Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

analize convert
by Gabriel Go.Es. 12 Mar '09

12 Mar '09

hello everybody i'n trying to convert a FS average to *.img, when i use mriconvert with one subject i put the rawavg.mgz, but in the average subject this file does not exist, so how can i make it? to convert the Fs average to an *.img Regards Gabriel _________________________________________________________________ Descubre todas las formas en que puedes estar en contacto con amigos y familiares. http://www.microsoft.com/windows/windowslive/default.aspx

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Aparcstats question
by Nathan Dankner 12 Mar '09

12 Mar '09

I have a couple of questions regarding the stats files. First, at the beginning of the aparc.stats tables, there is a measure that is labeled ³unknown.² Is this total average thickness throughout the cortex, or just some throw-away measure? Secondly, I have heard that there are command line flags that can be used to find things such as total white matter volume, etc. What are these flags? Thank you in advance, Nathan

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A question about symmetry between two hemispheres
by carl＠nmr.mgh.harvard.edu 11 Mar '09

11 Mar '09

Hi Lars, In the interim you might want to take a look at thread below about this issue where I discuss some admittedly imperfect approaches pending doug's tool carl schwartz On 3/11/09 3:32 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: Not yet. I have some experimental software to do this but it is not ready for release. "Soon". doug Lars M. Rimol wrote: > Hi, > This is perhaps a tricky problem. I have created a lh STG label using > "custom fill" and the "up to functional threshold" option and > retrieved the data from those vertices. This label is just a minor > portion of the entire STG parcellation. Now I would like to compare to > the homologous area in the right hemisphere. Short of using the > annotation labels and thereby chosing the entire parcellation, is > there any way to get the vertex numbers for "the same" area in the > right hemisphere? > > > Thank you! > > > -- > yours, > LMR > ------------------------------------------------------------------------ >>>>>>>>>>>>>>>>> ---------------------------- Original Message ---------------------------- Subject: [Freesurfer] A question about symmetry between two hemisphere From: carl(a)nmr.mgh.harvard.edu Date: Mon, January 19, 2009 12:35 am To: freesurfer(a)nmr.mgh.harvard.edu -------------------------------------------------------------------------- hi yczhang, see also my reply on Dec 2 2008 to frederic.andersson(a)univ-tours.fr re similar question -- search freesurfer archives on "comparing hemispheres" Ultimately to look at the symmetry question properly, we will need Doug's tool. In the interim, below is one, admittedly imperfect approach. Suppose you have a cluster of thickness difference (or bold signal) in one hemisphere between 2 groups. Create your own average subject (to increase accuracy of visualization (but fs average would work as well). Then hand-draw the analogous cluster in the other hemisphere. To do so, you would need to determine the min and max values that occur in x, y, z in talairach space and additional control points as required for the cluster or region where the primary finding occurs . Then flip the sign on the x coordinates and hand draw the cluster in the opposite hemisphere, guided by the tal coodinates. Determine the variable of interest (mean thickness, mean bold signal, etc) in the "mirror" cluster. Input that variable into a glm/anova (outside of freesurfer) where side, group, variable of interest and test for whether there is a side x variable interaction, suggestive of a truly lateralized finding. Remember that the test statistic/significance level for the PRIMARY hemisphere finding is not appropriate to report as it is inherently biased (it is defined as the region where there is a significant between group difference. It is the "mirror" contra-lateral and the presence or absence of a side x variable interaction that is the focus. You might also be able to simply analyze the mirror cluster alone without putting the other side into the anova since it, unlike the primary finding cluster, is not a biased metric. best, carl schwartz >>>>>>>>>>>> no, the vertex index is essentially arbitrary and you can't use it to compare left and right. Doug had some tools for this, but I'm not sure whether they are ready for primetime yet. cheers, Bruce On Sun, 18 Jan 2009, Zhangyuanchao wrote: > Dear Expert, > > I want to exame the symmetry property of two hemispheres,for example, symmetry of cortical thickness or lgi, I want to know whether the same ID of the two hemispheres after resampling using the average pial surface corespond to the same anatomical region. > > > > For example, > > ID=1000, > For the left hemisphere, the vertex 1000 corespond to 'medial_wall'; what about the vertex 1000 on the right hemisphere? Is it also corespond to the same anatomical region "medial_wall" so that we can compare their cortical thickness of vertex 1000 on both left and right hemisphere to exame the symmetry property. > > > Thanks a lot! > yczhang >

