Freesurfer December 2009

freesurfer@nmr.mgh.harvard.edu

77 participants
105 discussions

GM & WM bitmaps; different from FAST(FSL)?
by Julie McEntee 04 Dec '09

04 Dec '09

Hi, So far, I have results from autorecon1 & -subcortseg. The aseg.stats that are obtained following these procedures contain measures of L & R-Cerebral-White-Matter and Cerebral Cortex. If I created masks (bitmaps) using these labels in FreeSurfer, would they be equivalent to whole-brain WM and GM, or do I need to use maps/surfaces created further along in the FreeSurfer processing stream (if so, which would be accurate)? In general, how would these differ from the tissue segmentations obtained using FSL-FAST? Thank-you for your help, Julie Julie E. McEntee, MA, CCRP Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676

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Neonatal Brain
by Naama Barnea-Goraly 03 Dec '09

03 Dec '09

Followup to yesterdays question - there is one Freesurfer paper I know of that did segmentation (and curvature analysis) of newborn brains. Bruce, you are a co-author, could you please comment on that approach? Int J Imaging Syst Technol. 2008 Jun 1;18(1):42-68. A METHODOLOGY FOR ANALYZING CURVATURE IN THE DEVELOPING BRAIN FROM PRETERM TO ADULT. Pienaar R, Fischl B, Caviness V, Makris N, Grant PE. Thanks, Naama Naama Barnea-Goraly M.D. Instructor Center for Interdisciplinary Brain Sciences Research Stanford University Division of Child and Adolescent Psychiatry 401 Quarry Rd. MC 5795 Stanford University School of Medicine Stanford, CA 94305-5795 Phone: (650) 736-1874, fax: (650) 724-4794 CONFIDENTIALITY NOTICE: This e-mail communication and any attachments may contain confidential information for the use of the designated recipients named above. If you are not the intended recipient, you are hereby notified that you have received this communication in error and that any review, disclosure, dissemination, distribution or copying of it or its contents is prohibited. If you have received this communication in error, please notify Stanford Medical Center immediately by telephone at (650) 725-5722 and destroy all copies of this communication and any attachments. Thank you.

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check talairach transform
by Anne Gallagher 03 Dec '09

03 Dec '09

Hi, I run recon-all -autorecon1 on my own data set. I want to check the talairach transformation using tkregister2, but I don't have the "surf orig" (green lines) yet. My questions are: 1- How can I aligned the TARGET and MOVEABLE without the green lines? 2- Which of the 30 steps of recon-all -all creates the "surf orig"? 3- Would the best way to proceed be to run recon-all -all first to create the "surf orig" and then check talairach transform? thanks for your help, anne... a new user!

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how to convert our own atlas to freesurfer
by Guang Zeng 03 Dec '09

03 Dec '09

Hello, there, We have a manualled labeled atlas, it is saved in a .nii file. We'd liek to use this atlas instead of FS's default atlas. If there are any commands or fucntions in FS can help us to do it. Thanks a lot! Guang _________________________________________________________________ Windows Live Hotmail gives you a free,exclusive gift. http://www.microsoft.com/windows/windowslive/hotmail_bl1/hotmail_bl1.aspx?o…

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surface
by j janssen 03 Dec '09

03 Dec '09

Hi, here's an email from Don Hagler from February 2009: It seems to me that vertex areas in the native subject space are not > meaningful. The orig surfaces should be uniformly tesselated; however, > topology correction and final surface finding should introduce complicated > and probably uninteresting variation. > i couldn't find a direct reply to this remark, hence my question: is this true? and if so, does this imply that native space surface measurements (as given in the aparc.stats file) are uninteresting for statistical analysis? best, -joost

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--paired-diff option
by Jürgen Hänggi 03 Dec '09

03 Dec '09

Dear FS experts If I use the --paired-diff option in mris_preproc, I know that the different time points of a subject has to be adjacent inputs in the FSGD file. Do I also have to specify the different time points as different classes or as only one class in the FSGD file? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. 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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ASCII to SURFACE
by João Ricardo Sato 02 Dec '09

