Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Surface area of ROI
by Barnali Basu 10 Sep '09

10 Sep '09

Experts, I have labels drawn on surfaces of individual subjects. I need to find the surface area of each (one on each surface). Is there a way I could do it? Thanks -- Barnali Basu Cell : 425 638 2936 Home: 206 257 0174

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problem of underestimate on pial surface
by yzhangd＠artsci.wustl.edu 10 Sep '09

10 Sep '09

Hi,everyone,I reconstruct a pial surface using freesurfer,and there are some dips which i want to get rid of, i.e: i want to smooth the pial surface in the area where the red arrow point at, as shown in the attached picture. what i can do on the brainmask.mgz to make it work ? Thanks a lot

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mris_volmask description
by Guang Zeng 10 Sep '09

10 Sep '09

Hello, there, Do you know where I can find a description for mris_volmask. The page on FreeSurferWiki about this is empty. Thanks a lot! Zeng _________________________________________________________________ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:O…

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Missing Volume Values
by Warner, Matthew A. 10 Sep '09

10 Sep '09

Hi Freesurfer team, Thank you in advance for your help. We are attempting to obtain left hemisphere and right hemisphere volumes for various grey and white matter structures in a variety of controls and brain injured patients. However, values for the corpus callosum are often not reported in aparc.stats files for either hemisphere. This has occurred for both patients and normal controls. Is there a reason why these values are not being computed? Also, in the aseg.stats for several patients, the Corpus Callosum mean values are reported as 0.0000 with SD, Min, and Max of 0 as well. Are the brains perhaps too structurally abnormal to report a reliable value? The subjects with this problem had a ventriculostomy, which damaged the corpus callosum to some extent. Should CC values for these patients be considered unusable? I have attached a T1-hdr file for your reference. In addition, I have attached the aseg.stats file for this subject(which reports a CC value of 0) and the lh.aparc.stats file (which did not report a corpus callosum value). If the ventriculostomy is to blame, can you provide a reason why for some normal controls the corpus callosum volume was not calculated for left and right hemispheres? Any insight you could provide would be greatly appreciated. Thank you very much for your time and help, Matt

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Post-surgery images
by Paula Diniz 10 Sep '09

10 Sep '09

Hello! I would like to know if someone has experience with segmentation of post-operative images using freesurfer. Thanks! Paula -- ================================== Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de São Paulo Hospital das Clínicas - Ribeirão Preto ==================================

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Intersection of labels with other labels or volumes
by James Porter 09 Sep '09

09 Sep '09

Hello- Is there a simple way to obtain the intersection of two labels, output into a third label? Or the intersection of a label and an .mgh file output by mri_surfcluster? For instance, I have a cluster defined by mri_glmfit/mri_surfcluster that spans multiple anatomical regions, and I want to investigate the values from subsections of the cluster. That is to say, I want to run mris_anatomical_stats on only the section of my cluster that covers, say, precentral cortex but not caudal middle frontal or pars opercularis. I've tried several strategies without success. The most promising seemed to be just having mri_surfcluster output an aparc file, and then pass that aparc file into mris_anatomical_stats. However, that aparc just puts the very first region definition to every vertex. The same happens if I run mri_label2aparc on the labels output by mri_surfcluster. This happens no matter which LUT or ctab I use, i.e., with aparc.annot.ctab the whole volume gets labeled "bankssts" and with FreeSurferColorLUT.txt every vertex in the cluster volume gets labeled "Left-Cerebral-Exterior." I guess there are a few issues in this email, but the most important one to me is being able to run mris_anatomical_stats on the union of a cluster file and the individual regions from the standard aparc atlas. Any suggestions? Thanks in advance, --------- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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Freesurfer installation on Ubuntu desktop or server?
by Burcu Ayşen Ürgen 09 Sep '09

09 Sep '09

Hi all, If one installs Freesurfer on Ubuntu, should he/she prefer the desktop version of Ubuntu or server edition? Does it matter? Thank you, Burcu Aysen Urgen.

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Averaging Labels
by David Brang 09 Sep '09

09 Sep '09

Hi, I’m trying to average 2 labels together, but haven’t seen any script out there that does this. Essentially we used ROI localizer tasks to create individual labels for each of our subjects. For visualization purposes, we created an average brain, and used mri_label2label to map each individual subjects’ label onto the group brain. But, now I’m not sure how to create an average of these labels. Thanks! David Brang

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Autoredraw in TKSurfer
by Pedro Paulo de Magalhães Oliveira Junior 09 Sep '09

09 Sep '09

Some people asked me how to enable Auto Redraw in TKSurfer in the virtual machine distribution of FreeSurfer. A video tutorial was placed in YouTube: http://www.youtube.com/watch?v=9573UYJxlok ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

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Temporal lobe surface problem
by Chris Adamson 09 Sep '09

09 Sep '09

Everyone, I am having problems with Freesurfer not seemingly appreciating the WM/GM boundary in the temporal lobe. I have attached a screenshot of the problem area which is in the bottom right of the pic. A large portion of the grey matter is outside the pial surface and the inner boundary does not extend to the edge of the white matter. I have checked the white matter segmentation and edited the aseg volume to correct this problem but after running recon-all again I get the same result. Any ideas? Chris. -- Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash) Research Officer Developmental and Functional Brain Imaging, Critical Care and Neurosciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9345 4306 M XXXX XXX XXX E chris.adamson(a)mcri.edu.au www.mcri.edu.au

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