeSurfer chapter
Sorry Andrew. I didn't know. -- iOS 4.3 Em 16/07/2011, às 14:28, Simmons, Andy andy.simm...@kcl.ac.uk escreveu: There are also several other chapters of the same book using Freesurfer in AD, including Magnetic Resonance Imaging and Magnetic Resonance Spectroscopy for Detection of Early Alzheimer's Disease / Eric Westman, Lars-Olof Wahlund, Catherine Foy, Michaela Poppe, Allison Cooper, Declan Murphy, Christian Spenger, Simon Lovestone and Andrew Simmons Combinatorial Markers of Mild Cognitive Impairment Conversion to Alzheimer's Disease - Cytokines and MRI Measures Together Predict Disease Progression / Simon J. Furney, Deborah Kronenberg, Andrew Simmons, Andreas Güntert, Richard J. Dobson, Petroula Proitsi, Lars-Olof Wahlund, Iwona Kloszewska, Patrizia Mecocci, Hilkka Soininen, Magda Tsolaki, Bruno Vellas, Christian Spenger and Simon Lovestone Best wishes, Andy Simmons - Date: Fri, 15 Jul 2011 20:36:01 -0300 From: Pedro Paulo de Magalh?es Oliveira Junior p...@netfilter.com.br Subject: [Freesurfer] Book with FreeSurfer chapter To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Message-ID: CAPSXCjqtiYDJMAFvxGWu=k9nute8zf1jdoawmv3hsbiuawq...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Just for information: *Handbook of Imaging the Alzheimer Brain* * Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley, O. Sabri, A. Furst, S.E. Black and M. Weiner July 2011, 824 pp., hardcover ISBN 978-1-60750-792-5 (print) ** The chapter that describes the usage of FreeSurfer in AD is Automated Volumetric Methods to Detect Alzheimer's Disease / Pedro Paulo de Magalh?es Oliveira Jr. et al. * Dr Andy Simmons Reader in Neuroimaging Consultant Clinical Scientist Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre Institute of Psychiatry, Box P089 Kings College London De Crespigny Park London, SE5 8AF, UK Email - andy.simm...@kcl.ac.uk Webpage - http://www.iop.kcl.ac.uk/staff/profile/default.aspx?go=10338 Directions - http://www.iop.kcl.ac.uk/virtual/?path=/about/how-to-find-the-institute-of-psychiatry/ ResearcherID - http://www.researcherid.com/rid/B-8848-2008 Fax +44 (0)203 228 2116 image001.png http://msc-neuroimaging.com/ ___ 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] Book with FreeSurfer chapter
Just for information: *Handbook of Imaging the Alzheimer Brain* * Editors: J.W. Ashford, A. Rosen, M. Adamson, P. Bayley, O. Sabri, A. Furst, S.E. Black and M. Weiner July 2011, 824 pp., hardcover ISBN 978-1-60750-792-5 (print) ** The chapter that describes the usage of FreeSurfer in AD is Automated Volumetric Methods to Detect Alzheimer's Disease / Pedro Paulo de Magalhães Oliveira Jr. et al. * ___ 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] muliple fressurfer instance and cuda
Try running only one GPU-assisted recon-all On Fri, Jul 8, 2011 at 10:02, Knut J Bjuland knut...@hotmail.com wrote: Hi When I have ran two or more Freesurfer instance in pc with one geforce gtx 460. I usually get a abort or memory corruption when running two or more Freesurfer instance. I usually get trouble when two ore more Freesurfer instance is in autocon3 phase of the recon-all protocol. Cheers Knut J ___ 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] cortical dysplasia
Carolina, We have worked with several cases of MCD (including cortical dysplasia). We have published this paper: https://surfer.nmr.mgh.harvard.edu/pub/articles/jon_372_LR.pdf It may help. But in most cases of cortical dysplasia (not Gray matter heterotopia cases) you'll find a ticker cortex not a thinner one. But maybe you could post one image illustrate this problem. PPJ On Thu, Jul 7, 2011 at 10:39, Carolina Valencia cvalen...@linkdx.com.cowrote: Hello FSexperts I have a MPRAGE image of cortical dysplasia, I have some regions of grey matter within the white matter, and I measured the cortical thickness in the projections of those regions and I expected to find a thinnercortex instead I found a cortical thickening. FS takes into account the embedded region of the grey matter to measure the cortical thickness? Best regards, Carolina ___ 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] measuring cortical thickness using FreeSurfer
