Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

Re: [Freesurfer] mri_aparc2aseg issue
by Paul Beach 06 Apr '13

06 Apr '13

Hi Freesurfers, I'm currently trying to take manually made ROIs (label files) that have been incorporated into new annotation files (one for each hemisphere - rh.aug_aparc.annot & lh.aug_aparc.annot) and turn them into a new (augmented) annotation into a aseg file (an aug_aparc+aseg.mgz file). To do so I've been using the mri_aparc2aseg command and, at face value, it works well. However, some of my ROIs (specifically my insular ROIs) are being either shifted or lost in the transition from annotation to segmentation. Note that each hemisphere's new annotation files look perfect on tksurfer (which is where they were originally drawn). It's only when I try and make them fill the full cortical ribbon with the mri_aparc2aseg command that I get this issue. I piloted everything out on averaged subject and it all worked perfectly. However, when I attempted things on individual subject data I received the problem described above. I've attached a picture illustrating the discrepancy between the an averaged subject and a single subject. I have also attached my script code. The overall goal is to create a gmroi_volume which will allow me to determine an aux number of each manual ROI so as to export each one to AFNI space. I'd *really* appreciate help on how to fix this. Thanks, Paul -- Paul Beach DO/PhD candidate - Year V Michigan State University

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bblabels??
by Anupa AV 06 Apr '13

06 Apr '13

Hello experts, I'm in a process to make coronal cuts using tksurfer Please help me with the following questions: 1. How to map the label(merged) to fsaverage? 2. How to use bblabels? 3. How to map back to the individuals? What is the coomand line function used for the above questions? Any help will be appreciated.!!

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Error map
by Valtina Pouegue 06 Apr '13

06 Apr '13

Hi, I am looking for a tool of FreeSurfer. In fact, the tool is supposed to take in input 2 surfaces ( hemispheres) of subjects, registrate the surfaces and display the difference between the 2surfaces ( like 'euclidian distance'). What I want is exactly that output (http://www.sciencedirect.com/science/article/pii/S1053811909010064) availablein this article (http://www.sciencedirect.com/science/article/pii/S1053811909010064).Do you know the tool in question ?Thanks,VP

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R: Re: R: Re: incomplete tracts
by stdp82＠virgilio.it 05 Apr '13

05 Apr '13

Hi Anastasia, yes, for some subject the low-b volume is in the end.Some subjects have again incomplete tracts.I'm attacking an example of configuration file that I'm using.I hope that you can check it please. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 5-apr-2013 18.45 A: <stdp82(a)virgilio.it> Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] incomplete tracts Hi Stefano - In your case we determined that the ones that had the low-b volume in the end didn't run correctly, right? In that case, I didn't need to see anything, you were going to try running 5.2. a.y On Fri, 5 Apr 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > could I send you the data of a subject that I don't run correctly? > > I still have some subjects with tracts incomplete and I do not know if it depends from > my analysis or whether the images are not good. > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 5-apr-2013 17.37 > A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] incomplete tracts > > > Hi Gerit - If it's not an issue with the gradient table but instead a > tractography initialization issue, I strongly recommend running 5.2 with > bbregister for the registration (which is the default in 5.2 anyway). > > You can also upload an example data set with issues (include: dmri, > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > Hope this helps, > a.y > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > > > Dear Anastasia, > > > > thanks for the help. There is also a line option in freeview. However we still have > > brains with missing tracks, I rerun them with increasing the ncpts and registering > to > > bbr (since that is default in Tracula 5.2.). We are reasonable confident that our > bvel > > and bvac are correct, since we have roughly 20 cases out of 90 processed brains > where > > there are no missing tracts. Further sometimes only one tract is missing, sometimes > it > > is more severe. We could not find any correlation with recon-all problems or DTI raw > > data issues (all but one were without moving artefacts). Since we are running > bedpostx > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) might it be an > issue > > that is solved with installing the 5.2. version? Would that run in freesurfer 5.1.0? > > I guess we need to change the dcmrirc files only a bit. > > > > Kind regards > > Gerit Pfuhl > > > > > > On 3 April 2013 16:59, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > Hi Benjamin - I'd look in a coronal view to see if the lines in the corpus > > callosum follow the curvature of the corpus callosum, and in a sagittal > > view to see if the lines in the cingulum follow the curvature of the > > cingulum. Does this make sense? > > > > a.y > > > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > > > Dear Anastasia, > > > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because our > > gradient table is wrong but I am not really sure how to analyse > > these informations. You wrote to Stefano the lines have to point in > > the right direction and that the eigenvectors are not pointing along > > his corpus callosum. Can you give me a more detailed description > > what I have to do when I dislpay dtifit_V1 as lines, overlaid on > > dtifit_FA. > > > > Thanks and kind regards > > Benjamin > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. > > > > > > > > > > -- > > http://gerit-orientation.blogspot.com > > http://team-arzgebirg.blogspot.com > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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R: Re: incomplete tracts
by stdp82＠virgilio.it 05 Apr '13

