Freesurfer April 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
147 discussions

ICV meaning...
by Gonzalo Rojas 28 Apr '10

28 Apr '10

Hi: Which is the meaning of the Intracaranial Volume (ICV) ?... it includes only the brain, or also the skull ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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ICV meaning...
by Gonzalo Rojas 28 Apr '10

28 Apr '10

Hi: In aseg.stats file, appears "lh-cerebral-white-matter" and "Left-Cerebral-White-matter": which are the difference between both values?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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converting label to binary mask.mgh
by Ritobrato Datta 28 Apr '10

28 Apr '10

Hello All, I have created a V1 label using Hinds and Fischl Method. Is a label a .mgh file as well ?? How do I convert this label to a binary mask mgh file ? Please let me know. Thanks much Rito

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Question about cortical surface area
by Massieh Moayedi 28 Apr '10

28 Apr '10

Hi everyone, I had two questions: 1) I was wondering if it's ok to run a glm to compare cortical surface areas between two groups on a vertex-wide basis (just like a thickness analysis). Or is it better to extract the area of a label (as is the output of mri_anatomical_stats)? 2) The mri_anatomical_stats output includes 4 measures of curvature: MeanCurv, GausCurv, Van Essen Folding index and Curvature Index. There was some discussion as to which of these was most appropriate for comparing sulcal folding (that is, essentially what they measure, correct?)- was there ever any final consensus? Thank you. Regards, Massieh Moayedi B.Sc. (Hons) PhD Student Dr. Karen Davis' Lab Institute of Medical Science University of Toronto Brain, Imaging and Behaviour- Systems Neuroscience MP 14-301 Toronto Western Research Institute University Health Network 399 Bathurst Street Toronto, Ontario Canada M5T 2S8 Tel: 416-603-5882 massih.moayedi(a)utoronto.ca mmoayedi(a)uhnres.utoronto.ca http://individual.utoronto.ca/PSMJC

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Group comparison -qdec clarification
by Rajagopalan, Venkateswaran 28 Apr '10

28 Apr '10

Dear All, I want to perform group comparison of cortical thickness between my patient and control group. I read qdec tutorial regarding how to do this. I was little bit puzzled and not able to understand the following. Before creating qdec table of patient data, fsaverage was suggested to run, so that the data will be resampled and smoothed. If i understand correctly this is to have all the data in the same space so that we can perform statistical tests on them I am new to freesurfer and entire processing steps. Also I would like to know if patient data is resampled and smoothed using fsaverage then my files in stats folder namely aparac.stats will have values little bit different from the ones after the recon-all -all step am i right. One other question i have 4 different patients groups so for instance if i want to compare whether group 1 >group 2 then my contrast will be 1 -1, if also want to check whether group 2>group1 then my contrast will be -1 1 am I right. Thanks in advance 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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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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Freesurfer April 2010