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Are accurate volumes necessary for accurate surfaces?
by Jeff Sadino 11 Mar '09

11 Mar '09

Hello Surfers, I want to do a study on the cortical thickness for some new subjects. As I understand the Recon process, the surface files get their information from the volume files. If I want to increase the accuracy of my thickness files, do I first need to manually check the accuracy of the volume segmentations? Thank you, Jeff _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=TXT_TAGLM_WL_HM_70faster_032009

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qcache error
by Dankner, Nathan (NIH/NIMH) [F] 11 Mar '09

11 Mar '09

Hello All, While running qcache on a subject, I received this error: ERROR: number of vertices in [subj path]/surf/rh.thickness does not match surface (152261,152724)ERROR: reading curvature file This has only happened with this one particular scan. Is this something that can be resolved? Thanks in advance, Nathan

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homologous lh and rh labels
by Lars M. Rimol 11 Mar '09

11 Mar '09

Hi, This is perhaps a tricky problem. I have created a lh STG label using "custom fill" and the "up to functional threshold" option and retrieved the data from those vertices. This label is just a minor portion of the entire STG parcellation. Now I would like to compare to the homologous area in the right hemisphere. Short of using the annotation labels and thereby chosing the entire parcellation, is there any way to get the vertex numbers for "the same" area in the right hemisphere? Thank you! -- yours, LMR

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Adding papers to the Wiki
by Pedro Paulo de Magalhães Oliveira Junior 11 Mar '09

11 Mar '09

Hi, Can you add this paper to the Wiki page? "Cortical thickness reduction of normal appearing cortex in patients with polymicrogyria" - Oliveira Jr, Pedro Paulo; Leite, Claudia; Valente, Kette; Shergill, Sukhwinder; Amaro Jr, Edson; - Journal of Neuroimaging - 2008 - In Press Tks PPJ ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom

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Re: [Freesurfer] Voxel size smaller than 1x1x1mm?
by Bruce Fischl 11 Mar '09

11 Mar '09

Hi Falk, yes, you can use the "conform to min" (-cm I think) switch in recon-all. Can you cover the whole brain at .7mm iso? That's hard. And 7T is hard for whole brain morphometry because of dielectric effects. Good luck. Bruce On Fri, 6 Mar 2009, Falk Lüsebrink wrote: > Hi Freesurfers, > > I'm currently doing my bachelors thesis in medical engineering and I'm > trying to measure the cortical thickness of scans acquired by a 7T MRT. > > A colleague of mine has used Freesurfer (v4.0.5) before and mentioned that > high resolution scans with a voxel size smaller than 1x1x1mm (like > .7x.7x.7mm) are converted to 1x1x1mm during a processing stage of autorecon > - I think during the mri_convert process. > > Is it possible to keep the native size or does Freesurfer need to change the > voxel size to 1mm in order to do the segmentation correctly? > > Regards, > Falk > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Average MRI
by SHRIKANTH KULASHEKHAR 11 Mar '09

11 Mar '09

Hi, I have 2 sets of MRI measurements with the same measurement sequence per subject. I was wondering if there would be any use of averaging these 2 sets, before the surface reconstructions? If yes how is this averaging achieved in freesurfer. Thanks in advance. Shriks Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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recon surf folder is missing data
by jake＠nmr.mgh.harvard.edu 10 Mar '09

10 Mar '09

Hi All, I was just wondering if anyone has had data missing from the surf directory in the recon folder of a subject, ie- right hemisphere data is missing, or no data at all. Here is the path to a recon where I recently have found missing data: /space/amaebi/35/users/ablood/R01_Botox/R01BTX_recons/CD_R01BTX_pat2_sess4_recon_missing_surfdata Any help would be greatly appreciated, thanks Jake

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