Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

VBM in SPM and FreeSurfer
by soft.join Huang 18 Feb '11

18 Feb '11

Hi, FreeSurfer and VBM experts I'm a newer in the field, and not sure if this question is relevant to the list - any help will be appreciated. I am wondering about the difference between the data of FS and that of VBM in SPM. After searching in Google, I find a topic following, url: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-May/007710.html, and have some different opinions. In the discussion in above link, all believe that FS and VBM could give the same measurement - volume, yet I don't think so. I admit that we could get the volume of specific ROI by multiplying the thickness by the surface area, but through VBM in SPM, we get the mass( something like it) of the gray matter( multiply the density of gray matter by the volume). They have different meaning, to the best of my knowledge. I don't know if I get the right understanding. Thanks a lot in advance. Lijie Huang email: huanglijie.seal(a)gmail.com State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing China

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manual
by Pom Sailasuta 17 Feb '11

17 Feb '11

Is there a later FreeSurfer manual other than version 0.8? The instruction in this version called file that does not exist (FreeSurferDefs.csh). -- Pom

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skullstrip manual editing with tkmedit: will 5.0 results be compatible with 5.1?
by Hyunwoo Lee 17 Feb '11

17 Feb '11

Hello, I see that the new 5.1 version may be available soon. Thererfore, I was wondering if the brainmask.mgz file that contains the manual editing (using tkmedit from FS 5.0) will be compatible with the forthcoming FS 5.1 version. I am planning to use the 5.1 version for the longitudinal processing, and as the manual editing requires significant amount of time, I don't think it would be wise to do the manual editing with the 5.0 version if it is not going to be compatible. Thank you very much, and I look forward to hearing from you. Hyunwoo Lee

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retrieving persistent edits from manually edited reruns
by Binod Thapa-Chhetry 17 Feb '11

17 Feb '11

Hi, We are trying to set up a freesurfer pipeline to measure cortical thickness for a multisite project. I came across the show-edits option in freesurfer 5.0.0. My understanding from herehttp://surfer.nmr.mgh.harvard.edu/fswiki/Edits is that running show-edits is supposed to give a edits.mgz file with regions where user intervention has been performed. I am not able to figure out why edits.mgz for a freesurfer output without any user intervention is still showing some regions(on the brain's edge approximately). Also, edits.mgz for a freesurfer output with user intervention, is able to show edited brain regions(great!!) with the unexpected persistent regions close to what were present in unedited freesurfer output. I am not sure if I am using/interpreting things the right way. Any suggestion on this will be highly appreciated. Thanks, Binod Molecular Imaging and Neuropathology Division Department of Psychiatry, Columbia University New York, NY (212)543-5659

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freesurfer 4.5 download
by Yuko Yotsumoto 17 Feb '11

17 Feb '11

Hi, I'm trying to download freesurfer 4.5 for leopard-ppc, but connection keeps failing. Could someone check the link? http://www.freesurfer.net/pub/dist/freesurfer/4.5.0/ Thank you, Yuko Yotsumoto

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mc-z precached and FWHM
by Chris Hyatt 17 Feb '11

17 Feb '11

When the GLM for a group of subjects is computed using mri_glmfit, a residual FWHM value is computed and stored in the file 'FWHM.dat'. When running a subsequent mri_glmfit-sim, using a pre-cached Monte-Carlo Z (mc-z) simulation for clusterwise correction for multiple comparisons, there appear to be separate simulations for a range of FWHM values stored (for each hemisphere, lh and rh) in /freesurfer/average/mult-comp-cor/fsaverage/?h/cortex/ from 01 to 30 (1 to 30 mm? - fwhm01, fwhm02, etc). My question is, if the value in FWHM.dat for the original mri_glmfit for a hemisphere is say, 15.294 mm, does mri_glmfit-sim (mc-z) use interpolated data from fwhm15/ and fwhm16/ in its calculations, or does it choose the nearest value (in this case, fwhm15)? Thanks, Chris Hyatt Olin Neuropsychiatry Research Center Institute of Living

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converting a vertex (or a set of vertices) from one space to another
by Joonkoo Park 17 Feb '11

17 Feb '11

Dear FreeSurfers, I have a set of vertices in the fsaverage surface space that I want to convert (or remap) to each subject's native surface space. What's the easiest way to do this? I thought of mri_label2label, and this will involve making label files. Are there any easier methods, either using FS directly or using matlab? Joon

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output of mris_anatomical_stats
by Marco Loggia, PhD 16 Feb '11

16 Feb '11

Dear all, In mris_anatomical_stats, the "average cortical thickness" value comes with a measure of dispersion around the mean. Is this Standard Deviation? If so, is there a way to plot the 95% confidence intervals instead? Thanks, Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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Between Task Analysis
by Mandy Nagy 16 Feb '11

16 Feb '11

Hi all, We are attempting to do an analysis for subjects that came in on two different days to perform two similar but different tasks (one learning condition, one control). Each of the tasks is structured such that there are 30sec rest epochs alternating with 30sec active (typing) epochs for a total of 12.5 minutes (the task begins and ends with rest). We are trying to compare the typing period for the control task to the typing period for the learning task. We currently have first-level analyses of each of the tasks (active condition vs. null rest condition). Can we do within-subject comparisons and then do a group analysis on those? Or did we need to concatenate the learning and control conditions in the first-level analysis? If that is the case, how would you suggest that we do this? Paradigm file: 0 0 30 1 Rest 30 1 30 1 Typing 60 0 30 1 Rest 90 1 30 1 Typing 120 0 30 1 Rest 150 1 30 1 Typing 180 0 30 1 Rest 210 1 30 1 Typing 240 0 30 1 Rest 270 1 30 1 Typing 300 0 30 1 Rest 330 1 30 1 Typing 360 0 30 1 Rest 390 1 30 1 Typing 420 0 30 1 Rest 450 1 30 1 Typing 480 0 30 1 Rest 510 1 30 1 Typing 540 0 30 1 Rest 570 1 30 1 Typing 600 0 30 1 Rest 630 1 30 1 Typing 660 0 30 1 Rest 690 1 30 1 Typing 720 0 30 1 Rest Thanks in advance! --Mandy Nagy

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question regarding T1-data quality
by Eveline Geiser 16 Feb '11

16 Feb '11

Dear List, we recorded this anatomical data on a clinical scanner (Philips Achieva 3T) with the following parameters: eight-channel sense head coil, TE 2.3 ms TR = 20ms, angle = 20degree. do you think it is usable? thanks for your reply -- --------------------- Eveline Geiser PhD Massachusetts Institute of Technology Department of Brain and Cognitive Sciences phone: +617 324 63 71 e-mail: egeiser(a)mit.edu http://web.mit.edu/gabrieli-lab/

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Freesurfer February 2011