Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Announcement of HBM satellite conference on the DMN and other Intrinsic Networks
by Erick Jorge Canales 28 Apr '10

28 Apr '10

Dear FreeSurfer list, Just to let you know that soon it will be a conference on the Default Mode and other intrinsic networks in Barcelona. It is a satellite of the HBM conference. Please, take a look at the program (see links below) since many interesting people are comming to present their latest results and developments on brain networks. I hope you come too, Raymond Salvador Dear Sir / Madam, It is our pleasure to announce the congress *"Default Mode Network and other Intrinsic Networks in health and disease"* to be held in St. Boi de Llobregat (Barcelona, Spain) on *June 4th and 5th, 2010.* The Scientific Committee has put together an ambitious and attractive programme for professionals in neuroimaging, psychiatry and neuroscience. This congress will be a previous activity to the *"16th Annual Meeting of the Organization for Human Brain Mapping" *which will take place in Barcelona between the 6th and 10th of June, 2010. With some of the world’s leading experts speaking, we are confident that the meeting will provide a unique opportunity to broaden our knowledge and formulate future perspectives in this rapidly developing field. In the following link you can find the preliminary programme: Preliminary Programme <http://www.viajesiberiacongresos.net/Default/> If you would like to register on-line, please use the following link: On-line Registration<https://events.viajesiberiacongresos.com/ei/getdemo.ei?id=412&s=_1W010OXRL> Fo rmore information visit the website: http://www.defaultmodenetwork.com/ We hope to see you soon! Estimado Sr. / Sra., Es para nosotros un placer comunicarle que los próximos días *4 y 5 de junio de 2010* se celebrará en St. Boi de Llobregat (Barcelona) el congreso *"Red Neuronal por Defecto y otras redes intrínsecas en la salud y la enfermedad". * El Comité Científico ha elaborado un ambicioso y atractivo programa para los profesionales en neuroimagen, psiquiatría y neurociencias. Este Congreso será un acto previo al *"16th Annual Meeting of the Organization for Human Brain Mapping"*, que se celebra en Barcelona los días 6 a 10 de junio de 2010. Estamos seguros de que este Congreso, con la presencia de los más destacados especialistas de todo el mundo va a brindarnos una ocasión única para profundizar en el conocimiento y en las perspectivas futuras en esta área en constante evolución. En el siguiente enlace encontrará el programa preliminar del congreso: Programa Preliminar <http://www.viajesiberiacongresos.net/Default/> Si desea realizar su inscripción on-line, puede hacerlo a través del siguiente enlace: Formulario On-Line<https://events.viajesiberiacongresos.com/ei/getdemo.ei?id=412&s=_1J80RK61R> Para más información visite la web: http://www.defaultmodenetwork.com/ Le esperamos! <congresos.barcelona(a)viajesiberia.com> Technical Secretariat: *VIAJES IBERIA CONGRESOS* c/Pallars 193 - 2nd Floor 08005 - Barcelona, Spain Tel. +34 93 510 10 05 Fax. +34 93 510 10 09 congresos.barcelona(a)viajesiberia.com * * ------------------------------ Este mensaje se dirige exclusivamente a su destinatario y puede contener información privilegiada o confidencial. Si no es vd. el destinatario indicado, queda notificado de que la utilización, divulgación y/o copia sin autorización está prohibida en virtud de la legislación vigente. Si ha recibido este mensaje por error, le rogamos que nos lo comunique inmediatamente por esta misma vía y proceda a su destrucción. Aquest missatge va dirigit exclusivament al seu destinatari i pot contenir informació privilegiada o confidencial. Si vosté no és el destinatari indicat, li notifiquem que la utilització, divulgació i/o còpia sense autorització està prohibida en virtud de la legislació vigent. Si ha rebut aquest missatge per error, li preguem que ens ho comuniqui el més aviat possible.

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Saving time in longitudinal processing
by Jordan Poppenk 27 Apr '10

27 Apr '10

Dear list, I am about to start processing a largish longitudinal dataset and wondered whether I could save some processing time in the following ways: 1) I have seen written in a few places that only norm.mgz is used from the cross-sectional stream during base template creation at the next stage. Does that mean I can run "-autorecon1" only on each of the timepoints during the cross-sectional processing stage rather than "-all"? 2) As I am only interested in the subcortical output of the longitudinal processing, can I include the flags "-autorecon1 -subcortseg" in all remaining steps in the longitudinal stream to skip cortical processing, or will that cause problems? Thanks for your help, Jordan

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fail to open .mgz data in tkmedit: DICOM image data in the sagittal view
by liyari5018 27 Apr '10

27 Apr '10

hi FS experts, FS can't recognize the file which was covert from a DICOM data in sagital view, here is an example of failure：（see the annex for more detail ） root@lijin-desktop:/usr/local/freesurfer/subjects/fuzhou_test# tkmedit bai_hong_jun mri/orig/001.mgz ERROR: cannot find /usr/local/freesurfer/subjects/fuzhou_test/bai_hong_jun/mri/mri/orig/001.mgz Error: Loading volume mri/orig/001.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. how can i do to solve this problem? thanks for your reply! LJ

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recon-all error autorecon3
by Antoine Leflon 27 Apr '10

27 Apr '10

hi , I was processing autorecon3 and it screened me this error : #@# Cortical ribbon mask Tue Apr 27 19:44:20 IST 2010 /home/cami/freesurfer/subjects/ant/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance ant mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux pride 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Tue Apr 27 19:44:20 IST 2010 ______________________________________________________________________ Is it something important ? Antoine