05 Apr '13

Hi Anastasia, could I send you the data of a subject that I don't run correctly? I still have some subjects with tracts incomplete and I do not know if it depends from my analysis or whether the images are not good. Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 5-apr-2013 17.37 A: "Gerit Pfuhl"<gerit.pfuhl(a)gmail.com> Cc: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] incomplete tracts Hi Gerit - If it's not an issue with the gradient table but instead a tractography initialization issue, I strongly recommend running 5.2 with bbregister for the registration (which is the default in 5.2 anyway). You can also upload an example data set with issues (include: dmri, dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Hope this helps, a.y On Fri, 5 Apr 2013, Gerit Pfuhl wrote: > Dear Anastasia, > > thanks for the help. There is also a line option in freeview. However we still have > brains with missing tracks, I rerun them with increasing the ncpts and registering to > bbr (since that is default in Tracula 5.2.). We are reasonable confident that our bvel > and bvac are correct, since we have roughly 20 cases out of 90 processed brains where > there are no missing tracts. Further sometimes only one tract is missing, sometimes it > is more severe. We could not find any correlation with recon-all problems or DTI raw > data issues (all but one were without moving artefacts). Since we are running bedpostx > outside of trac-all (i.e. trac-prep then bedpostx then trac-path) might it be an issue > that is solved with installing the 5.2. version? Would that run in freesurfer 5.1.0? > I guess we need to change the dcmrirc files only a bit. > > Kind regards > Gerit Pfuhl > > > On 3 April 2013 16:59, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Benjamin - I'd look in a coronal view to see if the lines in the corpus > callosum follow the curvature of the corpus callosum, and in a sagittal > view to see if the lines in the cingulum follow the curvature of the > cingulum. Does this make sense? > > a.y > > On Wed, 3 Apr 2013, Roschinski, Benjamin wrote: > > Dear Anastasia, > > we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because our > gradient table is wrong but I am not really sure how to analyse > these informations. You wrote to Stefano the lines have to point in > the right direction and that the eigenvectors are not pointing along > his corpus callosum. Can you give me a more detailed description > what I have to do when I dislpay dtifit_V1 as lines, overlaid on > dtifit_FA. > > Thanks and kind regards > Benjamin > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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. > > > > > -- > http://gerit-orientation.blogspot.com > http://team-arzgebirg.blogspot.com > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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MNI template
by Chrysa Lithari 05 Apr '13

05 Apr '13

Hi FreeSurfers, I want to obtain a template mri annotated according to the Destrieux atlas. I found an mgz file in FreeSurfer/subjects/cvs_avg35_inMNI152/aparc.a2009s+aseg.mgz. I read it with a FieldTrip function (ft_read_mri) and I get an atlas with 16777216 voxels. On the other hand, when I read the annotation files (?h.aparc.a2009s.annot), I get 16399385 voxels. Can anybody help me by indicating the correct file? I am also confused if the file should be an annot file or an mgz one. I am quite ignorant but I hope I am clear enough. thank you in advance, Chrysa -- Chrysa Lithari, PhD CIMeC - Center for Mind/Brain Sciences Via Delle Regole 101, 38123 Mattarello Trento, Italy tel. +39 0461 283083

