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30056 discussions

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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Re: [Freesurfer] Normalization of mris_anatomical_stats
by Bruce Fischl 08 Dec '05

08 Dec '05

Hi Glenn, we have some estimated total intracranial volume (eTIV) in the new stuff using something that Randy Buckner showed recently - the determinant of the tal transform is predictive of TIV. Should be out soon. It's not clear however that thickness needs to be corrected by it. The MNI folks have shown in some cases that it does not, and thickness certainly doesn't scale with TIV linearly as many people have shown. Bruce On Thu, 8 Dec 2005, Glenn Lawyer wrote: > Bruce, I don't know how you manage to always get back to me so quickly, but I > sure do appreciate it! > > Yes, we were thinking of ICV. We are using the automatically generated > surface labels and looking at the grey matter volumes. > > Thanks again, > > +glenn > > Bruce Fischl wrote: > >> you mean by ICV? No, although in our new versions we compute ICV/TIV. Do >> you mean volume labels or surface labels? Volume of volume labels can be >> computed with mri_label_volume, surfaces can be given to >> mris_anatomical_stats -l <label name> >> >> cheers, >> Bruce >> >> On Thu, 8 Dec 2005, Glenn Lawyer wrote: >> >>> 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 >>> >>> > >

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talairach transform with brain.mgz as input file
by Lars M. Rimol 08 Dec '05

08 Dec '05

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

2 1

how to get .mgz files
by peggy christidis 07 Dec '05

07 Dec '05

Hi there, I'm starting off with an AFNI dataset (e.g., fred+orig.BRIK) and I want to convert this file to FreeSurfer's .mgz format. When I run the command "mri_convert fred+orig.BRIK fred_surf/mri/orig", I end up with 256 .COR files. How do I get .mgz files instead? Do I need to add something to the command line? I've checked mri_convert's help manual but I still can't figure out how to do this. Thanks, Peggy

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which version is recommended, and any way to avoid -conform?
by Sebastian Moeller 07 Dec '05

07 Dec '05

Hi All, which version of freesurfer is the one recommended to be used, the v2.2 stable from November 20. or still the development version from October 3rd? I guess it is still the dev version. My second question is about the conform step implicit to recon-all -motioncor, as I used a 0.5mm^3 resolution for scanning my monkey brains, it would be a pitty to conform this data to 1mm^3 for further steps. So far the only way I know, how to avoid this is using the -iis -ijs -iks switches to mri_convert to actively lie to freesurfer, that the scans already conform to 1mm^3. Is there a nicer way to achieve the use of non-conformed resolution, like doing the -motioncor step of recon-all -autorecon1 manually? Or is the use of the standard process not recommended for monkey data anyway? Regards Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 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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mask_label in script
by Henrik Ormåsen 07 Dec '05

07 Dec '05

We use mask_label in the prompt to load this file. How can we load it from a tksurfer tcl script? - Henrik

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