I usually can run one instance of FreeSurfer with 1GB if I use the -no-gut flag I have a benchmark of 4 recon-all running in a 4 Core AMD with 4GB RAM that took only 10% more time than one recon-all alone. 2011/7/6 John Jan Drozd john.dr...@gmail.com Hi Bruce, Thanks for pointing this out to me about the RAM. I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects simultaneously if each subject requires 2 to 3 Gb of RAM. Thanks, John Sent from my iPhone On 2011-07-05, at 6:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: how much ram do you have? You'll need at least 2G/subject if not 3 On Tue, 5 Jul 2011, John Drozd wrote: Hi Bruce, Thanks for the suggestion, Bruce. I'll run 8 different subjects at once. Take care, John 2011/7/5 Bruce Fischl fis...@nmr.mgh.harvard.edu Sorry, that won't help a single subject much, although there are options to run the hemis in parallel. You can run multiple subjects at the same time, which is what we usually do. Or you can use cuss On Jul 5, 2011, at 5:11 PM, John Drozd john.dr...@gmail.com wrote: Hi Bruce, Okay, thank you. I understand and can see that to do an accurate job, the pipeline must be complicated. I have eight processors on my linux desktop computer. Maybe some parts of recon-all are multi-threaded which could speed things up for me :-) Thank you, John 2011/7/5 Bruce Fischl fis...@nmr.mgh.harvard.edu sorry, but the majority of the time is required. We're working to speed things up, but it is complicated software with multiple nonlinear warps, segmentation procedures, etc Bruce On Tue, 5 Jul 2011, John Drozd wrote: Hi Bruce and Pedro, Thank you both for sending me your suggestions. Just to let you know, because my .dcm (dicom) files had a space and two dots in the filenames: (e.g. 2008_12_08.ek -0035-0001-1.dcm ) (and using quotes around the file name or \ within the filename without the quotes did not work with recon-all), recon-all truncated the filename before the space as 2008_12_08.ek feeding it to an mri_convert command and gave an error message. So I worked around this problem as follows: I converted the .dcm series to a nifti .nii volume using 3D Slicer, and then used mri_convert to convert the .nii format to .mgz format. Then I ran recon-all on the .mgz formatted file and it is now running successfully. I see on the online tutorials and slides, that this process takes about 20 hours. Is there a way to only run partial steps pertaining only to the cortical thickness? Pedro also suggested that I go through the FreeSurferBeginnersGuide wiki which I am doing now. Also, reading some mailing lists emails, I noticed that matlab can be used to analyze the cortical thickness statistiics, and also freesurfer comes with matlab scripts. I will try these tools out as well. Thank you for your time, John On Tue, Jul 5, 2011 at 1:18 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: recon-all \ -i one slice in the anatomical dicom series \ -s subject id that you make up \ -sd directory to put the subject folder in \ -all cheers Bruce On Tue, 5 Jul 2011, John Drozd wrote: Hi, I am running freesurfer on 64 bit Fedora 10 linux. I am using version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. Can anyone point me to a reference web page listing what steps I need to type to process a series of MRI dicom slices and use FreeSurfer to measure cortical thickness for this dicom series? Thank you, John -- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm ___ 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. -- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm -- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm -- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm
Re: [Freesurfer] Fwd: freesurfer recon error
Have you tried including the flag -cw256 with the recon-all command? On Tue, Jul 5, 2011 at 10:18, Sarah Rappaport - UoB` sjr...@bham.ac.ukwrote: Hi!, I am new to FreeSurfer and I am having some difficulty with the T1 reconstruction. My MRI files were Par Rec and converted to nii. I successfully converted the nii file to mgz but had errors when running the recon -all command (see screen print attached). I have tried re-exporting the files in case there was an inital error at this stage but it returned the same error. I would appreciate any help with this. thanks Sarah ___ 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] measuring cortical thickness using FreeSurfer
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide On Tue, Jul 5, 2011 at 13:14, John Drozd john.dr...@gmail.com wrote: Hi, I am running freesurfer on 64 bit Fedora 10 linux. I am using version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. Can anyone point me to a reference web page listing what steps I need to type to process a series of MRI dicom slices and use FreeSurfer to measure cortical thickness for this dicom series? Thank you, John -- John Drozd Post-Doctoral Fellow, Robarts Research Institute The University of Western Ontario London, ON, Canada http://publish.uwo.ca/~jdrozd2/index.htm ___ 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] Difference in hippocampal volume between scanners
This is not normal. Maybe you should check the aseg volume for improper segmentation. On Thu, Jun 23, 2011 at 19:27, Jessica Liu jessicali...@gmail.com wrote: Hi everyone! I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks! Jessica Liu ___ 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] How to obtain volume of specific structure