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incomplete tracts
by Roschinski, Benjamin 05 Apr '13

05 Apr '13

Dear Anastasia, we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because our gradient table is wrong but I am not really sure how to analyse these informations. You wrote to Stefano the lines have to point in the right direction and that the eigenvectors are not pointing along his corpus callosum. Can you give me a more detailed description what I have to do when I dislpay dtifit_V1 as lines, overlaid on dtifit_FA. Thanks and kind regards Benjamin

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Cannot login to CVS repo
by Chris Roat 05 Apr '13

05 Apr '13

$ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login Logging in to :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:2401/usr/fscvsroot CVS password: [hidden] cvs [login aborted]: connect to fsvm.nmr.mgh.harvard.edu(155.52.242.23):2401 failed: Connection timed out Is this a known problem?

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Five PhD positions are available in Brainnetome Center
by Yong Liu 05 Apr '13

05 Apr '13

Dear all, Five PhD positions are available in our lab, the deadline for the first round is April 15. Please find the details below: http://www.brainnetome.org/job-bulletin.html *Job1: PhD Positions are available in Neuroimaging and Brainnetome* Applications close: *April 15th, 2013* for the first round. *CAS-TWAS President’s Fellowship Programme Downlod<http://www.brainnetome.org/job/01_fellowship.docx> * *APPLICATION FORM FOR CAS-TWAS PRESIDENT’S FELLOWSHIP PROGRAMME Download<http://www.brainnetome.org/job/02_fellowship_form.docx> * *UCAS Admission Application Form Download<http://www.brainnetome.org/job/03_admission_form.docx> * ** Five PhD positions are available at Brainnetome Center of CASIA to utilise neuroimaging technologies to discover mechanisms of brain wiring. These positions will be supported by CAS-TWAS President’s Fellowship Programme for PhD Candidates from Developing Countries and other grants. They involve developing neuroimage analysis methods and tools and applying them to neuroscience and clinical problems. In this role the students will develop skills in developing computational algorithms and computer programming in neuroimage analysis that could be utilised in both basic research and clinical areas. The Person Applicants should meet the requirements of “CAS-TWAS President’s Fellowship Programme for PhD Candidates from Developing Countries” and have MSc degree in one of the following fields: mathematics, physics, neuroimaging, computer science, electronic engineering, neurobiology, psychology, cognitive neuroscience, psychiatry, and neurology. Outstanding C/C++ programming skills in Linux are highly desired. Enquiries Please contact Professor Tianzi Jiang at jiangtz(a)nlpr.ia.ac.cn . In order to complete the form application process, please fill in the - Fellowship form(www.brainnetome.org/job/02_fellowship_form.docx) - Admission form (www.brainnetome.org/job/03_admission_form.docx) Applications close: *April 15th, 2013* for the first round. ------------------------------ *Job2: Faculty Members in Brainnetome Center* Brainnetome Center is a new founded department of Institute of Automation of the Chinese Academy of Sciences (CASIA). It consists of 15 faculty members and more than 30 PhD students. Researchers at the Brainnetome Center work on a wide topics in neuroimaging and brainnetome, such as, Basic Theory of Brain Netowks, Equipments and Technologies of Brain Netowks, Simulating and Modeling Brain Networks, and Translational Medicine Based on Brainnetome, to discover the molecular, cellular, and brain network mechanisms that underlie the ability of the brain to function. In 2013, Brainnetome Center seeks 5 faculty members from assistant to full professor levels in neuroimaging, neuroscience, neuroanatomy, neuropsychiatry and related fields. We specifically seek individuals with expertise in one of the following fields: magnetic resonance imaging, especially diffusion MRI and functional MRI, optical imaging, medical image processing and analysis, pattern recognition and supercomputing. The candidates with expertise in psychology, cognitive neuroscience, physics and mathematics are also welcome. A PhD in a relevant field is required. Brainnetome Center (www.brainnetome.org ) at CASIA has established its international reputation in neuroimaging, brain networks, and their applications in mental diseases. It also has established strong collaboration networks with a number of prestigious national and international laboratories and hospitals through brainnetome consortium ( www.brainnetome.org ). The faculty members have chance to work in an Australian partner laboratory on Neuroimaging and Brainnetome at Queensland Brain Institute (www.qbi.uq.edu.au) For the outstanding candidates, we will assist them to obtain the support from the Hundred Talents Program of the Chinese Academy of Sciences or Program of Global Experts. Interested individuals are encouraged to contact with Professor Tianzi Jiang, for further information and informal enquiry at +86 10 82614469. Applicants should send an e-mail attachment of full dossiers, including a curriculum vita, statement of research goals, and pertinent preprints and publications to jiangtz(a)nlpr.ia.ac.cn<jiangtz(a)nlpr.ia.ac.cn?subject=jiangtz> or tainzi.jiang(a)gmail.com <tianzi.jiang(a)gmail.com?subject=tianzi.jiang> for the first screen. The search will continue until all the positions are filled. -- Best wishes. -------------------------------------------------------------------- Liu Yong Brainnetome Center National Laboratory of Pattern Recognition (NLPR) Institute of Automation, Chinese Academy of Sciences (CASIA) www.brainnetome.org/yongliu

