Freesurfer

freesurfer@nmr.mgh.harvard.edu

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FSL & FreeSurfer Couse 2006 - Siena, Italy
by Stephen Smith 06 Dec '05

06 Dec '05

--------------------------------------------------------------------- Announcing: FSL & FreeSurfer Course 19-23 June 2006 - Siena, Italy Organised by FMRIB Centre, University of Oxford, Martinos Center for Biomedical Imaging, MGH & Quantitative Neuroimaging Laboratory, Siena Local Organiser: Prof. Nicola De Stefano, Siena http://www.fmrib.ox.ac.uk/fslcourse/2006 --------------------------------------------------------------------- We are pleased to announce the 2006 FSL & FreeSurfer course in Siena, Italy. It will run immediately after the Human Brain Mapping conference in nearby Florence. The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with at most two attendees per computer. By the end of the course, attendees should be able to fully analyse their own FMRI and MRI data sets. The course is aimed at both new and existing users of these packages and will cover both basic and advanced features. The methods covered include * Functional MRI analysis: - GLM-based analysis of FMRI data including Bayesian multi-subject statistics (FSL - FEAT) - Model-free (ICA) analysis of FMRI data (FSL - MELODIC) * Structural MRI analysis: - Image registration and unwarping (FSL - FLIRT/FUGUE) - Brain extraction and tissue-type segmentation (FSL - BET/FAST) - Structural spatial statistical analysis e.g. atrophy (FSL - SIENA/SIENAX) - Automatic subcortical segmentation / alignment (FreeSurfer ASEG) * Cortical-flattening of images and its applications (FreeSurfer): - Cortical flattening for improved FMRI analysis, including inter-subject averaging - Group studies of cortical morphometry; thickness, folding, surface area, volume * Analysis of diffusion-weighted imaging data, including tractography and related applications (FSL - FDT/TBSS) * Paradigm optimisation (Optseq) --------------------------------------------------------------------- For more information and to register, visit: http://www.fmrib.ox.ac.uk/fslcourse/2006/ ---------------------------------------------------------------------

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Video card/linux distro for 3D dual monitors: Recommendations?
by Graham Wideman 06 Dec '05

06 Dec '05

Folks: Having developed high blood pressure due to the incredible time waste involved in trying to get anything other than lowest-common-denominator video running on linux... I thought I'd ask you all for recommendations that you know *do* work. So I'm looking for some combination of video card, drivers/libraries and linux distribution that can be installed and configured in time guaranteed to be less than infinite... 1. Must support dual monitors (ie: for 2560 x 1024 desktop). 2. Vid card must have some features that make 3D operations speedy. 3. Must have actual non-buggy drivers that allow FreeSurfer to drive the vid card's 3D features. 4. All should be relatively recent so that they don't preclude getting other things running due to being obsolete. Any suggestions? Thanks, Graham

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N3 in FreeSurfer
by Michele Perry 05 Dec '05

05 Dec '05

Is the normalization software called N3 a standard part of the dev release of Freesurfer? Michele

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Control-points
by Martin Ystad 05 Dec '05

05 Dec '05

Hi, I'm using a lot of control-points (typically 200-500) to compensate for intensity inhomogeneities in my images. This tends to create a rather uniformly looking white matter without any clearly discernible anatomical landmarks, such as the basal ganglia, etc. Does this mean that the subcortical segmentation won't work properly? Will this munificent use of control-points constitute a source of error for the cortical segmentation, or are the protocols relatively robust? Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies vei 91, 5009 Bergen, Norway.

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mri_ms_fitparms output volumes
by Christian Haselgrove 02 Dec '05

02 Dec '05

Hi, What exactly is contained in the outputs of mri_ms_fitparms? Specifically: the T1 volume looks like it might have T1 times in ms -- is this correct? And I assume that PD is proton density -- is there a specific unit attached to these voxel values as well? Thanks, Christian -- Christian Haselgrove Center for Morphometric Analysis ch(a)cma.mgh.harvard.edu Massachusetts General Hospital 617-726-6018 Building 149, 13th St. 617-726-5743 Charlestown, MA 02129

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motion correction during recon-all
by Don Hagler 02 Dec '05

