Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

Re: [Freesurfer] recon-all -mprage flag
by Judith Segall 03 Feb '10

03 Feb '10

Hi Freesurfer users. I recently noticed the "-mprage" option when running recon-all. Is this the same multi-echo mprage developed by Andre van der Kouwe? Also, what are the advantages for using the -mprage option if you are using the mgh developed mprage? Thanks, Judith S Mind Research Network

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FreeSurferColorLUT label Unkown in annotation file
by Guang Zeng 03 Feb '10

03 Feb '10

Hi, there, I have question about FreeSurferColorLUT label Unkown in annotation file. In FreeSurferColorLUT, I read that #No. Label Name: R G B A 0 Unknown 0 0 0 0 I load the inflated surface of a subject, import lh.aparc.annot file. All the subcortical region are labelled as "Unknown" Then I load the lh.aparc.annot file using read_annotation.m to MATLAB as [vertices, label_val, colortable] = read_annotation(annotation_filename); Since the RGB of label Unknown is zero, then its label value in read_annotation.m should also be zero, since annotation value = (R) + (G * 256) + (B * 256^2) However, there are no vertices with label_val = 0 when I use unknown = find(label_val == 0). I also check the label_val of several randomly picked verteices in unkown (subcortical) region, they gave me different values. I thought I should find the same values, although they may not equal to zero. So, my question is how to find the vertices which are labelled as unknown in annotation file? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469226/direct/01/

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scrambled boundaries
by Brendan Robert Ansell 02 Feb '10

02 Feb '10

Hi, I have a set of fairly old MRIs which have been run on freesurfer. Occasionally scans have scrambled pial or white matter boundaries - a knot-like appearance especially in sulci. I am wondering how freesurfer estimates cortical thickness in these regions. For example, does it take the pial boundary closest to the white boundary i.e. the outer surface of the 'pial knot'? Are the encapsulated GM voxels included in the overall cortical thickness measurement? Thanks- Brendan Ansell MNC

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GM volume and cortical thickness
by keepmoon 02 Feb '10

02 Feb '10

Dear developer, I want to compare the grey matter volume by VBM to cortical thickness by freesurfer. But in this process, I meet a problem: how to change the points number of grey matter into the same with the vertex of thickness by freesurfer? Any help will be appreciated! Best regards Joe

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Freesurfer , wfu pick atlas
by Sharmili 57 02 Feb '10

02 Feb '10

Hey, I want to do Cortical thickness analysis for regions defined by the wfu atlas in a MEG study. How can I define these areas in Freesurfer? It is imprecise to use the atlases implemented in Freesurfer, isn't it? Thanks for your help Sharmili _________________________________________________________________ http://redirect.gimas.net/?n=M1001xIMFb2 Was machst Du grad bei Facebook? So erfahren es alle im Messenger

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Painting two contrasts simultaneously
by John Gelburg 02 Feb '10

02 Feb '10

Dear all, I am using tksurfer to paint in single subject contrast (step 6 here: http://surfer.nmr.mgh.harvard.edu/fswiki/SpmPainting) However, I would like to see two contrasts simultaneously, like here: http://web.mit.edu/mcgovern/images/News_and_Publications/0512_kanwisher.gif In other words I want to see let's say face selective regions and scene selective regions at the same time. There are many papers, which show it this way, though I suspect they do it BrainVoyager. What is the way to do it FreeSurfer? Thanks for help, John

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segmentation without conform
by magnet scanner 02 Feb '10

02 Feb '10

Hi, Please excuse me if this is an old question. I was wondering if there is a way of not doing conform when segmentation on the whole brain since I am dealing with spectroscopy data and need affine matrix. So I have to make sure the matrix is the same. Thanks, Mag

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unpacksdcm/mri_convert question
by Sebastian Moeller 02 Feb '10

02 Feb '10

Dear List, I got a question/problem regarding unpacksdcmdir and mri_convert (of version 4.5.0 centos4_x86_64). When I unpack the siemens DICOMs (syngo B17, from a recent tim trio) as bshorts, mri_info reports the proper FOV of 96; when I unpack them as nii, I get a wrong FOV of 64 (also the xstart, ystart and zstart are wrong for nii as unpack target). In both cases does the unpack log give 96 as FOV. Is this something to be alarmed about? Should I send example DICOMS? Best Regards & many thanks for the great tools Sebastian -- Sebastian Moeller telephone: 626-395-6713 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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why FreeSurfer Surface Atlas does not contain subcortical region
by Guang Zeng 02 Feb '10

02 Feb '10

Hi, there, Kind of wondering, why FreeSurfer Surface Atlas does not contain subcortical region? Thanks! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/201469228/direct/01/

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Postdoctoral position in multimodal imaging (autism) available
by Herbert, Martha R.,M.D.,Ph.D. 02 Feb '10

02 Feb '10

Postdoctoral position in multimodal imaging (autism) available I would like to make known the availability of a two year postdoctoral position in my laboratory. Strong MRI/DTI/Spectroscopy signal processing analysis skills plus experience with and commitment to multimodal imaging are required; EEG or MEG experience is an advantage. The TRANSCEND Research Program (http://www.nmr.mgh.harvard.edu/transcend/ and www.mghneuro.transcendresearch.org <http://www.mghneuro.transcendresearch.org/> ) performs multimodal imaging and biomaterial collection with a central focus on neurodevelopmental disorders in general, and autism in particular. Our main location is at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org <http://www.martinos.org/> ) which is affiliated with Massachusetts General Hospital, Harvard Medical School and MIT. We have a second location at a clinical site, the Lurie Family Center for Autism where we have a 128 lead EGI EEG in a shielded room as well as a photogrammetry machine. This position will involve analysis of multimodal imaging data, integrating EEG data with multimodal MRI and behavioral data, and collection of new data. Our research projects include MRI (volumetrics, diffusion, MRS, etc.) and MEG (usually on the same subjects allowing coregistration) as well as EEG from early infancy through mid-childhood; the subjects are all carefully phenotyped. We additionally analyze clinical EEG and imaging data. An additional interest in metabolic, toxicological or molecular measures and imaging will be welcomed. The Martinos Center provides ample opportunities for interacting with outstanding colleagues. Please direct any interested members of your lab or anyone else amongst your colleagues or colleagues' labs to write to me at mherbert1(a)partners.org and please cc transcend(a)partners.org. Please forward to any potentially interested colleagues. Thank you. Yours truly, Martha R. Herbert, MD, PhD

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