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Problem adding control points
by Sasa Kivisaari 27 Apr '10

27 Apr '10

Dear FreeSurfers, I'm a postgraduate student and recently started with FreeSurfer. I have problems adding control points to the volumes I have loaded into tkmedit. For some reason, after selecting the Edit Control Points -tool and clicking the white matter voxels, I do not get the green crosses I should. Instead, I see a red cross (the same I get when I choose e.g. the edit voxels tool), which disappears after clicking another voxel. No control points are saved, although I'm able to create the control.dat file. I'm running Freesurfer on Mac Snow Leopard. Thank you for your help! Sincerely, Sasa Kivisaari

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missing stats files
by Rajagopalan, Venkateswaran 27 Apr '10

27 Apr '10

Hi All, In some of our subjects in stats folder i don't see lh and rh .curv.stats files (so only 6 stats files in total whereas in others i have 8 stats files in total) why is that. Recon-all finishes without any error what am i doing wrong. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Re: [Freesurfer] nu-correct parameters
by Nick Schmansky 27 Apr '10

27 Apr '10

for 3T scans, try this modification to the nu_correct usage in recon-all. first, create a file called 'xopts' with this one line: mri_nu_correct.mni --proto-iters 1000 --distance 50 then, run recon-all with these params: recon-all -s subjid \ -nuintensitycor \ -nuiterations 1 \ -expert <path>/<to>/xopts the new flags being '-nuiterations 1 -expert ./xopts'. these params are taken from a new paper: http://web.mysites.ntu.edu.sg/zvitali/publications/documents/N3_NI.pdf also, mri_nu_correct.mni --help provides help info. n. On Mon, 2010-04-26 at 21:48 +0200, Leonardo Chesi wrote: > Dear all, > > I’m Leonardo, a student of the University of Pisa. We study AD’s > patients by MRI. In the last days I had have many problems with the > segmentation because of the B0 inhomogeneity with a 8 channel phased > array coil on a 3.0 T General Electric machine. In some articles I > have found the nu_correct command that provide to normalize the image. > I’m writing to you to ask if some of you know the optimal parameters > to give input to nu_correct to normalize as well as it possible the > image. I’ve try with the default parameters and my segmentation is > already better than the previous. > > Moreover I’d like to know if there is a manual of this command because > on the FreeSurfer Wiki I can’t find detailed information. > > I’m waiting for your corteous help. > > Greetings > > Leonardo > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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question about clustering simulation
by Anthony Dick 27 Apr '10

27 Apr '10

Hello all, I am interested in using the mri_glmfit simulation to control for multiple comparisons in data I have run on the surface in AFNI. Before doing this, I have a few questions: 1. What does the simulation with the mc-z flag do, exactly? It claims to be comparable to AFNI's AlphaSim, but it takes a maximum cluster area for each iteration, which is not exactly what AlphaSim does. Here is my guess: Given a surface, a given smoothness of the data, and a given per-vertex threshold, for each iteration the simulation populates that surface with random data taken from a normal distribution, thresholds the data, and applies the smoothness of the actual data (supplied as an input parameter). It then computes the maximum cluster size in area for that "image". Doing this n iterations gives a distribution of maximum cluster sizes that occur for random data of a given smoothness, and taking cluster sizes above a certain percentile rank controls for the FWE at a level equal to that percentile rank (e.g., 95th% controls for FWE = .05). AlphaSim does something similar, although instead of taking maximum cluster sizes at each iteration it computes all given cluster sizes. AlphaSim also allows for different cluster connectivity radius, but it seems Freesurfer computes only for neighboring vertices. All in all, if this is correct, it seems like a good implementation. 2. It is my understanding that one could bypass running the glm in Freesurfer and only compute the simulation, as the simulation only needs information about the surface, and the smoothness of the data (which are supplied by the user). To do so, you have to "fake out" Freesurfer to bypass glm, but that turns out to be pretty painless. 3. In a future distribution, is it possible to modify this procedure to also output maximum cluster sizes in terms of number of nodes, rather than area? Can you please let me know if I am mistaken in any of these assumptions? Thanks in advance. Anthony -- Anthony Steven Dick, Ph.D. Post-Doctoral Fellow Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: adick(a)uchicago.edu Web: http://home.uchicago.edu/~adick/

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FOV error
by Antoine Leflon 27 Apr '10

27 Apr '10

Hi all , I have got a problem with the field of view which is told to be 300 (instead of 240 ou 256) and when running tkmedit it's impossible to have good views ... Can someone tell me the error I did ? Because with other data everything is working . thanks

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Talairach to vertex index: selec_talairach_point?
by Arslan, Ali 26 Apr '10

26 Apr '10

Hi, I'm trying to go over a long list of talairach coordinates and to find their vertex indices. I did a bit of research and saw a previous question on the same topic: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12550.html So I went on to write a tcl script in order to write the corresponding vertex indices to a file. But the problem is, the function selec_talairach_point gives 4 successive outputs, therefore I can't parse the vertex number because it gets overwritten. such as these: % select_talairach_point 66.18 -14.56 39.06 surfer: vertex 68342: dist = 0.002702 % surfer: dmin=0.0027, vno=68342, x=43.6843, y=-11.1042, z=35.8562 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % 0 (0 0 0) My questions are: 1) is there an easier way of doing this besides writing a tcl script? 2) how can I access the function "selec_talairach_point" to modify it temporarily (so that it outputs ONLY vertex indices and not anything else) 3) is there a way to parse the output of this function in tcl? Ali B. Arslan Graduate Student in Cognitive & Linguistic Sciences

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