Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

white matter volume - version 3.0.5 vs 4.0.5
by Paul Greenberg 23 Jun '08

23 Jun '08

Dear Freesurfers, Is it acceptable to use the program "mris_wm_volume" from version 4.0.5 (Cent OS, x86_64) to calculate total white matter volume from data processed with version 3.0.5? Would I need to subtract any subcortical volumes such as ventricles, basal ganglia, etc, from the output of mris_wm_volume (version 4.0.5) in order to get the most accurate measurement of total white matter volume? Thanks! Paul -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg(a)ucsd.edu

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inorm-sess error
by Leila Reddy 23 Jun '08

23 Jun '08

Hi, I'm trying to get around the problems from my previous post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07669.html I am now trying to use mri_convert to convert from nifti to bshort using the following command: mri_convert -i rfkoch-0021-00144-000144-00.nii -it nii -o fspm2_000.bshort -ot bshort The bshort files seem to be created but then when I run inorm-sess I get the following error. The odd thing is that when I used mri_concat on exactly the same .nii files (as mentioned in my previous post) I was able to run inorm-sess with no errors... What is the difference between these two commands? The inorm error: Warning: Matrix is singular to working precision. > In fast_inorm at 196 ??? Error using ==> betainc at 35 X must be in the interval [0,1]. The exact output from the command is pasted below. Here is the output of bugr: --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5 Kernel info: Darwin 8.11.1 i386 --------------------------------------------------------------------- If anyone has any suggestions I'd be grateful to hear them! Thanks! inorm-sess -sf sessid -df sessdir -rlf runlist_inormcheck -funcstem fspm2 ------------------------------------------------ ------------------------------------------------ ------------------------------------------------ /Volumes/donnees/Imagery/imagery_data/RF005 Thu Jun 19 17:43:17 CEST 2008 Filesystem 512-blocks Used Avail Capacity Mounted on /dev/disk0s3 808067040 465870224 342196816 58% /Volumes/donnees RunList 021 ---------------------------------------------- /Volumes/donnees/Imagery/imagery_data/RF005/bold inorm -i 021/fspm2 -umask 22 -TR 2.0000 -ipr 3 -bpr 2.9999998958184 -seqname PerImg ---------------------------------------------- Log file is 021/inorm.log inorm matlab file is /tmp/inorm_21280.m ----------- Matlab file -------------- %%% ----------------- %% % matlab file to run inorm % This is a temporary file and may be deleted % /tmp/inorm_21280.m global QuitOnError; QuitOnError = 1; r = fast_inorm( '-i', '021/fspm2', '-umask', '22', '-TR', '2.0000', '-ipr', '3', '-bpr', '2.9999998958184', ' ', 'PerImg'); quit; ----------------------------------- ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007 Warning: Duplicate directory name: /Users/lreddy/matlab. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> $Id Parsing Arguments Checking Parameters invol 021/fspm2 firstslice 0 nslices 32 relthresh 0.750000 reportfile 021/fspm2.report meanvalfile 021/fspm2.meanval twfstem 021/fspm2.twf TR 2.000000 First Pass: Computing global mean 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Second Pass: Segmenting 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Warning: Matrix is singular to working precision. > In fast_inorm at 125 Warning: Matrix is singular to working precision. > In fast_inorm at 146 Warning: Matrix is singular to working precision. > In fast_inorm at 175 Warning: Matrix is singular to working precision. > In fast_inorm at 196 ??? Error using ==> betainc at 35 X must be in the interval [0,1]. Error in ==> tTest at 37 p = betainc(z,dof/2,0.5); Error in ==> fast_inorm at 223 tSigCor = tTest(s.ntp-2,tCor); >> 2008-06-19 17:43:31.661 MATLAB[21307] Process manager already initialized -- can't fully enable headless m

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Reanalyzing some OASIS cases
by Martin Kavec 23 Jun '08

23 Jun '08

Hi, I would like to rerun recon-all (from the latest freesurfer) on a few cases from OASIS brains study, to get control values for my patient group. Since my computational options are rather limitted, I would like to avoid running redundant steps, which would anyway give me the same results, or to repeat possible surface editing. Anybody could please suggest me where to start the analysis or in general how to tackle this problem? Thanks in advance, Martin

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cortical measures - normalised?
by Narly A Golestani 21 Jun '08

21 Jun '08

Dear all, Am I correct in thinking that the measures of cortical volume, area, and thickness, as well as subcortical volumes obtained after running the reconall pipeline (and found in the 'aparc' and 'aseg' files, respectively) are native ones? Or are they based on normalised brains, thus 'controlling' for overall brain volume differences? thanks, Narly.

6 6

Erosion of Fill Volume/Pial Surface
by Cochrane Jamison 19 Jun '08

19 Jun '08

I have been working on getting a volume created by mris_fill from the pial surfaces exported to be used in a dipole/current density analysis software package. I have succeeded in being able to concat both halves and have gotten the volumes loaded successfully into the software, but I need a bit better resolution. My question is this: Is there a way to erode the pial surface either before or after its creation? I need maybe 0.5 - 1mm of erosion so that each sulci is a bit more defined. The surface looks great, but in order to consider the grey matter in each sulci for the dipole/current density calculation, each sulci needs to be distinct. The only way that I can think about it is by eroding the grey matter by 0.5-1mm before I use the mris_fill command. I am not sure if this is even possible, or if it is where it would need to be done. Thanks for any help. Cochrane

