Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

partial volume effects
by Jose Luis Cantero Lorente 23 Feb '09

23 Feb '09

Hi there, I would like to reduce the bias between FDG uptake and cortical thickness changes in my dataset. Would it possible to correct partial volume effects after registering FDG-PET and MR images (using bbregister) with Freesurfer? I am trying not to use other software packages to perform this task, since all my MRI images were already segmented and registered with Freesurfer. Thanks in advance. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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need T-values
by Wang, Xin 23 Feb '09

23 Feb '09

Hello, Freesurfer group, I need T values instead of F values for a one-sample T test GLM. How can I convert the values in F.mgh or sig.mgh (for 12 subjects one group no factor) to T values and overlay them on the surface? I found the similar questions in the following emails posted on freesurfer email list. I want to follow up these questions. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-September/00619… https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-September/00611… Thank you in advance, Xin

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facebook strike 2
by Sam Mehl 23 Feb '09

23 Feb '09

test

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facebook
by Sam Mehl 23 Feb '09

23 Feb '09

test

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Doubt manual segmentation
by Kelly Silva 23 Feb '09

23 Feb '09

Hello, 1) We have done the manual segmentation of one subcortical structure and we have observed that when we erase some area, it appears "none" in the "sgmtn label" from tkmedit window. Is there any problem whit this? 2) When we install the new version of freesurfer (4.2), is it necessary to put the fixes that appears on the freesurfer web? Thanks and best regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Échale un vistazo a mi perfil de Facebook
by Gabriel Gonzalez E 21 Feb '09

21 Feb '09

Hola, Free: He creado un perfil en Facebook donde puedo publicar mis fotos, vídeos y eventos, y quiero añadirte a mis amigos para que puedas verlo. Para ello, necesitas registrarte en Facebook y, después, podrás crear también tu propio perfil. Gracias, Gabriel Para registrarte en Facebook, sigue este enlace: http://www.facebook.com/p.php?i=660875920&k=53FZZXQZ356M5BFAWBZ3QV&r Este correo puede contener material publicitario. Si no deseas recibir mensajes comerciales de Facebook en el futuro, por favor haz clic en el siguiente enlace. Las oficinas de Facebook están situadas en 156 University Ave., Palo Alto, CA 94301. http://www.facebook.com/o.php?k=5f2dd3&u=1021605002

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question about time courses..
by Srihasam, Krishna 20 Feb '09

20 Feb '09

Hi, Is there any way I can overlay the time course of events defined in the paradigm file on to the time course of blood flow? I am using tkmedit's "load time course" button to load the raw time courses. I would like my paradigm to be overlaid on this. - Krishna

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questions about SPM surfrend
by Wang, Xin 20 Feb '09

20 Feb '09

Dear Dr. Kahn, I have a few question about your surfrend. I attended Freesurfer workshop a month ago, but I did not know your SPM surfrend tool at that time. So I send you this email to seek your help. 1) could you give some details about the surfrend? I am interested in the procedures and commands used in this tool. 2) I compared surfrend registration and the registration using bbregister SPM_fixedscapled_T1.img to my average. Some active ROIs are splited onto adjecent gyri after using .bat file produced by bbregister. In contrast, the active ROIs are continuous through sulcus using surfrend. Could you explain how did you correct for the cross sulcual spliting? 3) do you know anything like surfrend for FSL? I am looking forward to hearing from you. Thank you in advance, Xin Wang

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Cluster analysis using mri-glmfit-sim
by Devdutta W 20 Feb '09

20 Feb '09

Hi, I have been following the documentation for mri_glmfit-sim and need a bit of clarification. The point where we run tksurfer with the -annot option, it seems that it displays all the clusters (regardess of the significance) on the average brain. When I run it, it looks like cortical parcellations are being displayed on the brain. It also displays the clusters (within the parcellations); so it seems to be working. I am just curious as to why the parcellations are being displayed. Here is the command I am using. *tksurfer fsaverage rh inflated -annot mc-z.abs.2.sig.ocn.annot -fthresh 2 -curv -gray* But more importantly, I would like to know how to interpret what I am seeing correctly. I understand that the p-value threshold can be set by -fthresh (2 corresponds to p value of 0.01). In the cluster summary (it found 25 clusters), I am seeing CWP of 0.001 for 24 of the 25 clusters. What does this significance mean as calculated by the command? Is this corrected across the whole brain? Thank you, Devdutta

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Registration when producing a z-score thickness map of a single subject
by Jürgen Hänggi 20 Feb '09

20 Feb '09

Dear FS experts I would like to compare a single subject's thickness map against a group's thickness map by using z-score transformations. I already produced a mean and a standard deviation thickness map of the controls. Now I struggle in how to register the single subject's thickness map to the mean group thickness map. Which is the most easy way to do this? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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