Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

Surface-Based Group Analysis Results --> Original coordinate space
by emoulton＠mclean.harvard.edu 08 Nov '06

08 Nov '06

Hello, Is there a straightforward way to convert Surface-based Group Analysis results (e.g. sig.mgh) to ANALYZE format in conventional coordinate space (i.e. viewable with FSL)? It seems to require a bit more gymnastics than a simple mri_convert command to properly convert these surface maps. What steps, and what tools, should I use to perform such a conversion? Thanks, Eric Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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3D visualisation
by Nicolas Cherbuin 07 Nov '06

07 Nov '06

Hello, I would like to visualize subcortical structures, particularly the hippocampus, in 3D. Is there an available function to display a glass brain with solid internal structures and/or is it possible to extract this information from the freesurfer files? If yes where could I find the file format to extract the info? Also, is it possible to perform surface analyses on the subcortical structures (e.g. hippocampus) instead of on the inflated brain, for example to show differences in volume related to memory measures? Thanks Nic

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Re: [Freesurfer] is this ok?
by Chacko Cherian 06 Nov '06

06 Nov '06

Thanks Bruce. I Am using version 3.0.3,..wat can i do to to get better pial surface images? IS it something to do with the skull stripping stage or is it the motion artifacts which cause a reduction in the overall resoution of the image? Chacko. ----- Original Message ---- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Chacko Cherian <chacko_cherian(a)yahoo.com> Cc: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Monday, November 6, 2006 4:25:05 PM Subject: Re: [Freesurfer] is this ok? Hi Chako, I wouldn't worry too much about the inflated - it looks okay. Probably a result of the large motion artifact in your data. The pial surface is more worrisome - what version are you running? They are usually *much* better than this. Bruce On Mon, 6 Nov 2006, Chacko Cherian wrote: > Hello freesurer users, > > Is it ok to have such edges on the inflated surface?Is there something I can do to rectify this? > THe second image is the brainmask and wm volume as seen using tkmedit. > > (tkmedit subj1 brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white) > > THanks in advance > > Best, > > Chacko Cherian > > > >

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is this ok?
by Chacko Cherian 06 Nov '06

06 Nov '06

Hello freesurer users, Is it ok to have such edges on the inflated surface?Is there something I can do to rectify this? THe second image is the brainmask and wm volume as seen using tkmedit. (tkmedit subj1 brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white) THanks in advance Best, Chacko Cherian

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Scan quality
by Derin Cobia 06 Nov '06

06 Nov '06

Should I expect this kind of quality/resolution from my FS images based on the original scan (see attached images)? These are older scans that I've been given, and I just want to make sure that the image quality isn't introducing any unnecessary error, or is not "good enough" for FS. Thanks. -Derin

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N3 options (was: [Freesurfer] parameters for N3 correction)
by Sebastian Moeller 03 Nov '06

03 Nov '06

Hi List, On 3. Nov 2006, at 19:48 Uhr, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 10 > Date: Fri, 03 Nov 2006 13:48:18 -0500 > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] parameters for N3 correction > To: Chacko Cherian <chacko_cherian(a)yahoo.com> > Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <1162579698.27296.26.camel(a)minerva.nmr.mgh.harvard.edu> > Content-Type: text/plain > > also, the command: > > recon-all -s <subjid> -nuintensitycor > > will run just that stage. > Something relted on the topic of N3. Using the default settings with surface coils (RX and TX through the same coil in our case) ends up looking ugly no matter the number of -nuiterations specified in recon-all. Hacking mri_nu_correct.mni to include "-iterations 150 -stop 0.0001" in the invocation of nu_correct, ends up with better results. Just as the N3 documentation recommends for surface coils ;). Now would it be possible to get a "-surfacecoil" argument for mri_nu_correct.mni (or even better recon_all via the experts options mechanism?) included into the distribution. If yes I would be willing to hack something up (at least including this properly into mri_nu_correct.mni). This might be helpful for other surface coil users out there... ahoi & sorry -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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parameters for N3 correction
by Chacko Cherian 03 Nov '06

03 Nov '06

Hello users, Is there any information available regarding the parameters used for N3 correction in the autorecon process? Thanks, Chacko.

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Doubt on spherical coordinates
by jorge luis 03 Nov '06

03 Nov '06

Hello all I would like to know what kind of coordinates (RAS, Talairach, Spherical) are saved in the AsCII file resulting from: mris_convert lh.sphere.reg lh.sphere.reg.asc I could not find correspondence among the resulting coordinates and those that are shown in Tksurfer. If they are not the spherical ones, how can I get an ASCII file with the spherical coordinates ( XYZ) or (Rho,Theta) in order to work on the spherical world? In advance Thank you a lot ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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freesurfer course
by Nicolas Cherbuin 01 Nov '06

01 Nov '06

Dear Freesurfers, I am trying to plan international travel for next year. Can somebody inform me of when the next freesurfer courses will take place in 2007? Thanks Nic

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mris_anatomical_stats error
by Johannes Klein 01 Nov '06

01 Nov '06

Hi everyone, I'm trying to calculate surface areas for some labels I've drawn on an averaged subject created with mrake_average_surface, and mris_anatomical_stats seems the way to go. Unfortunately, it needs a file called wm.mgz, which doesn't exist for my averaged subject. The mri subdir contains T1, brain, mni305.cor and orig.mgz, but no wm.mgz. Is there a way to create this file from the data I've got? Thanks for your help, Johannes

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