Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

Oblique slices with pial and white matter surface
by Oya, Hiroyuki 05 Dec '09

05 Dec '09

Dear all, I'd like to make serial oblique slices with pial surface resampled into the slice. Would it be possible to do this with tkmedit ? Any suggestion would be appreciated. Hiroyuki

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QDEC
by liyari5018 04 Dec '09

04 Dec '09

Hi all, I got a troble when I tried to use QDEC, an error occurred( My computer system: ubuntu 9.10, platform: CentOS4.8_x86_64_public): qdec.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory How can I slove this problem? J

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Gray-White boundary question
by Meghana Karnik 04 Dec '09

04 Dec '09

Hello. I'm a new Freesurfer question, and I was wondering if you could answer a couple of questions for me. First some background: After having done the autorecon1 and autorecon2 steps successfully, and after also checking and making sure that the original white matter surface registered well to Talairach space, I am now at the point of checking the white matter surface. There are definitely places that should be included as white matter that were left out. In those spots, I have added control points and have had no trouble. My questions though are about spots in the cortex where the white matter surface has included gray matter. I believe I should use the Edit Voxels Tool to fix this, but I am not entirely sure how I should "Configure the Brush Info" or "Configure the Volume Brush". For the Brush Info, should I set the Target as the Main Volume, the Aux Volume or the Main and Aux Volume? I am not sure which I should select. From the tutorial ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits) it looks like I should select the Aux Volume and then save that in order to run: recon-all -autorecon2-wm -autorecon3 -subjid wm2_edits_before. But, I'm concerned about what the tutorial means as the deletion of voxels by this editing tool. Would reclassifying these voxels as non-white matter automatically render them as part of the pial surface when the above script is run? Or, would they be reclassified as non-brain tissue? Also, I would appreciate it if you could direct me on how to set the Volume Brush Info appropriately. Thank you in advance for your help, Meghana -- Meghana Karnik-Henry, Ph.D. Research Associate University of Texas at Dallas Center for Brain Health Department of Behavioral and Brain Sciences

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white matter edits
by Jesse Bledsoe 04 Dec '09

04 Dec '09

Hi experts, Should I be concerned about the number of white matter errors in the attached tif? Is it normal or unusual to have this many white matter errors after reconstruction? It seems like discussions on editing white matter suggest there are usually only a handful, if any errors to the wm.mgz. Thanks so much, Jesse

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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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