Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

mri_normalization, what do the command line switches do?
by Sebastian Moeller 29 Apr '09

29 Apr '09

Aloha, fellow freesurfers, currently I am in the process of switching from freesurfer 3.0.5 to 4.3.0 (hopefully I can do the same for fsfast later). In that process I am revisiting mzy old scripts and try to improve them (or at least get rid of some cargo-cult coding). One of the more crirtical early steps for processing monkey brains, at least that is my experience, are the two normalization steps. Now here is the help from mri_normalize: mri_normalize input output -n <int n> use n 3d normalization iterations (default=2) -no1d disable 1d normalization -conform interpolate and embed volume to be 256^3 -noconform do not conform the volume -gentle perform kinder gentler normalization -f <path to file> use control points file (usually control.dat) -fonly <fname> use only control points file -w <mri_vol c> <mri_vol b> : write ctrl point(c) and bias field(b) volumes -a <float a> use control point with intensity a above target (default=25.0) -b <float b> use control point with intensity b below target (default=10.0) -g <float g> use max intensity/mm gradient g (default=1.000) -prune <boolean> turn pruning of control points on/off (default=off). pruning useful if white is expanding into gm -MASK maskfile -monkey turns off 1d, sets num_3d_iter=1 -nosnr disable snr normalization -sigma sigma smooth bias field -aseg aseg -v Gvx Gvy Gvz for debugging -d Gx Gy Gz for debugging -r controlpoints biasfield : for reading -u or -h print usage initially I use "mri_normalize -n 1 -no1d -gentle nu.mgz $T1.mgz", this invocation was handed down to me and I always just used it. Could someone in the know, explain, why monkey data should be processed without 1d normalization (and what is 1d normalization), and why only one iteration of 3d normalization is recommended; and what is the difference between a default normalization and a normaization using - gentle? (Since I mainly use the T1 for skull stripping and as underlay I guess I can just play around with the parameters to optimize the skull strip). I wonder especially, as I usually take monkey data at 0.5mm resolution, but fudge the header information so freesurfer thinks it is at 1.0mm, that way the size difference between human and monkey data is much less, compared to using monkey data at real 1.0mm resolution. And I have a hunch that the size difference might be the reason for special casing monkey data during normalization. Later I use "mri_normalize -f ${controlpoints} -monkey -MASK ${mask} nu.mgz brain.unmasked.mgz". Again I am interested to learn whether there is any reasoning to use the -monkey parameter here. (Since the full recon takes a while, doing trial and error here is a bit less attractive) Thank you very much in advance for any insight, aloha Sebastian -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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corpus callosum segmentation
by Wayne Su 29 Apr '09

29 Apr '09

The Freesurfer 4.3 segments the cc into 5 parts. But the wmparc.mgz has both 5 parts along with ctx-?h-corpuscallosum/ wm-?h-corpuscallosum. I think they should not co-exist. Maybe I¹m wrong. Wayne

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Volume-based Monte Carlo Restricted to a within mask area
by Dave Brohawn 29 Apr '09

29 Apr '09

Hello, Here is my bugr info if you need it: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090428 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /autofs/space/ventzl_016/users/ PWD: /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s ssh seymour setenv SUBJECTS_DIR /autofs/space/ventzl_016/users/ cd $SUBJECTS_DIR I have made a mask version of subcortical regions using mri_binarize: mri_binarize --i aseg.mgz --match 16 --match 10 --match 49 --match 13 --match 52 --match 12 --match 51 --match 11 --match 50 --match 18 --match 54 --match 17 --match 53 --match 26 --match 58 --match 28 --match 60 --o Subcortical.nii I am able to load this file into tkmedit over fsaverage and I see that it has all the structures I want to use as a mask for my volume-based monte carlo command. I tried running my monte carlo command as follows: mri_glmfit --y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii --fsgd $SUBJECTS_DIR/fsgd/All-18.fsgd --C $SUBJECTS_DIR/fsgd/All-18.mat --mask $SUBJECTS_DIR/fsaverage/mri/Subcortical.nii --sim mc-full 1000 2 $SUBJECTS_DIR/All-18/monte_carlo_01_V/SubCortVol_MCSIM1 --fwhm 13.37 It looks like it wants to work, but will say: gdfReadHeader: reading /autofs/space/ventzl_016/users//fsgd/All-18.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 CC 2 T INFO: gd2mtx_method is dods simbase /autofs/space/ventzl_016/users//All-18/monte_carlo_01_V/SubCortVol_MCSIM1 $Id: mri_glmfit.c,v 1.138.2.9 2009/01/17 02:08:58 greve Exp $ cwd /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s cmdline mri_glmfit --y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii --fsgd /autofs/space/ventzl_016/users//fsgd/All-18.fsgd --C /autofs/space/ventzl_016/users//fsgd/All-18.mat --mask /autofs/space/ventzl_016/users//fsaverage/mri/Subcortical.nii --sim mc-full 1000 2 /autofs/space/ventzl_016/users//All-18/monte_carlo_01_V/SubCortVol_MCSIM1 --fwhm 13.37 sysname Linux hostname seymour machine i686 user jroffman FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 13.370000 OneSampleGroupMean 0 y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii logyflag 0 usedti 0 FSGD /autofs/space/ventzl_016/users//fsgd/All-18.fsgd mask /autofs/space/ventzl_016/users//fsaverage/mri/Subcortical.nii maskinv 0 glmdir (null) IllCondOK 0 DoFFx 0 Loading y from /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii INFO: gd2mtx_method is dods Matrix condition is 1 ERROR: dimension mismatch 1 between y and mask Do you have any ideas about how to fix this? I am not sure how to look at the matrix dimension mismatches, nor am I sure how to alter the mask I made to fit the dimensions of the ces.nii file for the analysis. Please let me know. Thanks! Dave

