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running my own data
by Mark.Gay＠unlv.edu 23 Nov '09

23 Nov '09

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Error in template initialization.
by Hui Zheng 23 Nov '09

23 Nov '09

Hi all, We have a problem in longitudinal processing. The mri_robust_template somehow chopped off a part of the brain (attached image). Any idea how to correct this? With this "partial" template, the longitudinal processing of phase 1 and 2 data were also wrong. This is the second subject I was checking. I hope it is not a common problem. I can provide the subject's data if necessary. Thanks, Zheng Hui

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create volumes from surfaces
by Martin Ystad 23 Nov '09

23 Nov '09

Hi, I'm working on a fractal dimension analysis of the pial- and white-matter surface. The matlab script that calculates the fractal dimension needs binary nifti-files as input. Since FreeSurfer creates the surfaces I need, here's what I want to do: I'd like to convert the pial and white-matter surfaces (separately) to .nii-volumes (e.g. 256x256) where the voxels intersected by the respective surfaces are white, and everything else is black. Furthermore, I'd like to do this for individual subregions of each surface; for example only the precentral gyrus or the whole frontal lobe, so that only the voxels intersected by the surface belonging to the specific label I choose appear white, and everything else is black. How do I get this output from FreeSurfer? Thanks, Martin Ystad PhD-candidate, University of Bergen, Norway

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Research Assistant/ Lab Manager Position at OSU
by Ruchika Shaurya Prakash 22 Nov '09

22 Nov '09

Full-time Research Assistant/Lab Manager temporary position available in the Clinical Neuroscience Laboratory at Ohio State University. We employ both fMRI and behavioral paradigms to investigate the efficacy of psychosocial interventions on brain and cognitive plasticity. The job involves both administrative and research duties, with the potential candidate being involved in participant recruitment, maintenance of lab databases, data collection and analyses. A bachelor's degree in psychology, neuroscience or a related field is required. Prior research experience, background in computer programming is preferable. Start date is negotiable and the position can start as early as first week of January. For more information, interested candidates may contact Ruchika Prakash at prakash.30(a)osu.edu. To apply for the position, please visit : http://jobs.osu.edu/; (Job # : 348100) Ruchika Shaurya Prakash, Ph.D. Assistant Professor Department of Psychology Ohio State University Email: prakash.30(a)osu.edu Phone: (614) 292-8462 URL: http://faculty.psy.ohio-state.edu/prakash/lab/The_Lab.html

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missing vertices in mri_glmfit
by Julien Cohen-Adad 22 Nov '09

22 Nov '09

Hi, I'm using 'mri_glmfit' with surface inputs. However, from subject to subject, some vertices have zero-values. One solution is to use the 'prune' flag to keep only non-zeros vertices across subjects. However, this solution seems too conservative as too many vertices are discarded, producing gruyère-like significance maps. Is it possible to adopt a softer version of prune, i.e., only do the inference on non-zeros frames, without including frames that have null signal? In other words, this solution would consist in having different degrees of freedom throughout the surface. thanks, julien -- Julien Cohen-Adad, PhD Athinoula A. Martinos Center for Biomedical Imaging MGH, Harvard Medical School 149 Thirteen St, Charlestown, MA 02129, USA Work: +1 617 724 2463 ; Cell: +1 857 544 6110 ; Fax: +1 617 726 1383

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Bonferroni multiple comparison correction
by Jonathan DuBois 21 Nov '09

21 Nov '09

When correcting for multiple comparisons with Bonferroni for FS parcilation statistics, is it necessary to adjust for all parcellations (35) or just the variables (in our case mean thickness and surface area)? Assuming that no prior hypothesis is used to constrain the number of parcellations. Thanks for you input! Jon

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how to use my own template
by Guang Zeng 20 Nov '09

20 Nov '09

Hello, there, I built our own template, and gonna use it to test some subjects. Currently, I have two questions, (1) How can I use my template, In "recon-all.sh", I found that their two places where ?h.average.curvature.filled.buckner40.tif are called, so I just need to change all the "?h.average.curvature.filled.buckner40.tif" in "recon-all.sh" to "?h.average.curvature.filled.owntemplate.tif", is it correct? I think I need not do anything to ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs, right? How about RB_all_withskull_2007-08-08.gca? (2) How can I test if my template is good? I am going to test some subjects using my template and the FS default template, measure the volumes of some ROIS, compare the percentage overlapping ratio and correlation coef, does it sound reasonable? Thanks a lot! Guang _________________________________________________________________ Windows 7: It works the way you want. Learn more. http://www.microsoft.com/Windows/windows-7/default.aspx?ocid=PID24727::T:WL…

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mri_robust_register
by Jared Price 20 Nov '09

20 Nov '09

Hi gurus, The output of mri_robust_register includes some instruction for checking the registration. In my case the ouput said I could check the registration by running "tkregister2 --mov 0110837_20090425/mri/001.anatomicalspace.mgz --targ 0311501_scan1_20061205/mri/001.anatomicalspace.mgz --lta 0110837_20090425/mri/transforms/robustreg.lta --reg 0110837_20090425/mri/transforms/robustreg.reg" However, when I run this I get the error that file 0110837_20090425/mri/transforms/robustreg.reg does not exist. Mri_robust_register appears to exit without error and creates the linear transform array file, but it did not create a file called robustreg.reg. Did something go wrong?

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talairach registration-result
by Rajagopalan, Venkateswaran 19 Nov '09

19 Nov '09

Dear Freesurfer Users, Could anyone please tell me what is the name of the image file after talairach registration for instance like nu.mgz (after intensity correction). Thanks venkateswaran =================================== 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.

2 4

Question about longitudinal outputs
by Weisinger, Brian (NIH/OD) [E] 19 Nov '09

19 Nov '09

Is there any way to view the change in deeper cortical structures in freesurfer in a longitudinal stream run study like you can see with tksurfer and cortical thickness?

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