Take a look in aseg.stats file -- iOS 4.3 Em 22/06/2011, às 23:09, ZhiLiangLong lagosslong1...@163.com escreveu: Hi all: After all recon-all -all processing has been completed for all subjects ,I want to obtain volume of specific structure of each subject(e.g., the volume of Caudate Nucleus). But i have no idea about it,Are there some tools or commands that can help? I hope you can give me some suggestions . Thanks! ___ 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] recon-all -s exited with ERRORS
recon-all -s bert -all -use-gpu -- iOS 4.3 Em 13/06/2011, às 21:30, Leo Souza lso...@nvidia.com escreveu: /recon-all -use-gpu ___ 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] FreeSurfer Tutorial and Workshop
I think you should send an e-mail to Allison (astevens) On Fri, May 27, 2011 at 13:34, Eisenstein, Sarah eisenste...@npg.wustl.eduwrote: Does anyone know how to register for the FreeSurfer Tutorial and Workshop scheduled for September, 2011? I cannot find a link or a phone number to do this on the Course Description page ( http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription). Thanks! Sarah Sarah A. Eisenstein, Ph.D. Postdoctoral Scholar Hershey Lab Psychiatry/Neuroimaging Lab Washington University in St. Louis St. Louis, MO eisenste...@npg.wustl.edu ___ 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] Error from cudadetect
5.1 was released yesterday -- iOS 4.3 Em 25/05/2011, às 09:42, R Edgar freesurfer@gmail.com escreveu: On Wed, May 25, 2011 at 7:59 AM, Howison, Mark mhowi...@brown.edu wrote: We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute cluster at Brown and are seeing the following error when running 'cudadetect': ERROR: cuda driver does not appear to be installed! Detecting CUDA... There are 2 devices supporting CUDA: Device 0: Tesla M2050 CUDA Driver Version: 3.20 (etc.) Did you do a binary install, or compile from source? If the former, then it might be a problem with us using a different version of CUDA at the time of compilation. Things are supposed to work, but we've seen a lot of problems like this. I believe that 5.1 is about to be released, which should be compiled against the driver/library you're using. Otherwise, the best solution might be to get the source, and compile directly from that. Richard ___ 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] FS5.1 for CentOS4 works for CentOS5-like OS?
Yes. It works -- iOS 4.3 Em 25/05/2011, às 10:14, Xinian Zuo zuoxin...@gmail.com escreveu: Dear FS team, Only see new 5.1 version for CentOS4 in the website. Thanks, XN. -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) ___ 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] Running FreeSurfer Remotely
It will probably work. However the experience can be sluggish On Mon, May 23, 2011 at 11:34, obre...@nmr.mgh.harvard.edu wrote: Hi, Will FreeSurfer run remotely using NX Client for OSX or should I employ VNC only? Thanks, Gabriel ___ 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] [Major Upgrade] - iSurf Brainview 3.0.0
Today it was released the version 3.0.0 of iSurf Brainview, it's a major version release for IPad, IPhone and IPod Touch. Major New Features - Quiz for Brain structures (you can take a Quiz with 10 random questions about structure locations. The current database has more than 40 questions) - Select the brain structure by name - You have a list of available structures. Minor Changes - Visual Improvements - Memory usage improvement - Paper of Destrieux, C. - Versioning As usual suggestions and feedbacks are welcome. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423mt=8 A personal note: Some residents in Radiology of our med school found the quiz challenging. I think it can be a very good tool to teach neuroanatomy in MRI - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile ___ 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: mpr2mni305 failed, see transforms/talairach_avi.log
I'm having this error in the recon-all # #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti image as ga_2010.nii Any hints? ___ 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] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
The images are: 0.5 x 0.5 x 1.0 Can mri_convert fix it or should I edit the Nifti header? 2011/5/16 Nick Schmansky ni...@nmr.mgh.harvard.edu PPJ, Hi, mri_info /space/incoming/ga_2010.nii shows that the image is 0.5 x 0.5 x 0.5. but when viewing in freeview or tkmedit, the brain seems 'squashed', as if there is a slice gap. do you know the details of how this was acquired? N. On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm having this error in the recon-all # #@# Talairach Mon May 16 16:38:01 EDT 2011 /usr/local/freesurfer/subjects/GAGRICOLA/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the original nifti image as ga_2010.nii Any hints? ___ 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] Smaller Virtual Machine
