Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

FreeSurfer license
by Stefano Galletti 20 Apr '10

20 Apr '10

Hello, i purchased the license below on january 2010. In the next days i will change my OS so i have to download and reinstall the software. The new OS version will be Ubuntu 10.04 (Long Term Support): i would like to Know if the software is compatible with this version and what i have to do for the license. I also would like to now if there will be any problems if i will update the OS in the future. Thank you Stefano Galletti FreeSurfer Registration ha scritto: > Here is your FreeSurfer license. Place the three lines between the > CUT HERE markers in a file named ".license" in the directory pointed to > by the $FREESURFER_HOME environment variable (see the FreeSurfer > documentation). > > #---------------CUT HERE--------------- > stefano.galletti(a)scientificbiomedical.com > 8273 > *CqhZfxfmi2t2 > #---------------CUT HERE--------------- > > The information you submitted was: > > title=mr > firstname=Stefano > lastname=Galletti > institution_name=Fondazione Biomedica Europea > institution_type=nonprofit_education_research > user_email=stefano.galletti(a)scientificbiomedical.com > address1= > address2= > city=Roma > state=Lazio > zipcode=00198 > country=Italia > telephone=0685304575 > fax=0685800461 > OS/Platform=Linux/Intel > >

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CUDAEnabling for FreeSurfer 4.5.0
by wen miao 20 Apr '10

20 Apr '10

Hello Freesurfer experts. I'm recently woking on CUDA<http://developer.nvidia.com/object/cuda_3_0_downloads.html#MacOS>enabling for Freesurfer 4.5.0. I got CUDA installed on my computer and it works well as I tested the Examples of CUDA SDK. I find out some information in freesurfer wiki( http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide/CUDAEnabling) about CUDA Enabling, but it seems that the infomation here is insufficient for my work. Is it needed to programming to enable CUDA for freesurfer? Or can I get my work done by just do some configurations of FreeSurfer 4.5.0. Thanks in advance. Wen Miao

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Re: [Freesurfer] CUDAEnabling for FreeSurfer 4.5.0
by Pedro Paulo de Magalhães Oliveira Junior 20 Apr '10

20 Apr '10

The author of the blog (Thomas) is the person who's working on the port of FreeSurfer to GPU technology at Martinos Center/MGH. ---------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.4 www.Netfilter.com.br --- Novo Netfilter Small Business 2010/4/20 wen miao <mwinvent(a)gmail.com> > Thank you for your reply. I know that Freesurfer 4.5.0, which is the latest > version don't support CUDA. But some guys like this one( > http://twboutnothing.blogspot.com/2009/07/cuda-freesurfer-fun.html) have > work it out perfectly. I just can't wait to try. > > 2010/4/20 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > > Hi >> >> This wiki page is for internal development. The FreeSurfer version >> that will have a partial support for CUDA is the upcoming 5.0 >> >> cheers >> >> PPJ >> >> On Tuesday, April 20, 2010, wen miao <mwinvent(a)gmail.com> wrote: >> > Hello Freesurfer experts. >> > >> > I'm recently woking on CUDA < >> http://developer.nvidia.com/object/cuda_3_0_downloads.html#MacOS> >> enabling for Freesurfer 4.5.0. I got CUDA installed on my computer and it >> works well as I tested the Examples of CUDA SDK. >> > I find out some information in freesurfer wiki( >> http://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide/CUDAEnabling) >> about CUDA Enabling, but it seems that the infomation here is insufficient >> for my work. >> > Is it needed to programming to enable CUDA for freesurfer? Or can I get >> my work done by just do some configurations of FreeSurfer 4.5.0. >> > Thanks in advance. >> > >> > Wen Miao >> > >> >> -- >> ---------------------------------------------------------- >> Pedro Paulo de M. Oliveira Junior >> Diretor de Operações >> Netfilter & SpeedComm Telecom >> --- Novo Netfilter 3.4 www.Netfilter.com.br >> --- Novo Netfilter Small Business >> > > > > -- > Lab of Complex System and Artificial Intelligence, > Institute of Automation,Chinese Academy of Sciences(CASIA) > Beijing, 100190,P.R.CHINA >

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normal value of "Brain Segmentation Volume Without Ventricles" value ?
by Gonzalo Rojas Costa 19 Apr '10

19 Apr '10

Hi: I need to know which is the normal value of BrainSegVolNotVent (Brain Segmentation Volume Without Ventricles) of patients with 70 years aprox ?... Any paper ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile

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normal value of Bra
by Gonzalo Rojas Costa 19 Apr '10

19 Apr '10

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Which volumes to sum to obtain cereberal and cerebellar GM/WM volumes?
by Jory Hoogendam 19 Apr '10

19 Apr '10

Hello Freesurfer experts, We have generated a list of volumes, using asegstats2table (based on aseg.stats files). We want to compute total grey matter and white matter volumes for right and left hemispheres, separately for the cerebebrum and cerebellum. Which volumes from the list should we sum to generate these grey matter and white matter volumes? And which volumes should be included to calculate CSF for the whole brain? Is it allowed to sum all volumes to obtain intracranial volume? And why does this differ from the last variable of the list (IntraCranialVol)? Thanks in advance, Jory Hoogendam

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Re: [Freesurfer] The error about recon-all -s subjid -autorecon1
by Antoine Leflon 19 Apr '10

19 Apr '10

thanks Can you post these to the list? Nick would be able to help you, or others. On Mon, 19 Apr 2010, Antoine Leflon wrote: [Cacher les citations] Hi Bruce , I use a virtual machine , the Hard Disk simulated is 8GB but there're 1.7GB remaining on it . Is it enough ? Antoine Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> a écrit : Hi Antoine is your partition full? Bruce On Mon, 19 Apr 2010, Antoine Leflon wrote: sorry this error was : ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/s2/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1657531 voxels, voxel volume = 1.000 mm3 = 1657531 mmm3 = 1657.531 cm3 mri_watershed Error: read failed Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Sep 9 15:08:15 CST 2009 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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Re: [Freesurfer] The error about recon-all -s subjid -autorecon1
by Antoine Leflon 19 Apr '10

19 Apr '10

Hi Bruce , I use a virtual machine , the Hard Disk simulated is 8GB but there're 1.7GB remaining on it . Is it enough ? Antoine

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Re: [Freesurfer] The error about recon-all -s subjid -autorecon1
by Antoine Leflon 19 Apr '10

19 Apr '10

sorry this error was : ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/s2/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1657531 voxels, voxel volume = 1.000 mm3 = 1657531 mmm3 = 1657.531 cm3 mri_watershed Error: read failed Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Sep 9 15:08:15 CST 2009

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recon-all with nifti
by Christophe Chênes 19 Apr '10

19 Apr '10

For the input,I try using this command: # recon-all -s $MY_SUBJECT -i $SUBJECT_DIR/$MY_SUBJECT/mri/ orig/sujet01.nii.gz -all -notal-check -no-isrunning It returns the following error: # ERROR: /home/christophe/con/dvlp/pipe/FS/subjects/sujet01 exists, delete or re-run with -force ...

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