Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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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Reorientation of raw images?
by chenchunhuichina 02 Feb '10

02 Feb '10

Hello Bruce, and Freesurfers, Sorry for asking an old question, but I really need more confirmation. I am running recon-all to processing my structural data, but i am not sure do I have to reorient the data or not. The data were acquired in sagital view, and dicom data were converted into nift format using dcm2nii, the transformed nii file (called original image below) are in wrong orienation, in fslview, it's X axis is acturally from anterior to posterior, the Y, Z axises were also wrong. dcm2nii also created a o*.nii image, which is in right orientation. I run recon-all using both images, and the results (volume for each region) are a little bit different, about 0.25%, for example, volume of a brain rigion got with original image is 2000 , but got with o*.nii image is 1995. It's not a big problem, but since they are exactly the same data, why the results are not exactly the same? is it better to use original image or even dicom files or to use reoriented data? the resolution of my data is 1*1*2 mm. Another related quetion is, if data are left-right fliped, do I have to flip the raw data and run recon-all again or can I just flip left-right of results, i.e., consider volume got for a left region as that of the corresponding right region? Thank you very much! 2010-02-02 Chunhui Chen _________________ Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人： Bruce Fischl 发送时间： 2010-01-22 12:38:11 收件人： chenchunhuichina 抄送：主题： Re: Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data no, that shouldn't matter On Fri, 22 Jan 2010, chenchunhuichina wrote: > May I ask a related question? > > My structural data are acquired in sagital view, do I have to re-orient it before I run recon-all? In fslview, it's X axis is acturally from anterior to posterior. > > Thanks! > > > 2010-01-22 > > > > chenchunhuichina > > > > 发件人： Bruce Fischl > 发送时间： 2010-01-22 07:06:58 > 收件人： yzhangd(a)artsci.wustl.edu > 抄送： freesurfer(a)nmr.mgh.harvard.edu > 主题： Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data > > How do you know? It should be in the same space. > Bruce > > > > On Jan 21, 2010, at 5:01 PM, yzhangd(a)artsci.wustl.edu wrote: > > > I have run the following command to create a 001.mgz file from raw > > *.dcm > > data: > > > > recon-all -s <subjid > -i <path to *.dcm data > > > > > The output 001.mgz file is not in the same native space as the > > original > > *.dcm data. Could anyone tell me what space the 001.mgz file is in? > > Does > > the above command change the orientation (i.e does it rotate/ > > translate) > > besides simply converting from .dcm to 001.mgz > > > > thanks a lot > > > > yuning > > > > > > _______________________________________________ > > 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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Re: [Freesurfer] Reorientation of raw images?
by chenchunhuichina 02 Feb '10

02 Feb '10

in some regions like left amygdata, the difference exceed 5% 2010-02-02 Chunhui Chen _________________ Institute of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 发件人： Bruce Fischl 发送时间： 2010-01-22 12:38:11 收件人： chenchunhuichina 抄送：主题： Re: Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data no, that shouldn't matter On Fri, 22 Jan 2010, chenchunhuichina wrote: > May I ask a related question? > > My structural data are acquired in sagital view, do I have to re-orient it before I run recon-all? In fslview, it's X axis is acturally from anterior to posterior. > > Thanks! > > > 2010-01-22 > > > > chenchunhuichina > > > > 发件人： Bruce Fischl > 发送时间： 2010-01-22 07:06:58 > 收件人： yzhangd(a)artsci.wustl.edu > 抄送： freesurfer(a)nmr.mgh.harvard.edu > 主题： Re: [Freesurfer] Orientation of 001.mgz versus raw dicom data > > How do you know? It should be in the same space. > Bruce > > > > On Jan 21, 2010, at 5:01 PM, yzhangd(a)artsci.wustl.edu wrote: > > > I have run the following command to create a 001.mgz file from raw > > *.dcm > > data: > > > > recon-all -s <subjid > -i <path to *.dcm data > > > > > The output 001.mgz file is not in the same native space as the > > original > > *.dcm data. Could anyone tell me what space the 001.mgz file is in? > > Does > > the above command change the orientation (i.e does it rotate/ > > translate) > > besides simply converting from .dcm to 001.mgz > > > > thanks a lot > > > > yuning > > > > > > _______________________________________________ > > 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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FreeSurfer & Matlab
by Raghav Puranmalka 01 Feb '10

01 Feb '10

Hi all, I am working on a project that aims to: (1) Use an MRI image, skullstrip and convert the brain volume to a surface (2) Import that surface onto Matlab and visualize it there. (3) On top of that surface in Matlab, add pictures of electrodes as well as 3D "heat maps" of neural activity. It seems that FreeSurfer may be an option for me. I have a few questions that I have been unable to find the answers to: (1) Can one visualize the surface created by FreeSurface in Matlab? If so, would somebody be able to point me to the documentation? (2) Can one start the freesurfer from Matlab? It seems that the matlab files that come with freesurfer are more for reading and writing data rather than using/starting the freesurfer binaries. Thanks for your help! Best, Raghav Raghav Puranmalka Candidate B.S. Engineering | Major: Bioengineering Candidate M.S. Engineering | Major: Bioengineering SEAS | University of Pennsylvania raghav.puranmalka(a)gmail.com

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Freesurfer