I have distributed another EC2 image. I think you can now start FreeSurfer instances at Amazon EC2 On Tue, May 3, 2011 at 06:25, Fidel falf...@hggm.es wrote: So... What about this? Cheers :) El 29/04/2011 16:43, Pedro Paulo de Magalhães Oliveira Junior escribió: I'll check if it's public On Fri, Apr 29, 2011 at 11:40, Fidel falf...@hggm.es wrote: Thanks PPJ, I have made a fast search in Amazon's page and via google and I did not find it. Do i have to be registered to find it? Can anyone use a copy of your virtual machine, or do we have to create our own and then, upload it to Amazon? Thanks again. Fidel. El 29/04/2011 16:25, Pedro Paulo de Magalhães Oliveira Junior escribió: Yes. But that machine distributed by FreeSurfer is the one with full GUI to run under Windows. I have a machine for cloud processing in Amazon EC2 (you can look up for FreeSurfer DMI in Amazon EC2) PPJ On Fri, Apr 29, 2011 at 11:15, Fidel falf...@hggm.es wrote: Hi all, I have been trying the virtual disk image, and it works well. Nevertheless, I think that more than 7GB is a lot of space if somebody wants to use it as a Virtual Machine in a cloud environment, in which you are charged for used storage and maybe for used bandwidth in the data communication. Is anybody thinking about creating a lighter version of this virtual disk image? Thanks and best regards, 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 listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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 mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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 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
[Freesurfer] [New release] - iSurf Brainview 2.1.1
Today it was released a new upgrade of iSurf Brainview. (2.1.1) *New features: * Phone / IPod Touch - IPhone now show webpage with structure description when you tap the name of the structure All iOS - More structures with webpage description - Cache webpages for speedup As usual suggestions are welcome. Upcoming features should include 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423mt=8 Cheers Pedro Paulo Jr. ___ 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] Smaller Virtual Machine
Yes. But that machine distributed by FreeSurfer is the one with full GUI to run under Windows. I have a machine for cloud processing in Amazon EC2 (you can look up for FreeSurfer DMI in Amazon EC2) PPJ On Fri, Apr 29, 2011 at 11:15, Fidel falf...@hggm.es wrote: Hi all, I have been trying the virtual disk image, and it works well. Nevertheless, I think that more than 7GB is a lot of space if somebody wants to use it as a Virtual Machine in a cloud environment, in which you are charged for used storage and maybe for used bandwidth in the data communication. Is anybody thinking about creating a lighter version of this virtual disk image? Thanks and best regards, 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 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] Smaller Virtual Machine
I'll check if it's public On Fri, Apr 29, 2011 at 11:40, Fidel falf...@hggm.es wrote: Thanks PPJ, I have made a fast search in Amazon's page and via google and I did not find it. Do i have to be registered to find it? Can anyone use a copy of your virtual machine, or do we have to create our own and then, upload it to Amazon? Thanks again. Fidel. El 29/04/2011 16:25, Pedro Paulo de Magalhães Oliveira Junior escribió: Yes. But that machine distributed by FreeSurfer is the one with full GUI to run under Windows. I have a machine for cloud processing in Amazon EC2 (you can look up for FreeSurfer DMI in Amazon EC2) PPJ On Fri, Apr 29, 2011 at 11:15, Fidel falf...@hggm.es wrote: Hi all, I have been trying the virtual disk image, and it works well. Nevertheless, I think that more than 7GB is a lot of space if somebody wants to use it as a Virtual Machine in a cloud environment, in which you are charged for used storage and maybe for used bandwidth in the data communication. Is anybody thinking about creating a lighter version of this virtual disk image? Thanks and best regards, 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 listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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 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 movie generation recipe
Some months ago it was asked in this list how to make a Movie of he process
of the inflation of the brain.