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longitudinal processing
by Dana W. Moore 29 Apr '09

29 Apr '09

FreeSurfers, I am using the longitudinal processing stream to look at change in the lateral ventricles at several timepoints. As a control measure, we are running two consecutive baseline images in the scanner. These images were done back-to-back, exactly the same, and the subject did not get out of the scanner nor reposition. Motion was not a problem. I have processed this first subject, and the longitudinal stream gives me a 2% change in lateral ventricular volume, comparing the two baseline scans. This is bigger than I'd like to see, as we are interested in changes over time as small as 2%. Is this kind of variability expected, or am I doing something wrong? I just used the first baseline as tp1, processed it cross-sectionally, and then longitudinally, and then I used the second baseline as tp2. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

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(no subject)
by Elina Pitri 29 Apr '09

29 Apr '09

Hello Freesurfer Creators, I am wondering how much time should Volume and Surface processing (using recon-all commands) take. thanks, Elina

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(no subject)
by Elina Pitri 29 Apr '09

29 Apr '09

Hello, Do you know how can I convert my images which are in ctf format to a freesurfer compatible format? thanks, Elina

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longitudinal stream
by Bruce Fischl 28 Apr '09

28 Apr '09

Hi All, We have recently tracked down a bias in the longitudinal processing stream. We believe we have a fix for the problem, but it will take us a bit of time to get it working and well-tested. We'll keep you posted as to when we will have a new version. Feel free to email me if you have any questions. sorry :<. Bruce

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skull strip problem
by Wilson, Benjamin 28 Apr '09

28 Apr '09

Hi, I am trying to run freesurfer on some SPGR sequences that I have on a few subjects. I managed to import and convert the DICOM files to .mgz with success, but when I ran the skull strip I have a significant amount of skull left in some places and a large chunk of brain missing in other planes on the same brain. I am wondering if there is a problem with intensity normalization (most of my brain appears to be close to an intensity of 110), but I do not know how to fix the problem. Can anybody offer some suggestions on how to fix the problem? Thanks. Sincerely, Ben Wilson

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Custom Aseg Atlas Question.
by Jamie Hanson 28 Apr '09

28 Apr '09

Hi Freesurfer folks- I am in the midst of creating a custom aseg atlas and had a quick question regarding when to use v. discard subjects. I just ran the second iterations of mri_ca_train (when you use all the subjects in subjects.csh and are training from segmented subjects using M3D_ONE) and I have 6 (of 18) subjects "with bad labels". Is it best to discard those subjects and just use the successfully labeled subjects? I wasn't sure if only included those good subjects would perhaps boost my aseg atlas accuracy. Thanks much. Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

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Freesurfer Brain Region Ontology
by Stephan Gerhard 28 Apr '09

28 Apr '09

Hi! I am rather new to the Freesurfer Software, so I'll start with an easy question. Currently I am involved in a SemanticWiki project called ConnetomeWiki, which deals with Brain Regions and their connectivity. This needs to setup a good ontology to start with and I am in the process of merging some of the Neuroscience Information Framework, Wikipedia, Foundational Model of Anatomy and some other vocabularies. Since there is a big community behind Freesurfer, I also looked into what is available here and I found the files: FreeSurferColorLUT.txt and surface_labels.txt. Am I missing some important files related to this? Now I thought that it would be nice to "align" my work with the FreeSurfers vocabulary for the benefit of everybody. So could anybody point me to the people that are involved in building the ontologies and inform about the current state of research in this field? Thanks to anybody helping me with this issues! Stephan

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