[Freesurfer] How to transfer the VTK cortical surface to the diffusion space?
Hi there! Since this is my first time using FreeSurfer, I found it quite challenging to get the handle on the different coordinate systems used. My goal is to generate vtk files where the vtk cortical surface and the vtk fiber tracts are in the same space (for one individual subject). Basically, I used recon-all to generate the cortical surfaces and trac-all to generate dtifit_FA.mgz and dtifit_V1.mgz for tractography in the original diffusion space. I used the transformation matrices generated in dmri/xmfs to transfer the cortical surface into the diffusion space, but not of them seem to work. What I find quite confusing is that when I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to lh.pial.vtk and brainmask.mgz to brainmask.mha and visualize them using Paraview, they are in different spaces. To do so, I used the command line mri_surf2surf so the surface will overlay with brainmask.mha image when using Paraview, but none of the transformation matrices seems to warp the surface onto the anatomical (structural FreeSurfer) space. I also tried to warp it to the diffusion space and the anatomical original space, but it never overlapped with the images nested in these respective spaces. It is always floating somewhere else! I would like to know which transformation I need to: 1. apply to have the VTK surface overlap with the brainmask.mha image in the anatomical space and, 2. apply another transformation to transfer the VTK surface to the diffusion space where I perform tractography. Also, does TRACULA perfom whole brain tractography? I really appreciate your help! Kindly, Islem ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Questions about surface coordanates
Hi all, I have a similar problem using Paraview: When I visualize the surface lh.pial and the anatomical image brainmask.mgz using FreeView they nicely overlap; however, after I convert lh.pial to lh.pial.vtk and brainmask*.mgz* to brainmask*.mha* and visualize them using Paraview, they are in different spaces. Do I need to apply a transformation matrix to lh.pial using the command line mri_surf2surf so the VTK surface will overlap with the image when using Paraview? I find this quite confusing. Thanks! Kindly, Islem On Tue, Aug 30, 2016 at 9:21 AM, Douglas Greve wrote: > tksurfer always uses the ?h.orig coordinates. Also keep in mind that the > vertex index is 0-based whereas matlab is 1-based. When you click on a > point, you should see something like the following print out > selected vertex 123491 out of 163842 > current -39.11 15.65 11.26 > orig -55.67 -10.37 19.95 > pial 0.00 0.00 0.00 > white-55.76 -10.29 19.93 > > > > > On 8/30/16 5:12 AM, Dongnandi wrote: > > Dear Experts, > > I tried to extract vertex coordinates information from > ‘fsaverage/surf/lh.pial’ file using matlab function ‘read_surf’, but I > found that the coordinates returned by the function are different from what > I saw in tksurfer, here are the screenshots: > > The vertex index starts from 0 in tksurfer, so I select the second > elements in matlab. Why is the result different from what has been shown in > tksurfer(also different in freeview)? Which one should I report? > > Is there any way to transform the surface coordinates to the MNI152 space? > > > > Thank you very much! > > Dong > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Dr. Islem Rekik; MSc, PhD IDEA Lab, UNC-Chapel Hill Biomedical Research Imaging Center Chapel Hill, NC 27599 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Call for Papers: Connectomics in NeuroImaging Workshop at MICCAI 2018, Granada (Spain)
External Email - Use Caution Hello Colleagues, The attached call for full-length papers flyer provides information about the 2nd International Workshop on Connectomics in NeuroImaging (*CNI 2018*), which will be held in parallel with the 21st International Conference on Medical Image Computing and Computer-assisted Intervention (MICCAI 2018) in Granada Spain. CNI 2018 is a full day workshop that will take place September 20th, 2018. Our topics of interest cover (but are not limited to): (1) New developments in connectome construction from different imaging modalities, (2) Development of data driven techniques to identify biomarkers in connectome data, (3) Brain network modeling and formal conceptual models of connectome data, (4) Machine learning algorithms and connectome data analysis, and (5) Evaluation and validation of connectome models. If you have research that fits into the scope of our workshop detailed on our website ( http://munsellb.people.cofc.edu/cni.html), we encourage you to submit a paper or an abstract! *** Why submit to the CNI workshop? *** - Three great keynote speakers, presentations and poster