Some hints:
Create this tcl script and name it as script.tcl:
for {set x 0} {$x120} {incr x} {
set r [expr (round(1.2*$x + 3))]
shrink $r
redraw
save_tiff ${x}-img.tif
}
exit
Then use the commands:
tksurfer bert lh pial -annotation aparc.annot -tcl script.tcl
ffmpeg -r 15 -b 2500 -sameq -i %d-img.tif videoOutput.mp4
You can check the results at:
http://www.youtube.com/watch?v=aj-d8PZMXt8
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Re: [Freesurfer] FreeSurfer movie generation recipe
easier.
Can you inflate until you get the sphere?
2011/4/28 Bruce Fischl fis...@nmr.mgh.harvard.edu
or you can save snapshots from mris_inflate with
mris_inflate -w 1 -scale 1 ...
then render each of the resulting surfaces.
cheers,
Bruce
On Thu, 28 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior wrote:
Some months ago it was asked in this list how to make a Movie of he
process
of the inflation of the brain.
Some hints:
Create this tcl script and name it as script.tcl:
for {set x 0} {$x120} {incr x} {
set r [expr (round(1.2*$x + 3))]
shrink $r
redraw
save_tiff ${x}-img.tif
}
exit
Then use the commands:
tksurfer bert lh pial -annotation aparc.annot -tcl script.tcl
ffmpeg -r 15 -b 2500 -sameq -i %d-img.tif videoOutput.mp4
You can check the results at:
http://www.youtube.com/watch?v=aj-d8PZMXt8
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.
___
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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 analysis different scanner
Yes it does. However you can maybe use the scanner as a covariate. On Wed, Apr 27, 2011 at 09:24, John Fredy jfochoas...@gmail.com wrote: Hello all, In voxel based morphometry is not recommended use images from different scanners. This recommendation also apply in the qdec analysis? Thanks in advance John Ochoa Universidad de Antioquia Instituto Neurológico de Antioquia ___ 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] Unknown label in Parcellation
In one study we are conducting we found significant difference in cortical thickness between the two groups in some areas. One of those areas are lh_unknown. Is this an error or it's a still unlabelled area? thanks Pedro Paulo Jr ___ 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] Unknown label in Parcellation
lh.aparc.stats 2011/4/27 Bruce Fischl fis...@nmr.mgh.harvard.edu which parcellation are you using? On Wed, 27 Apr 2011, Pedro Paulo de Magalhães Oliveira Junior wrote: In one study we are conducting we found significant difference in cortical thickness between the two groups in some areas. One of those areas are lh_unknown. Is this an error or it's a still unlabelled area? thanks Pedro Paulo Jr 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] Fwd: display error
in tcsh try: setenv doublebufferflag 1 in bash it would be export doublebufferflag=1 before running tksurfer Refs: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11049.html http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems On Tue, Apr 26, 2011 at 10:35, Cris Lanting c.lant...@gmail.com wrote: In the hope that someone recognises the error as described in the attached email... (Sorry for the repost but I haven't found a solution yet and I'm quite sure someone will recognise it) Cris -- Forwarded message -- From: Cris Lanting c.lant...@gmail.com Date: Mon, Apr 11, 2011 at 1:50 PM Subject: display error To: freesurfer@nmr.mgh.harvard.edu Dear Freesurfer community, I have a display problem that affects especially tkmedit and tksurfer. We run freesurfer ( freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) on a remote unix server and use Exceed (v. 14.0.0.376) to port the display to a local (windows) computer. At first we got a openGL error stating that OpenGL was not supported when calling e.g. tksurfer. Now we have installed Exceed 3D to support OpenGL it seems to continue beyond the previous error message but comes up with a different one (see snippet) snippet subject is js hemiis rh surface is pial surfer: current subjects dir: /home/cris/freesurfer/subjects surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/cris Reading image info (/home/cris/freesurfer/subjects/js) Reading /home/cris/freesurfer/subjects/js/mri/orig.mgz surfer: Reading header info from /home/cris/freesurfer/subjects/js/mri/orig.mgz fsurfer: vertices=156376, faces=312748 surfer: single buffered window surfer: tkoInitWindow(js) Window type not found! surfer: failed, trying double buffered window Window type not found! surfer: failed, no suitable display found end snippet Any ideas? Note that other programs that do not use OpenGL seem to run fine (i.e. fslview and gedit) Kind regards, Cris Lanting Career Development Fellow MRC Institute of Hearing Research Science Road, University Park Nottingham NG7 2RD c...@ihr.mrc.ac.uk ___ 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] Could I run several freesurfers at the same time?