2 1

mri_convert from BRIK to NIFTI
by Lauren Ethridge 19 Jun '08

19 Jun '08

Hi, I'm relatively new to freesurfer, just learned about it at the Multi-modal course this year, and I'm trying to apply it to some of our own functional data. This may be a bit of a simple question, but here goes. I've tried to use mri_convert to change a brik file to nifti but I get the following error: [quackers@matlab anat_lauren]$ mri_convert fa+orig.BRIK fa.nii mri_convert fa+orig.BRIK fa.nii $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from fa+orig.BRIK... afniRead(): error opening file /birc/jemlab/anat_lauren/fa+orig.HEAD [quackers@matlab anat_lauren]$ The header file is located in the same folder as the brik file. Is there something I need to do to the header file in order to make it readable to fsfast? I've also tried using unpacksdcmdir to unpack the raw dicom files, but the data came from a GE scanner so it doesn't seem to recognize them. Any help would be much appreciated. Lauren ------ Lauren Ethridge Graduate Student - Neuroscience Franklin Foundation Fellow Biomedical and Health Sciences Institute University of Georgia 706-542-3128

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questions regarding freesurfer 4.0.5
by Sebastian Moeller 19 Jun '08

19 Jun '08

First, if this shows up twice, let m apologise for mixing up my email addresses... Aloha fellow surfers, I just installed ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-leopard-i686-st… on my: intel macbook, running 10.5.3 with 4GB of RAM. A few observations: 1) minor: freeview does not seem to be part of the dmg, probably expected, but from the release notes it is not obvious, whether the macos version should contain it or not 2) minor, minor: it seems like the whole macos version is built for 32bit only (at least that is what "file `which mri_convert`" and a few other binaries tell me); would it be possible to have a 64bit built (than my macbook might suffice for surface reconstruction as well). 3) scuba dies horribly (tkmedit and tksurfer, however seem to work, at least they start up and display something), here is the problem report: Path: /opt/freesurfer//bin/scuba.bin Identifier: scuba.bin Version: ??? (???) Code Type: X86 (Native) Parent Process: tcsh [18243] Date/Time: 2008-06-18 10:10:42.832 +0200 OS Version: Mac OS X 10.5.3 (9D34) Report Version: 6 Exception Type: EXC_BAD_ACCESS (SIGBUS) Exception Codes: KERN_PROTECTION_FAILURE at 0x0000000000000000 Crashed Thread: 0 Thread 0 Crashed: 0 scuba.bin 0x001e5764 0x1000 + 1984356 1 dyld 0x8fe0e723 ImageLoader::recursiveInitialization(ImageLoader::LinkContext const&, unsigned int) + 307 2 dyld 0x8fe0e809 ImageLoader::runInitializers(ImageLoader::LinkContext const&) + 57 3 dyld 0x8fe04102 dyld::initializeMainExecutable() + 146 4 dyld 0x8fe07b5f dyld::_main(mach_header const*, unsigned long, int, char const**, char const**, char const**) + 2975 5 dyld 0x8fe01872 dyldbootstrap::start(mach_header const*, int, char const**, long) + 818 6 dyld 0x8fe01037 _dyld_start + 39 Thread 0 crashed with X86 Thread State (32-bit): eax: 0x00000000 ebx: 0x001e570c ecx: 0x00000002 edx: 0x00000000 edi: 0x00000026 esi: 0x00001000 ebp: 0xbfffd548 esp: 0xbfffd4c0 ss: 0x0000001f efl: 0x00010282 eip: 0x001e5764 cs: 0x00000017 ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037 cr2: 0x00000000 Binary Images: 0x1000 - 0x23ffed +scuba.bin ??? 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(???) /System/Library/ Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib 0x96db5000 - 0x96e48fff com.apple.ink.framework 101.3 (86) <dfa9debcd7537849d228021d1d9c0f63> /System/Library/Frameworks/ Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink 0x96f3e000 - 0x96fc8fe3 com.apple.DesktopServices 1.4.6 (1.4.6) <94d1a28b351b7dff77becadab0967772> /System/Library/PrivateFrameworks/ DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv 0x96fc9000 - 0x96fd0fe9 libgcc_s.1.dylib ??? 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(???) /usr/lib/ libSystem.B.dylib -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 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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2D images
by jewet037＠umn.edu 18 Jun '08

18 Jun '08

Hi, I would like to create a properly proportioned 2-dimensional map of hemispheric surfaces to use for displaying average vertex values within parcellated regions or individual values for each vertex. At the moment, we can access the matrix of vertex values (i.e. the scalars computed at each vertex of the equilateral triangles along the surface), but we don't know how to associate these values with the regions they came from, or how to plot them on a 2D surface. Thanks, Ethan

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FreeSurfer tksurfer
by Pedro Brito Cruz 18 Jun '08

18 Jun '08

Dear all, i'm a newbie using FreeSurfer and recently installed the CentOS 4 x86_64 version on my 64 bit processor with Linux Ubuntu (dapper version). I followed the tutorial for testing the installation and tkmedit tool worked fine but tksurfer did not. I got the following error, tksurfer bert rh pial surfer: current subjects dir: $FREESURFER_HOME/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: Reading header info from $FREESURFER_HOME/subjects/bert/mri/T1.mgz surfer: vertices=131168, faces=262332 Received X error! Error code : 163 Request code : 148 Minor code : 2 Error text : 'GLXBadLargeRequest' Does anybody know what can i do to solve this problemL? Thanks in advance. Pedro

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ICV accuracy
by Jared Conley 18 Jun '08

18 Jun '08

FreeSurfer Community: A quick question for the group. Our lab was wondering if there is an easy way to assess the accuracy of the intracranial volume (ICV) measurement? Or is this not necessary (never any errors)? Thanks in advance, Jared -- Jared Conley Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave., RF 394 P: 617.525.6238

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