02 Dec '09

Dear Freesurfers, Is it possible to convert ascii files in surface files? I found some posts in this mailing list only about converting surfaces to ascii files using mris_convert. Actually, I would like to use the thickness ascii files (converted using mris_convert) to process the data in another software (such as R or Matlab), and then retrieve the results (in ascii) back to freesurfer, for visualisation in tksurfer. Could anyone help me, please? Thank you in advance! All the best João Ricardo Sato Universidade Federal do ABC Brazil

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"dummy variable" in mri-glmfit
by Stefan Brauns 02 Dec '09

02 Dec '09

Hi there, we would like to test the effect of a binary variable (genotype = carrier vs. homozygous) on cortical thicknes in mri-glmfit. Since we are also controlling for gender and aquisition site (4 sites) we already have 16 groups. In order to control for age as a covariate we need at least 2 subjects per group to be able to estimate an age slope. If we include the aforementioned binary variable (genotype) as a factor (two different "groups"), we would have 32 groups and unfortunately not enough subjects per group. Is it possible to include binary variables ("dummy variable" coded as 0 and 1) such as genotype or gender as covariates (slope), in order to reduce the number of groups and examine the effect on thickness? In simple regression this would not affect the results - what would we expect here? Many thanks, Stefan

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Flattening hemisphere: Lateral extents of cuts
by Dickinson, Annelise (NIH/NIMH) [F] 02 Dec '09

02 Dec '09

Hello, I'm making whole-hemisphere flat maps, and I've been referring to the 1999 paper as well as the FreeSurfer manual for where to place the cuts. However, my flat maps are not turning out like the examples and I suspect that has something to do with how far AROUND the brain the cuts should extend. I've just been making them go out to the edge, as shown in Picture 1 attached (this is Figure 4 from the 1999 Fischl et al. paper). To my knowledge, the only extant example views of the cuts are medial views, like this one. If anyone has a lateral view of the cuts (showing where they should terminate on the outer surface of the hemisphere), or an explanation of where they should go, I would really really appreciate it!! Please let me know, and thanks! -Elise ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

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Neonatal brain
by Schneider, Jacques 02 Dec '09

02 Dec '09

Hello to the freesurfer group, I would like to analyze neonatal cortices with freesurfer. I ran a test data with a 10 yo child which came through wihtout problem. But a neonatal data set failed the recon at the level of talairach transformation. I suspect that the adult template is inconsistent with the neonatal immature folding and makes the transformation impossible. Now, Kazemi et al in NeuroImage 2007 published a neonatal template, and gave me the files on a research basis. My question is: how to replace the talairach coordinates in freesurfer with these neonatal data to make it work for this population ? I suspect the answer is not easy. But we are willing to give it a try, or perhaps are you already working on it ? Cheers Jack Dr. J.F. Schneider Head of Pediatric Radiology University Children's Hospital UKBB CH-4005 Basel Switzerland Phone +41 61 685 6282 Fax +41 61 685 6015 e-mail: jacques.schneider(a)ukbb.ch Diese Mitteilung ist vertraulich. Sie kann durch das Berufsgeheimnis geschuetzte Informationen enthalten und dient nur zum Gebrauch durch den Adressaten. Sollte diese Mitteilung irrtuemlich an Sie erfolgt sein, informieren Sie uns bitte und loeschen Sie diese Mitteilung sowie allfaellige Anhaenge unverzueglich. Jedes Verbreiten, Weiterleiten oder Vervielfaeltigen dieser Mitteilung ist verboten. This message is confidential and may contain confidential information which is covered by legal or professional privilege. If you are not the intended addressee and have received this e-mail by error, please advise the sender and immediately delete this message and any attachments. Any dissemination, distribution or copying of this communication is prohibited.

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Freesurfer December 2009