Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

entorhinal surface and wm intensity
by Derin Cobia 07 Jul '10

07 Jul '10

I have questions regarding two issues we've run into processing dementia and age-matched healthy subjects: 1. For several of our subjects, we've noticed that an isolated region of the entorhinal pial surface becomes 'indented' towards the white surface (see in RH in attached pics- P5b*). Not sure what's going, I've tried to correct it by removing any extraneous neighboring voxels or other 'anomalies' (no voxel gaps in the wm volumes from lesions, etc). It almost reminds me of the insula 'spike' a few versions back. Thoughts? 2. After re-running a subject for cp and wm edits, the resulting white (and consequently pial) surface has become inaccurate for large portions of the anterior temporal and frontal lobes, but just in the LH (attached pics- P8b*). To clarify, this was not the case after the data's initial run, only once edits were made and incorporated. We've run into this before, but only after editing a subject multiple times (3-4x, thus more recons), or 'updating' subjects to a new FS version (e.g., re-running v4.1.0 data with v4.5.0). Are edits changing the intensity threshold? It's odd that it's asymmetric. Any help/thoughts would be appreciated, thanks. -Derin

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Help on QDEC: Obtainign mean, sd and p-values from glm result
by Fernanda Palhano 07 Jul '10

07 Jul '10

Hello, I've just started using freesurfer. I've reading the mail list wich helps me a lot, but I can't find how I can obtain a table with the values of my glm analysis. For exemple, in the Qdec's tutorial I have a surface that answer the question "Does the correlation between thickness and age differ from zero?" It's possible to see this data like a table: region mean sd p-value precentral xx x xxxx Or at least obtain those values individually? thank you very much in advance, Fernanda

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manual corregistration...
by Gonzalo Rojas 07 Jul '10

07 Jul '10

Hi: How can I do a manual corresistration with freesurfer ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Re: [Freesurfer] subcortical segmentation
by Bruce Fischl 07 Jul '10

07 Jul '10

Hi Salem, yes, you can run any individual options in recon-all. See the -help output and run it through step 11 if you want. Note that we do use the surfaces to improve the aseg accuracy at the very end, so you'll be giving that up. cheers Bruce On Wed, 7 Jul 2010, Hannoun wrote: > > > Hi, > > I am a new user of freesurfer. Is it possible to do just the volumetric > processing stages without the surface processing stages? > > In fact what I want is to segment the subcortical structures. > > Is there a command line for this purpose only or should we run all the > recon-all steps? > > Thank you for your help > > Salem > > > > > >

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Qdec - problem with the Generate Stats Data Import button.
by Gaëlle Leroux 07 Jul '10

07 Jul '10

Dear FS, I'm basically stocked with a problem when I press the "Generate Stats Data Import" in the Qdec GUI. I got the following error message as in the attached file. I'm running FS using a python 2.6 version. It seems that I do have a problem with the asegstat2table command line but I don't understand why... Any advice, please? Many thanks in advance for your help. Sincerely, Gaëlle Leroux.

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RV: FREESURFER
by SANTIAGO GONZALEZ CALERO 07 Jul '10

07 Jul '10

> Good morning,I am working on brain segmentation using freesurfer program. > I wonder if it is possible to turn an initial image with some tool freesurfer. Because my problem is that when I start to perform segmentation in freesurfer, I get an error and I think that is because dicom image format is a little crooked. If you can not rotate with tkmedit or similar tool. > The error I get is as follows: > > ERROR > cp transforms/talairach.auto.xfm transforms/talairach.xfm > > #-------------------------------------------- > #@# > Talairach Failure Detection Tue Jun 22 04:45:20 EDT 2010 > /usr/local/freesurfer/subjects/ome/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** > (p=0.0063, pval=0.0000 < threshold=0.0050) > > I have tested the segmentation with another patient and gives me the following error. > > ERROR > > ********FINAL ITERATIVE TEMPLATE DEFORMATION******** > Compute Local values csf/gray > Fine Segmentation...44 iterations > mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/francia/mri/T1.mgz',frame -1, errno 12 > > mri_strip_skull: done peeling brain > > Brain Size = 1260141 voxels, voxel volume = 1.000 mm3 > = 1260141 mmm3 = 1260.141 cm3 > > mri_watershed Error: read failed > > Linux freesurfer-virtual 2.6.28-19-generic #61-Ubuntu SMP Wed May 26 23:35:15 UTC 2010 i686 GNU/Linux > > recon-all exited with ERRORS at Tue Jun 22 08:27:59 EDT 2010 > > Do not know if these errors can be solved with some kind of tool or if on the contrary are due to initial images of patients are slightly slanted, and if the same could reorient vertically. > Thank you very much. A greeting. > Attentively

