Freesurfer December 2005

freesurfer@nmr.mgh.harvard.edu

35 participants
51 discussions

Dev vs Beta versions
by Katherine Perdue 13 Dec '05

13 Dec '05

Hello- What are the differences between the Freesurfer surfaces created with the development version and the surfaces created with the standard version? I am trying to use the new annotation files from the dev version and map them into SUMA to form ROIs. I think there are some problems with the alignment though- when I looking at the annotation files made with the development version on an average brain made with the standard version, the annotation files were shifted (which leads me to believe there are differences in the surface files that the SUMA command I was using was not taking into account). It would be really great if I could use the dev annotation files, but it has taken a lot of work to get the functional and structural data in line with each other, and I'd rather not throw that away. Is there a way to to this? Thanks for any suggestions, Katherine

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talairach
by Sasha Wolosin 12 Dec '05

12 Dec '05

Dear all, We are having some difficulties getting accurate talairach.xfm files. After running recon-all, the final objective function value for most of our brains was above .2 We then regenerated the transform using brain.mgz. This helped, but our final objective function values are still above .1, some are above 1.5 There don't seem to be any bright neck regions left in the brain volumes, so we don't think bright neck regions are causing the problem. Manual inspection shows that the fuzzy talairach brain is slightly smaller than the subjects' brains, but seems to be in the correct orientation. Is there anything else we should try before manually adjusting the xform? Is there any objective way to evaluate a manually adjusted xform? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. 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 e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Normalization of mris_anatomical_stats
by Glenn Lawyer 10 Dec '05

10 Dec '05

Hi, We want to compare grey matter volumes from specific labels. Is the output of mris_anatomical_stats normalized in any way? It doesn't appear to be. Thanks! +glenn -- I want to go farther, farther! A. E. L. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

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fieldsign broken with new surfaces
by Don Hagler 10 Dec '05

10 Dec '05

I tried to run fieldsign calculation using surfaces created with the new recon-all but the results look wrong, with some vertices that have a salt-and-peppery look to them. The code I'm using is ripped out of an older version of tksurfer and works fine on old surfaces. It seems that there is a lack of correspondence between vertex numbers in the flattened surface and orig or something. Another odd thing is that the ripflag is set for all vertices in the flat patch, but that is probably unrelated. We noticed that the file size of the different surfaces (e.g. orig, smoothwm, inflated) varies. In the older version, the surfaces all had an identical size. This suggests that the different surfaces have different number of vertices now, or you've changed the file format somewhat. Can you tell me what's going on there? My current work-around is to use recon-all up to the point of fill, taking advantage of the new aseg, but then I'm using the old programs to generate surfaces compatible with my fieldsign code.

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talairach
by Sasha Wolosin 09 Dec '05

09 Dec '05

Dear all, I am trying to improve talairach registration and I noticed the following suggestion in the freesurfer wiki: "If you suspect that the bad transform is the result of a bright neck region, edit the volume to erase the neck and run mritotal on the edited volume. This can be accomplished through simple volume editing: set all the regions to zero where y is greater than a certain value (around 170). This generally works better than using the brain volume. Check your transform using tkmedit" I would like to try this, but I don't know which command to use. Could someone please fill me in? Also, after fixing the talairach registration, is it necessary to re-run -autorecon2? Or is it sufficient to over-write the header files and talairach.xfm? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. 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 e-mail in error, please immediately notify the sender via telephone or return e-mail.

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cerebellum segmentation
by Lars M. Rimol 09 Dec '05

09 Dec '05

Hi Bruce and Satra, Our specific goal is to measure the vermis. It's time consuming to do it manually, so my idea was to ask if it could be possible to develop an automatic segmentation/parcellation procedure, similar to aseg, that includes also the vermis. (In addition, we have three subdivisions of vermis.) I do realize that reconstructing the cerebellar surface is a very difficult task because of the spatial resolution issue but maybe a volumetric approach similar to aseg could be feasible? >Hi Satra, > >we do segment the cerebellum with the aseg stuff into cerebellar gray and >white. I guess it's a question of what your goals are Lars. -- yours, Lars M. Rimol