You can set up multicore in VirtualBox or VMWare In my experience ( without the gcut) 1GB is enough -- iOS 4.3 Em 21/04/2011, às 13:53, Richard G. Edgar rg...@nmr.mgh.harvard.edu escreveu: On Thu, 2011-04-21 at 09:48 -0700, Rongxiang Tang wrote: I was wondering if I can run several freesurfers in my virtualbox simultaneously by setting up several virtual machines...my computer has 16G RAM and it's Windows 7 64-bit. Would working multiple freesurfers at the same time slow down the calculations? Moreover, I was wondering if my computer could afford these loads... I can't speak for the virtualisation side, but it's certainly possible (even advisable) to run more than one copy of Freesurfer on a machine. I ran an experiment, running a recon-all instance on each of my box's four cores, and they were all complete in about 110% of the time of a single run - a big win. Now with virtualisation, you'd also be running extra copies of the guest OS. Can you set up a single VM with multiple cores instead? If you have a quad core machine, give the VM three cores, and run three Freesurfer jobs on it. Trying it is the only way to be sure. Richard ___ 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] Could I run several freesurfers at the same time?
the figure below show memory consumption for 3 running process (the OS uses 400MB) 2011/4/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br: You can set up multicore in VirtualBox or VMWare In my experience ( without the gcut) 1GB is enough -- iOS 4.3 Em 21/04/2011, às 13:53, Richard G. Edgar rg...@nmr.mgh.harvard.edu escreveu: On Thu, 2011-04-21 at 09:48 -0700, Rongxiang Tang wrote: I was wondering if I can run several freesurfers in my virtualbox simultaneously by setting up several virtual machines...my computer has 16G RAM and it's Windows 7 64-bit. Would working multiple freesurfers at the same time slow down the calculations? Moreover, I was wondering if my computer could afford these loads... I can't speak for the virtualisation side, but it's certainly possible (even advisable) to run more than one copy of Freesurfer on a machine. I ran an experiment, running a recon-all instance on each of my box's four cores, and they were all complete in about 110% of the time of a single run - a big win. Now with virtualisation, you'd also be running extra copies of the guest OS. Can you set up a single VM with multiple cores instead? If you have a quad core machine, give the VM three cores, and run three Freesurfer jobs on it. Trying it is the only way to be sure. Richard ___ 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. attachment: ESJ68Y.png___ 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] Fedora 14
Yes. It works. -- iOS 4.3 Em 18/04/2011, às 21:13, roger@yale.edu roger@yale.edu escreveu: Hi all, Quick question: will the latest Linux 32-bit install work with Fedora 14? Please let me know if there are known issues. Thanks, Roger ___ 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
[Freesurfer] Course FreeSurfer - São Paulo, Brazil
Just to inform we still have two spots available for the course in São Paulo next week http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Brazil2011CourseSchedule If there's anyone interested write me for more details. cheers Pedro Paulo Jr. ___ 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] recommende pc and cuda
Maybe a NVidia GTX590 (it's a dual GPU) On Mon, Apr 4, 2011 at 08:13, Knut J Bjuland knut...@hotmail.com wrote: Hi I am in the process of acquiring a new computer to run freesurfer on. I am currently think about buying a PC with a geforce 4X0 and a Tesla card along with a two screen setup running either Ubuntu or Redhat Linux enterprise 6.0. I think the PC should be a core i7 with 6 core and above 12 gigs byte of ram. What kind of tesla card is recommend for using with Freesurfer? Will Freesurfer 5.1 also support cuda 4.0. Knut J ___ 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] data preparation for SVM classification
Sorry for the advertisement :) I wrote a paper using this technique: Use of SVM methods with surface-based cortical and volumetric subcortical measurements to detect Alzheimer's disease.http://www.ncbi.nlm.nih.gov/pubmed/20061613 Oliveira PP Jr, Nitrini R, Busatto G, Buchpiguel C, Sato JR, Amaro E Jr. J Alzheimers Dis. 2010;19(4):1263-72. PMID: 20061613 [PubMed - indexed for MEDLINE] On Thu, Mar 24, 2011 at 09:10, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: what are you trying to classify and what is your hypothesis? cheers, Bruce On Thu, 24 Mar 2011, Alexander Ivanov wrote: *Dear Freesurfers,* Could you please suggest me the best way to prepare structural data for SVM classification? I googled, searched the archives - there're no examples of such preparation using freesurfer algorithms (to my knowledge)... Thank you beforehand. --- *Regards,* *A. Hasfatin* ___ 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] single subject versus a group map in qdec