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PhD position available at Aix-Marseille University
by Olivier Coulon 05 Apr '13

05 Apr '13

Dear all, please find below a PhD position offer: _PhD position:_ shape analysis applied to neuroimaging. The LATP (http://latp.univ-mrs.fr) and LSIS (http://www.lsis.org) labs, Aix-Marseille University, France, are seeking a candidate for a PhD in the field of shape analysis applied to neuroimaging. _Candidate_: We are looking for an excellent Ph.D. candidate with a good background in applied mathematics and/or image analysis as well as an interest for neuroimaging. A minimum level of programming skills is required (Matlab, Python, C++). The applicant must have completed Master studies in applied mathematics, computer science, or image analysis prior to starting the program. Excellent academic results during the Master studies are required. The candidate is expected to start in September-October 2013. _Context_: The project is part of a collaboration between the two laboratories which will provide a co-supervision of the PhD student. The LATP lab is a fundamental and applied mathematics lab based in Marseille that includes a team specialised in probabilities, statistics, and signal processing. The LSIS lab is a computer science and information technology lab that includes a team specialised in image analysis with many years of experience in neuroimaging. _Salary_: roughly 1600EUR/month (before tax but including health insurance, social security and fees) _Project_: The project is dedicated to the study of shape representations and distances between shapes. In particular, shape representations using directly the surface of the shapes, such as currents, and those using scalar maps describing the geometry of the shapes, such as Laplacian eigenfunctions, curvelets or shearlets, need to be compared. Their ability to capture global, local, or multiscale directional information is of particular interest. The goal is to produce methods that can be used to perform cortical morphometrics and characterize cortical folding patterns. Both labs can provide a solid theoretical environment and access to large databases of neuroimaging data. _Information and applications:_ Please send your application including your CV with a letter of motivation, and a list of courses you followed with grades and evaluations to frederic.richard(a)univ-amu.fr <mailto:frederic.richard@univ-amu.fr> julien.lefevre(a)univ-amu.fr <mailto:julien.lefevre@univ-amu.fr> olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univ-amu.fr> -- signatureMail2011 Olivier Coulon, CNRS research Fellow, Head of the Images&Models team olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univmed.fr> Tel: +33491828527 fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr <http://olivier.coulon.perso.esil.univmed.fr/> LSIS Laboratory, I&M Team ESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE BrainMorph logo http://www.lsis.org/brainmorph

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