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talairach transform with brain.mgz
by Lars M. Rimol 09 Dec '05

09 Dec '05

Hi, We have 15 out of 16 data sets with Final Objective Function value 0.1. We also find some deviations from the talairach (or MNI) volume when we visually inspect the images (fixed vs. movable) in tkregister2. But we are unsure how large the deviations must be for it to be a problem, so we rely on the Final Objective Function value. When it comes to the intensity normalization, that's even harder to inspect visually, so we don't really know how to check that (unless there are really huge effects). But when we use the brain.mgz image as input for the talairach, the Final Objective Value improves, that's why we've started using that. So we need to know how to proceed from there. (We use the "recommended reconstruction," so we check the talairach and skullstrip after autorecon1.) Thanks! -- yours, Lars M. Rimol >depends why you needed to improve the talairach. If it's just for >reporting purposes and the filling/intensity normalization all worked >fine then you don't need to. > >cheers, >Bruce >> Hi, >> After having redone mri_convert with an edited brain.mgz as input file, in >> order to improve the talairach transform, and after having changed the file >> names (brain.xfm -> talairach.xfm), should we then go to autorecon2? (or do >> we need to re-run some more scripts from autorecon1?) >> >> >> -- >> yours, >> Lars M. Rimol >>

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Re: [Freesurfer] Cerebellum atlas
by Joongnam Yang 08 Dec '05

08 Dec '05

If it is in progress, it means that it is not usable by end-users yet? If so, when would the how-to guide be available? (This would be a wonderful tool for my project in which I need to see a particular region labeled, i.e., lateral portion of the areas between parietal and occipital lobes. I am talking about the 'purple-colored' region in the example image shown in the Wiki page) Thanks. Nam. >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 12/08/05 11:09 AM >>> Lars, The wiki page describing atlas-building is a work-in-progress, so it's not yet a how-to guide, but the essential information exists. See: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation If you decide to try to construct your own atlas, it would be helpful to email me particulars on trouble-spots, so that the wiki page can be improved. Nick On Thu, 2005-12-08 at 08:38 -0500, Bruce Fischl wrote: > Hi Lars, > > I guess in principal you could use it via the standard route for > spherical morphing if you segmented it yourself. In general we haven't > done a lot with cerebellum as you need something like .3 mm voxels in > plane to resolve the majority of the foliations. Could someone point Lars > at the wiki page describing how to build your own atlas? Analyze would > probably be okay if you keep the orientation info in an associate .mat file > (as SPM does) > > cheers, > Bruce > > > On Thu, 8 Dec 2005, Lars M. > Rimol wrote: > > > Hi, > > We have manual tracings of the cerebellum (approx. 100 brains), which were > > done in the Brains2 software. Could these tracings be used to construct an > > atlas for use with FreeSurfer? If so, which file format would be most > > convenient? Analyze? > > > > (The data have been described in: Okugawa G, Sedvall G, Agartz I. Smaller > > cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J > > Psychiatry, 2003; 160:1614-7) > > > > -- > > yours, > > Lars M. Rimol > > > _______________________________________________ > 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

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sub-cortical segmentation and primate volumes
by peggy christidis 08 Dec '05

08 Dec '05

I'm guessing the answer to this question is "no", but I'll ask it anyway. Does the sub-cortical segmentation program work on a primate volume? Or do we have to do things the old way (i.e., with manual editing)? Thanks for you time, Peggy

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Cerebellum atlas
by Lars M. Rimol 08 Dec '05

08 Dec '05

Hi, We have manual tracings of the cerebellum (approx. 100 brains), which were done in the Brains2 software. Could these tracings be used to construct an atlas for use with FreeSurfer? If so, which file format would be most convenient? Analyze? (The data have been described in: Okugawa G, Sedvall G, Agartz I. Smaller cerebellar vermis but not hemisphere volumes in chronic schizophrenia. Am J Psychiatry, 2003; 160:1614-7) -- yours, Lars M. Rimol

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Freesurfer December 2005