Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

Loading flattened surface in matlab
by f.leone＠donders.ru.nl 21 Apr '10

21 Apr '10

Hi everyone, I would like a 2D representation, hence a flattened version, of a surface in matlab, either the indices (a 2D map of 3D coordinates) or the actual values. Is this at all possible and if so, how? I see that read_surf gives vertex-indices back, but there is no 2D structure in there and MRIread is made for 3D-data only it seems. This post (which has similar aims as I have) http://groups.google.com/group/mvpa-toolbox/browse_thread/thread/dff9ba1008… suggests it isn't possible at all. And that it has serious disadvantages (the flattening process creating deformations of its own, which makes sense). That would be a pity. Then the best way would be to use the masked version of the 3D data: for that I can use the vertices given by read_surf, or is there an alternative/easier way? Hope it is possible, thanks a lot in advance, kind regards, Frank -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

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Spatial relation between brainmask and pial surface
by Milakara, Denny 21 Apr '10

21 Apr '10

Hi Bruce, Doug and community, When I compare brainmask (exported es nifti) with ascii pial surface it seems that brainmask(XZY) = ascii(XYZ), where the point of origin in the brainmask must be set to 128,128,128. Is this correct? If so, what is the maximal aberration expected in millimeters per axis and how to calculate it? Cheers, Denny

1 0

Re: [Freesurfer] negative thickness value problem
by EK Kim 21 Apr '10

21 Apr '10

Hello Nick. I'm really sorry for bothering you but I'm still waiting for your answer. :) Thank you 2010/4/6 eunkyung kim <ksea03(a)gmail.com>: > Hello Nick. > Bruce said you can give me the latest Freesurfer version. > Actually, as I already mentioned, I have a problem with negative > cortical thickness and it bothered me very much.. > but it's fixed in the most recent version of mris_make_surfaces and > mris_thickness. > Freesurfer wiki homepage doesn't contain fixed version.. > I know you are very busy, but May I receive a fixed version from you > as soon as possible? > > Thank you. > > Sincerely, EK > > > 2010/4/2 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >> Hi EK, >> >> Nick (ccd) can get you the new versions. >> >> cheers, >> Bruce >> >> On Fri, 2 Apr 2010, eunkyung kim wrote: >> >>> Hi Bruce. Thank you for your reply. >>> But I still wonder because I used the most recent version ' >>> freesurfer-Linux-centos4-stable-pub-v4.5.0'. >>> Did you mean future released version 5.0 ? >>> Please let me know right place that obtain the 'mris_make_surfaces' >>> and 'mris_thickness' files. >>> The released note page does not contain this files at now... >>> >>> >>> Sincerely, EK. >>> >>> >>> 2010/4/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: >>>> >>>> Hi EK, >>>> >>>> this was a bug I fixed a little while ago. The negative thicknesses >>>> should >>>> all be in non-cortical regions, but it's fixed in the most recent version >>>> of >>>> mris_make_surfaces and mris_thickness. The negative value should all be 0 >>>> >>>> cheers, >>>> Bruce >>>> >>>> On Thu, 1 Apr 2010, eunkyung kim wrote: >>>> >>>>> Dear all >>>>> I performed recon-all -s subjectID -qcache and obtained thickness data >>>>> which was normalized to fsaverage template. >>>>> I'd like to extract thickness value of the '-rh(or >>>>> lh).thickness.fwhm0.fsaverage.mgh' file in each subjects, so it was >>>>> transformed to the ascii file format. >>>>> However, the thickness data obtained from the ascii file did have some >>>>> negative values. !!! >>>>> Interestingly, the thickness value that was not normalized to the >>>>> fsaverage did not have negative values so I was very confused.. >>>>> Please let me know how can I treat the negative value. >>>>> >>>>> I really THANK YOU for your reply. >>>>> >>>>> Sincerely, EK. >>>>> _______________________________________________ >>>>> 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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intensity normalization and control points
by Jones, Kathryn L 20 Apr '10

20 Apr '10

Hello FS listers, I apologize if this has been asked before and I missed it in the archives. Can you use control points to correct intensity in overly bright scans. I've attached an example pic. Thanks for your help, Kathy

2 4

normal value of "Brain Segmentation Volume Without Ventricles" value ?
by Gonzalo Rojas Costa 20 Apr '10

20 Apr '10

Hi: I need to know which is the value of BrainSegVolNotVent (Brain Segmentation Volume Without Ventricles) of healthy volunteers at different ages... Any paper ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clinica Las Condes Santiago Chile

2 3

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 >

1 0

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

1 0

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

19 Apr '10

1 0

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Freesurfer April 2010