Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

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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aparc+aseg error
by Gabriel Go.Es. 20 Feb '09

20 Feb '09

dear Freesurfers i'm exiting subcortical segmentations with: tkmedit sk024 aparc+aseg.mgz -aparc+aseg and load as aux volume the T1.mgz then i recive the error message: $ tkmedit sk024 aparc+aseg.mgz -aparc+aseg Reading 1034 control points... LoadSegmentationVolume main aparc+aseg.mgz /root/trabajo/freesurfer/FreeSurferColorLUT.txt Reading 1034 control points... Reading /root/trabajo/freesurfer/lib/tcl/tkm_common.tcl Reading /root/trabajo/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /root/trabajo/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /root/trabajo/freesurfer/lib/tcl/tkUtils.tcl % =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to analysis-bugs(a)nmr.mgh.harvard.edu : : Now exiting... : regards Gabriel _________________________________________________________________ Consigue gratis el nuevo Messenger. ¡Descárgatelo! http://download.live.com/

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What is the transformation from surfaces vertices to volume voxel coordinates?
by Lloyd Elliott 19 Feb '09

19 Feb '09

I am trying to overlay surface information acquired with freesurfer on to the original MRI volume. I tried reading lh.orig with [vertices,faces] = freesurfer_read_surf('surf/lh.orig') and then transforming the vertices with the matrix: vertices_affine = [vertices' ; ones(1,size(vertices,1))] # append the affine coordinates overlay = (rsb2vox*inv(M)) * vertices_affine where M = xfm_read('mri/transforms/talairach.xfm') and rsb2vox = inv([ [-1 0 0 128 ; 0 0 1 -128; 0 -1 0 128; 0 0 0 1] ]) I was lead to believe that this is the correct procedure by reading the 'official' description of the coordinate systems on the freesurfer wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ). Unfortunately the scaling and translation is incorrect. I've also tried other permutations of the above matrix multiplication without any luck. Am I doing something incorrectly? Thanks, Lloyd Elliott

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cortical lesions with FS (T1+DIR sequences)
by Irene Mattisi 19 Feb '09

19 Feb '09

Hi all, I'm using Freesurfer to calculate cortical atrophy in patients with multiple sclerosis. These patients usually have also cortical lesions that I can see with DIR sequences. My question is: can I piece together the 2 sequences to see cortical lesions with FS? for FS we use a 3D fast-field echo (FFE) sequence: 120 contiguous axial slices with the off-centre positioned on zero, TR = 25 msec, TE = 4.6 msec, flip angle = 30°, slice thickness = 1.2 mm, matrix size = 256x256. DIR sequence: repetition time (TR) = 15631 msec, echo time (TE) = 25 msec, inversion time (TI) = 3400 msec, delay = 325 msec, echo train length (ETL) = 17, 50 contiguous axial slices with a thickness = 3 mm, a matrix size = 130 x 256, and a field of view (FOV) = 250 x 200 mm. Thanks, Irene Mattisi Multiple Sclerosis Centre Padua, Italy

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TKSurfer - Mean Thickness Overlay Display
by Bramen, Jennifer E. 19 Feb '09

19 Feb '09

Dear Freesurfer List I am trying to make some figures to display mean thickness for my different groups. I have the overlays, but no matter what I do, they look terrible. The only color scale that seems to work is the "hot" scale. Everything else looks completely wrong. Either they look grainy like this or I get a black image. I am attaching screenshot showing what I mean. I am also attaching an example of what I want taken from a paper that also uses Freesurfer. I am studying kids, who have much thicker cortex than adults. I would like to threshold thickness at 1.7, with a max value of 5. Otherwise, I want my figure to look exactly like this one. How can configure the overlay display so that my figures look similar? Thanks Jen Jennifer Bramen, Ph.D. Assistant Research Neuroscientist David Geffen School of Medicine at UCLA Developmental Cognitive Neuroimaging 635 Charles Young Drive South Los Angeles, CA 90095-7332 Phone: (310)267-5116 Fax: (310)525-0865 Email: jbramen(a)mednet.ucla.edu Campus Mail Code 176919 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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mris_divide_parcellation
by Jose Luis Cantero Lorente 19 Feb '09

19 Feb '09

Dear FS Team, I used mris_divide_parcellation to create a new parcelation with smaller regions, but all these regions seem to have a different size. I am interested to get smaller cortical parcellated regions, but all of them with the same area. How can I get it? Could I decide the area size? Thank you 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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Freesurfer February 2009