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subcortical segmentation
by Hannoun 07 Jul '10

07 Jul '10

Hi, I am a new user of freesurfer. Is it possible to do just the volumetric processing stages without the surface processing stages? In fact what I want is to segment the subcortical structures. Is there a command line for this purpose only or should we run all the recon-all steps? Thank you for your help Salem

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surface-based cytoarchitectonic map
by Danny Kim 06 Jul '10

06 Jul '10

Hi Freesurfer users, In the paper, "Cortical folding patterns and predicting cytoarchitecture" by Fischl et al (Cerebral Cortex, 2008), it's mentioned that "surface-based probabilistic maps of the cytoarchitectonics can be downloaded from http://surfer.nmr.mgh.harvard.edu/fswiki". I can't seem to find them there in the wiki.. anyone know where they might be? Thank you Best Regards, Danny Kim Brainmapping BC Children's Hospital

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Spatial info of vertices
by Dankner, Nathan (NIH/NIMH) [F] 06 Jul '10

06 Jul '10

Hi all, I'm hoping to extract the connections and distances (edge and weight) of the vertices for each of my individual subjects' surfaces. How can I go about doing this? Thanks! Nathan

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Post-doctoral Position in Vascular Dementia Research at the German Center for Neurodegenerative Diseases (DZNE) in Munich
by Graf, Christina /DZNE 06 Jul '10

06 Jul '10

Post-doctoral Position in Vascular Dementia Research at the German Center for Neurodegenerative Diseases (DZNE) in Munich The German Centre for Neurodegenerative Diseases (www.dzne.de<http://www.dzne.de/>) has been newly founded by the Helmholtz Foundation. The DZNE Munich is now offering a post-doctoral Position in Vascular Dementia Research. The mission of the DZNE is to investigate neurodegenerative diseases of the ageing human brain, in particular Alzheimer's and Parkinson's disease, while also studying interactions with other neurological disorders relevant to ageing and dementia. A joint project between three different sites of the DZNE will focus on mechanisms of vascular and mixed dementia. For a project on the neural correlates of cognitive and behavioral dysfunction in vascular cognitive impairment the DZNE Munich in collaboration with Institute for Stroke and Dementia Research (www.isd-muc.de<http://www.isd-muc.de/>) is searching for a scientist with a background in cognitive neuroscience and image post-processing. The candidate must have attained a PhD or MD degree and should have skills in the following areas: MR image post-processing (FSL, SPM, Matlab etc.); statistics, programming (optional), neuropsychology (optional). The Institute for Stroke and Dementia Research (ISD) / DZNE Munich closely collaborates with national and international partners thus providing a stimulating environment for highly motivated and creative scientists. The position is for 3 years and will be opened in September 2010. Employment, payment and social benefits are determined by the Public Sector Collective Agreement (Tarifvertrag für den öffentlichen Dienst - TVöD). The DZNE seeks to increase the number of female personnel in those areas where they are underrepresented and therefore explicitly encourages women to apply. The DZNE is committed to employing more disabled individuals and especially encourages them to apply. Applications including a CV, a list of publications and a research summary should be sent electronically to isd(at)med.uni-muenchen.de<mailto:isd@med.uni-muenchen.de>. The application deadline will be July, 31 2010 time limit: 31.07.2010 place: Munich contact: Prof. Martin Dichgans (isd(at)med.uni-muenchen.de<mailto:isd@med.uni-muenchen.de>) Kind regards Christina Graf Personal und Organisation * Human Resources Department Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

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