sessions with accompanying power pitches will provide you with ample opportunity for exchanges and discussions; - There will be an INCF sponsored Best Paper Award; - Accepted papers will be published in an LNCS proceedings and will be invited to submit to a special issue journal; - Discuss your science and collaborate with international computational neuroscientists and clinicians in an intimate setting. *** Full length paper submission *** Paper submission deadline, June 11 via https://cmt3.research.microsof t.com/CNI2018 *Download flyer using*: http://basira-lab.com/wp-content/uploads/2018/04/CNI-MICCAI-2018.tiff <http://basira-lab.com/wp-content/uploads/2018/04/CNI-MICCAI-2018.tiff> For more information visit http://munsellb.people.cofc.edu/cni.html *** Full length important dates *** Submission deadline: 11:59 PM PST, June 11th, 2018 Notification of acceptance: July 2nd, 2018 Camera-ready deadline: 11:59 PST, July 16th, 2018 Workshop date: Sept. 20th, 2018 *Also, if you know other colleagues that may be interested in submitting a full length paper, please feel free to pass along our workshop information to them. * We look forward to your participation! If you have any additional questions, please contact Brent Munsell ( munse...@cofc.edu) or Ai Wern Chung (aiwern.ch...@childrens.harvard.edu) = CNI 2018 Chairs Islem Rekik, University of Dundee Ai Wern Chung, Boston Children's Hospital, Harvard Medical School Markus Schirmer, Harvard Medical School Guorong Wu, University of North Carolina, Chapel Hill Brent Munsell, College of Charleston ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Call for PRIME-MICCAI 2018 papers **1st International Workshop on PRedictive Intelligence in MEdicine **
External Email - Use Caution Dear all, We present the 1st edition of the *PR*edictive *I*ntelligence in *ME*dicine (*PRIME*) workshop in conjunction with *MICCAI 2018* in Granada, Spain. The main aim of PRIME is to propel the advent of predictive models in a broad sense, with application to medical data. We hope that PRIME workshop becomes a nest for high-precision predictive medicine, one that is set to transform multiple fields of healthcare technologies in unprecedented ways. We welcome contributions fitting the following research topics (*but not limited to*): Modeling and predicting disease development or evolution from a limited number of observations; Computer-aided prognostic methods (e.g., for brain diseases, prostate cancer, dementia, acute diseases, neurodevelopmental disorders); Forecasting disease/cancer progression over time; Predicting low-dimensional data (e.g., behavioral scores, clinical outcome, age, gender); Predicting the evolution or development of high-dimensional data (e.g., shapes, graphs, images, patches, abstract features, learned features); Predicting high-resolution data from low-resolution data; Predicting image modality from a different modality (e.g., data synthesis); Predicting missing data (e.g., data imputation or data completion problems). - *** Paper Submission *** Paper submission deadline, June 11 via https://cmt3.research. microsoft.com/PRIME2018 <https://cmt3.research.microsoft.com/PRIME2018> <https://cmt3.research.microsoft.com/PRIME2018> For more information visit http://tiny.cc/prime2018 <http://tiny.cc/prime2018> <http://tiny.cc/prime2018> *Flyer (if not attached, **check)*: http://basira-lab.com/wp- content/uploads/2018/01/PRIME-MICCAI_2018_flyer_final.pdf <http://basira-lab.com/wp-content/uploads/2018/01/PRIME-MICCAI_2018_flyer_final.pdf> <http://basira-lab.com/wp-content/uploads/2018/01/PRIME-MICCAI_2018_flyer_final.pdf> - *** Important dates *** - Paper submission deadline: June 11, 2018 - Author notification: July 15, 2018 - Camera-ready: July 20, 2018 - Workshop date: September 16, 2018 - *** Keynote Speakers *** Prof Dinggang Shen (University of North Carolina) Dr Ender Konukoglu (ETH Zurich) Dr Ipek Oguz (University of Pennsylvania) Dr Kilian M. Pohl (Program Director in the Center of Health Sciences at SRI International) - *** Highlights *** - Proceedings will be published in *Springer Lecture Notes in Computer Science (LNCS)* (EI, ISTP indexed). - The PRIME 2018 *Best Paper Award* will be granted to the best overall scientific paper. If you have any questions, please contact me, Islem Rekik at ire...@dundee.ac.uk Please feel free to forward this email to those who might be interested. We are looking forward to your PRIME submissions! Sincerely, The PRIME 2018 Chairs -- Islem Rekik (University of Dundee, UK), Point of Contact: ire...@dundee.ac.uk Gozde Unal (Istanbul Technical University, Turkey) Ehsan Adeli (Stanford University, US) Sang-Hyun Park (Daegu Gyeongbuk Institute of Science and Technology, South Korea) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
