Freesurfer

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30091 discussions

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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Checking raw dicom files
by qtnguyen＠nmr.mgh.harvard.edu 04 Apr '13

04 Apr '13

Dear Freesurfer experts, After I ran the functional to structural registration using the bbregister command, it looks like the dorsal part of the brain for this participant is cut off in the BOLD images. When we ran the scan, we made sure that the slice prescription covered the entire brain. We also looked at the functional scan in the control room right after the scan and it looked ok. We aren't sure what went wrong and why the bold data is cut off. Is there any way I can look at the raw dicom files to check if it includes the entire brain? Thank you, Trang

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faster wfile reading in matlab
by Keith Jamison 04 Apr '13

04 Apr '13

I noticed it was taking 6-7 seconds to read in a wfile (scalar surface overlay) into matlab using fast_read_wfile.m. In case anybody else finds this annoying, here's a faster alternative that produces identical output: in fast_read_wfile.m, replace everything after the first fread line with: vnum = fast_fread3(fid) ; % Number of non-zero values A = uint32(fread(fid,vnum*7,'uchar')); fclose(fid); v = bitshift(A(1:7:end), 16) + bitshift(A(2:7:end),8) + A(3:7:end); w0 = bitshift(A(4:7:end),24) + bitshift(A(5:7:end),16) + bitshift(A(6:7:end),8) + A(7:7:end); w = zeros(max(v),1); w(v+1) = typecast(w0,'single'); -Keith

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R: Re: R: Re: cortical thickness normalization
by stdp82＠virgilio.it 04 Apr '13

04 Apr '13

I'm sorry. I'm performing the cortical thickness analysis on three groups (2 pathological groups and 1 control group). I'm interested mainly to the differences between the two groups of disease. These are my questions: 1- Is qdec a good option for my study design or I should use other glm option that contains all 3 groups in the same matrix design? 2-As you suggest I'm using always mean cortical thickness as nuisance factor in qdec. If I'd like added 2 or more covariates, is correct if I add each covariate separately in my matrix.dat or I should add all covariates together in my matrix.dat? Thanks, Stefano ----Messaggio originale---- Da: mharms(a)conte.wustl.edu Data: 4-apr-2013 18.23 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: cortical thickness normalization Hi,Sorry, but I don't understand what you're asking. -MH -- Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <stdp82(a)virgilio.it> Reply-To: <stdp82(a)virgilio.it> Date: Thursday, April 4, 2013 9:31 AM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] R: Re: cortical thickness normalization Thank you very much, Michael! I have just an other important question, please. I'm performing cortical thickness analysis on three groups. One of this is a control group and I'm using it as support because I'm interested only to difference between the two groups of disease. These are my questions: 1- Is correct if I'm applying qdec, testing before a) disease 1 vs disease 2; b) controls vs disease 1 and c) controls vs disease 2. 2- Addictionally to cortical thickness that I'm reporting always as nuisance factor in qdec, I'd test some covariates. Taking in account my study design, could I test each covariates separately on my model using qdec? Thanks, Stefano ----Messaggio originale---- Da: mharms(a)conte.wustl.edu Data: 4-apr-2013 15.45 A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] cortical thickness normalization If you're studying thickness, I'm a fan of using mean cortical thickness as the covariate (since thickness is what you're studying). I've posted on this in the past. cheers,-MH -- Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <stdp82(a)virgilio.it> Reply-To: <stdp82(a)virgilio.it> Date: Thursday, April 4, 2013 7:21 AM To: <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] cortical thickness normalization Hi list, I'm reading a lot of post on this list about cortical thickness normalization. I' m noting very different results on my data when I use mean thickness or ICV as nuisance factor than no factor. I'm confuse on this topic, could you advise the best way, please? Thanks, Stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://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 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.

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Permutation doubts
by Gabriel Gonzalez Escamilla 04 Apr '13

04 Apr '13

4 4

Re: [Freesurfer] Projection of markers from the scalp to cortical surfaces
by Douglas Greve 04 Apr '13

04 Apr '13

When you say it does not work, what do you mean? Did it not put the label in the right place? The number of vertices in the output label may be much less than in the input. label2label just finds the vertex that is closest to each label point. A multiple input label points may map to a single output label. doug On 4/3/13 4:24 PM, Eleonora Maggioni wrote: > Dear Doug, > thank you for the suggestion. > I used the new file that you sent me exactly as in the example 4, but > the labels which are effectively translated into the nearest vertex > surface labels are few. > I first selected the marker labels on the T1 image within tkmedit. As > the labels are outside the head volume, I put the maximum distance > --paint as 50 mm, to be sure that the distance is sufficient to find a > surface vertex. But anyway is still does not works. > Can this be due to the external position of the markers? Which kind of > projection is done by mri_label2label? > Thank you for your support! > > Eleonora > > 2013/4/2 Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > > Hi Eleonora, > > the easiest way to do this is to create a label of the electrodes, > then > use mri_label2label to map them to the nearest pial vertices. This > ability to map volume labels to nearest surface vertices is broken in > the current version. I've fixed this and put a new version here: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2lab… > > Run it with --help and use Example 4. > doug > > > > On 04/02/2013 08:19 AM, Eleonora Maggioni wrote: > > Hi Freesurfer experts, > > I am new to FreeSurfer and I have a question. > > I have markers of EEG electrodes on the T1 image of a subject and I > > want to project them from the scalp to his pial surface (that I > > reconstructed using the standard procedure). > > To do so, I manually selected the central point of each marker in > > tkmedit and I defined a control point. Then I red that control point > > with tksurfer on the corresponding pial surface. This should be the > > projection to the pial surface: is this procedure correct? If > yes, in > > which coordinate system is the projection made? > > Thank you in advance, > > Kind regards, > > > > -- > > Eleonora Maggioni > > > > BioEngineering PhD student > > Politecnico di Milano > > Istituto E.Medea, Bosisio Parini (LC) > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > > > > -- > Eleonora Maggioni > > BioEngineering PhD student > Politecnico di Milano > Istituto E.Medea, Bosisio Parini (LC) >

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