We have dono something like this in Cortical thickness reduction of normal appearing cortex in patients with polymicrogyriahttps://surfer.nmr.mgh.harvard.edu/pub/articles/corticalPedroSep08.pdf https://surfer.nmr.mgh.harvard.edu/pub/articles/corticalPedroSep08.pdf cheers, 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 Wed, Mar 23, 2011 at 14:21, Emily Rogalski erogal...@gmail.com wrote: Using q dec we have run a single patient versus a group of healthy control subjects (n=20ish) and found significant differences even after FDR correction. Could you describe the process qdec uses to compute these differences? Is it legitimate to report these single subject maps? Practically this is very useful for case reports but Im concerned about violating statistical rules. Thanks! -- Emily J Rogalski, PhD Assistant Research Professor Northwestern University Cognitive Neurology and Alzheimer's Disease Center (CNADC) 320 E Superior Street Searle Building 11th Floor Chicago, IL 60611 312-503-1155 phone 312-908-8789 fax erogal...@gmail.com ___ 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] [New release] - iSurf Brainview 2.1.0
Today it was released a new major upgrade of iSurf Brainview. (2.1.0) New features: - New Atlas: Chistophe Destrieux 2009 Atlas - Improved Interface - Retina Display - iOS 4.3 As usual suggestions are welcome. Upcoming features will include 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423mt=8 Cheers Pedro Paulo Jr. ___ 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] Mac Pro with 12cores
That's without GPU? On Thu, Mar 10, 2011 at 11:17, Richard G. Edgar rg...@nmr.mgh.harvard.eduwrote: On Thu, 2011-03-10 at 08:27 -0500, Bruce Fischl wrote: If you have enough memory! Maybe Richard can post current CPU recon times with the latest hardware and optimizations. I think they are much shorter than they used to be My workstation (3.2 GHz Nehalem) can do a recon-all ernie in about 8 hours. Running four in parallel (one for each core) bumps the total walltime up to about eight and a half hours. Regards, Richard ___ 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] CUDA comparable to non-CUDA?
We assume that. On Tue, Mar 8, 2011 at 09:58, Marcus N Schmidt m.schm...@erasmusmc.nlwrote: Hi FreeSurfer Experts, Just a quick question: Generally speaking, assuming everything else remains the same, are subjects run through a CUDA-enabled recon-all comparable to subjects run through recon-all without CUDA? Thanks, Marcus * Marcus N Schmidt* Department of Child Adolescent Psychiatry Erasmus MC Rotterdam, The Netherlands ___ 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] Newbie - problems compiling project tree
libnetcdf-dev or netcdf-dev will do the trick On Tue, Mar 8, 2011 at 19:42, Shay Ohayon shay.oha...@gmail.com wrote: Hi All, I am having some problems compiling freesurfer . I checked out the recent development version from the CVS, ran setup_configure successfully, but upon ./configure, I end up with the following annoying message: checking for nccreate in -lnetcdf... no configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir. I attempted to install the netcdf-bin and libnetcdf6 packages using Synaptic, but this did not seem to help. How do I continue from here? -- Shay ___ 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] aparc+aseg.mgz and aparc.a2009s+aseg.mgz
I was checking the values at both aparc.a2009s+aseg.mgz and aparc+aseg.mgz and comparing it with the labels in FreeSurferColorLUT.txt I have noticed some problems: 1) There are values out of the range specified in FreeSurferColorLUT.txt (in bert dataset there are 353528 voxels with values above 14999) 2) There are many areas in FreeSurferColorLUT.txt that don't appear neither in aparc+aseg nor in aparc.a2009s+aseg My main concern is with the out of range values, which structure they map to? thanks - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile ___ 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 Tutorial and Workshop April 16-18 in Sao Paulo, Brazil
The Freesurfer group and the Hospital das Clinicas from São Paulo University will be offering a three-day Freesurfer Tutorial and Workshop April 16-18 at the Radiology Institute in Sao Paulo, SP, Brazil. A description of the course and a list of the topics covered can be found soon at http://www.neuroimagem.com but it's based on the description of http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription The course will take three days this year and will be in English. The registration fee is 400 BRL. If you want to apply for a spot send an e-mail to ppj at netfilter.com.brwith your details. We'll have a form in the website soon. There is room for only 40 participants and registration is on a first-come, first-serve basis. If you are not one of the first 40, you will be put on a waiting list and will be notified if a spot becomes available. If you need any information about arranging payment for the course, accommodations,course location, as well traveling issues please contact me in the e-mail above. Regards, Pedro Paulo Oliveira Jr. - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile ___ 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] parellizing Freesurfer
You'll find some answers here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15728.html 2011/2/26 Pablo Polosecki ppolose...@mail.rockefeller.edu 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 p...@netfilter.com.br 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] 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 in ubuntu