02 Dec '05

I want to average multiple structural scans for input into the surface recon. Two are axial and one is sagittal. (I plan to correct for the gradient inhomogeneities in the sagittal images, so that shouldn't be an issue.) Anyway, the problem comes when recon-all does "motion correction" to align the scans. For some strange reason, the axial and sagittal scan protocols use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012). For some even stranger reason, this brings recon-all to a screaching halt. I'm guessing that this is actually a MINC problem but I wonder if there is a way to make it ignore the TR and TE when aligning two structural scans. My work around is to explicitly set the TR and TE for the sagittal scan when running mri_convert: mri_convert -tr 8.012 -te 3.136 -it dicom i\*.1 $destdir/$mgzname.mgz

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neuroimaging job announcement
by David Ziegler 30 Nov '05

30 Nov '05

The Behavioral Neuroscience Lab at MIT is seeking a technical assistant who will take a lead role in the design, implementation, and analysis of our structural and functional MRI studies. A candidate with Freesurfer/FSL experience will have a distinct advantage. Here is a link to the full job description and online application page: http://sh.webhire.com/servlet/av/jd?ai=631&ji=1642175&sn=I -- David A. Ziegler Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Building 46-5121, 32 Vassar St Cambridge, MA 02139 Tel: 617-258-0765 Fax: 617-253-1504 daz(a)mit.edu <mailto:daz@mit.edu>

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RE: [Freesurfer] version history question
by Goldman, Aaron (NIH/NIMH) 29 Nov '05

29 Nov '05

Okay. Related to that question, if I reran people with the latest tools, would it be possible/make sense to read in my control point files from the old version? Thanks, -Aaron- -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, November 29, 2005 4:17 PM To: Goldman, Aaron (NIH/NIMH) Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] version history question Hi Aaron, one of the things we are trying to put in place is something like recon-all -rerun that will retain all manual interventions but reapply the newest tool to all your data. And yes, those tools have changed in the last year so you don't want to compare across versions if you can help it. cheers, Bruce On Tue, 29 Nov 2005, Goldman, Aaron (NIH/NIMH) wrote: > Hi, I'm interested in analyzing subcortical segmentations, and have a question about potential systematic differences between freesurfer versions. Specifically, I have a large number of subjects who've been through a year-old version of recon-all -stage1 (the skull strip, normalization, etc), and was wondering if I need to keep using the old version for consistency's sake. Have those initial steps been substantially upgraded or changed over the past year? Also, is there somewhere I can find a guide to version history? > > > > The versions concerned are: > > OLD: 08/31/04, recon-all version 1.5, tosa > > NEW: 09/28/05, recon-all version 1.114, nicks > > > > Thanks, > > > > -Aaron- > > > > Aaron L. Goldman > > Post-Bacc IRTA > > Genes, Cognition and Psychosis Program, NIMH > > Building 10, Room 3C108 > > Phone: (301) 435-0944 > > Email: aarong(a)mail.nih.gov > > > >

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version history question
by Goldman, Aaron (NIH/NIMH) 29 Nov '05

29 Nov '05

Hi, I'm interested in analyzing subcortical segmentations, and have a question about potential systematic differences between freesurfer versions. Specifically, I have a large number of subjects who've been through a year-old version of recon-all -stage1 (the skull strip, normalization, etc), and was wondering if I need to keep using the old version for consistency's sake. Have those initial steps been substantially upgraded or changed over the past year? Also, is there somewhere I can find a guide to version history? The versions concerned are: OLD: 08/31/04, recon-all version 1.5, tosa NEW: 09/28/05, recon-all version 1.114, nicks Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov

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mri_ca_normalize error
by Michele Perry 28 Nov '05

28 Nov '05

Hi, mri_ca_normalize failed for a subject. Here is the CA normalize portion of recon-all.log: =========================================== CA Normalize Thu Nov 17 17:02:05 PST 2005 $SUBJECTS_DIR/<subjid>/mri mri_ca_normalize -mask brain.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz using MR volume brain.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64/average/RB40_talairach_2005-07-20.gca'... setting gca type = Normal gca type Direction cosines read: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000 x_a = 0.0000, y_a = 0.0000, z_a = 1.0000 x_s = 0.0000, y_s = -1.0000, z_s = 0.0000 c_r = 0.0000, c_a = 0.0000, c_s = 0.0000 reading transform from 'transforms/talairach.lta'... mghRead: encountered error executing: 'zcat $SUBJECTS_DIR/<subjid>/mri/nu.mgz',frame -1 mri_ca_normalize: could not read input MR volume from nu.mgz reading input volume from nu.mgz... ERROR: mri_ca_normalize with non-zero status ======================================================= $SUBJECTS_DIR/<subjid>/mri contains nu.mgz and the talairach looks normal. How do I fix this? Michele

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