Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

talairach transform with brain.mgz as input file
by Lars M. Rimol 08 Dec '05

08 Dec '05

Hi, After having redone mri_convert with an edited brain.mgz as input file, in order to improve the talairach transform, and after having changed the file names (brain.xfm -> talairach.xfm), should we then go to autorecon2? (or do we need to re-run some more scripts from autorecon1?) -- yours, Lars M. Rimol

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how to get .mgz files
by peggy christidis 07 Dec '05

07 Dec '05

Hi there, I'm starting off with an AFNI dataset (e.g., fred+orig.BRIK) and I want to convert this file to FreeSurfer's .mgz format. When I run the command "mri_convert fred+orig.BRIK fred_surf/mri/orig", I end up with 256 .COR files. How do I get .mgz files instead? Do I need to add something to the command line? I've checked mri_convert's help manual but I still can't figure out how to do this. Thanks, Peggy

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which version is recommended, and any way to avoid -conform?
by Sebastian Moeller 07 Dec '05

07 Dec '05

Hi All, which version of freesurfer is the one recommended to be used, the v2.2 stable from November 20. or still the development version from October 3rd? I guess it is still the dev version. My second question is about the conform step implicit to recon-all -motioncor, as I used a 0.5mm^3 resolution for scanning my monkey brains, it would be a pitty to conform this data to 1mm^3 for further steps. So far the only way I know, how to avoid this is using the -iis -ijs -iks switches to mri_convert to actively lie to freesurfer, that the scans already conform to 1mm^3. Is there a nicer way to achieve the use of non-conformed resolution, like doing the -motioncor step of recon-all -autorecon1 manually? Or is the use of the standard process not recommended for monkey data anyway? Regards Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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mask_label in script
by Henrik Ormåsen 07 Dec '05

07 Dec '05

We use mask_label in the prompt to load this file. How can we load it from a tksurfer tcl script? - Henrik

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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

4 9

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

2 1

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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