try the command: sudo apt-get install tcl -- PPJ Please: cc the freesurfer list when answering 2011/2/22 Carolina Valencia cvalen...@linkdx.com.co Hi Pedro, Finally, I could install it with the license file and the environment is properly set without warnings. But trying to test it, following the instruction on the wiki page I have a problem cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit bert orig.mgz /usr/local/freesurfer/bin/tcl_setup: No existe el fichero o el directorio. in the .bashrc I copy the right location of the freesurfer folder FREESURFER_HOME=/home/cvalencia/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br run this command sudo rm -rf $FREESURFER_HOME 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Thanks Pedro, How I uninstall that version to re-install the correct version? I look for some answers and try rm -rf $FREESURFER_HOME It says that I don't have permission,how I can unistall it, if i'm the admin user? Thanks in advance, Carolina 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux Thanks, 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.co wrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: 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 /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the 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 subjid -process directive…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! 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 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
Re: [Freesurfer] installation problem in ubuntu
Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.cowrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: 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 /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the 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 subjid -process directive…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! 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 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 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 in ubuntu
It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux Thanks, 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.co wrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: 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 /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the 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 subjid -process directive…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! 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 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 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 in ubuntu
run this command sudo rm -rf $FREESURFER_HOME 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Thanks Pedro, How I uninstall that version to re-install the correct version? I look for some answers and try rm -rf $FREESURFER_HOME It says that I don't have permission,how I can unistall it, if i'm the admin user? Thanks in advance, Carolina 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux Thanks, 2011/2/21 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.co wrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /home/cvalencia/Descargas/freesurfer/fsfast does not exist FREESURFER_HOME /home/cvalencia/Descargas/freesurfer FSFAST_HOME /home/cvalencia/Descargas/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /home/cvalencia/Descargas/freesurfer/subjects MNI_DIR /home/cvalencia/Descargas/freesurfer/mni FSL_DIR /usr/share/fsl/4.1 I try to test it and it shows cvalencia@cvalencia-Precision-WorkStation-T3400:~$ tkmedit /home/cvalencia/Descargas/freesurfer/bin/tkmedit.bin: Formato de ejecutable incorrecto. Binary file not executable. Thanks a lot, Carolina 2011/2/18 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: 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 /home/jie/Documents/freesurfer//mni Everything seems fine and I also added the .license file to the 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 subjid -process directive…... ” and the other arguments. How to fix the problem and make Fressurfer run? Any help is appreciated. Thanks a lot! 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 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 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] Paper amigdala volume
http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.2724.html http://www.nature.com/neuro/journal/vaop/ncurrent/extref/nn.2724-S1.pdf This paper made the first page in some major newspapers in Brazil today, and it uses FreeSurfer Cheers PPJ Enviado via iPad ___ 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] [New release] - iSurf Brainview 2.0.0
Today it was released a major upgrade of iSurf Brainview. Major improvements could be noticed on the IPad. Now you can click the name of the brain structure and have a popup control with the definition and references for the area. As usual suggestions are welcome. Upcoming features include the use of Destrieux atlas and 3D visualization. The link for download is: http://itunes.apple.com/WebObjects/MZStore.woa/wa/viewSoftware?id=381072423mt=8 Cheers Pedro Paulo Jr. -- iOS 4.2 ___ 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] aparc+aseg
Hi, One quick question: In the aparc+aseg file I suppose we have two volumes (one for aparc and other for aseg). Are those volumes overlapped or one after another? thanks 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 ___ 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.
