Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

WM intensity < CSF intensity?
by Juranek, Jenifer 03 Sep '08

03 Sep '08

Hi, I'm running fsv405 on RHEL5. I received the following message and reviewed the input images, but could not spot the problem. Any suggestions about where I should be looking in the T1.mgz? Many Thanks, Jenifer White matter intensity 0 is lower than CSF intensity 14. Please examine input images. Will terminate ... *********************************************** *********************************************** *********************************************** ********************************************************** MRIstripSkull failed. ************************************************************

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Surface area measurement
by Barkay, Gavriel 03 Sep '08

03 Sep '08

Can I do surface area measurement using freesurfer? -- Gavriel Barkay M.D. M.Sc. Psychopharmacology Fellow Office: 317-433-1771 Pager: 317-312-2448

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about white matter segmentation
by abel cruz vadell 02 Sep '08

02 Sep '08

Hi Checking the white matter segmentation of a subject I found the problem atacched (blue arrow in the axial, sagital and coronal views). I used controls points but the problem remains. Any idea? Thanks Abel

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Statistic in Freesurfer
by Massimiliano Calabrese 02 Sep '08

02 Sep '08

Dear Freesurfer users, probably this is for you a very simple question: we would like to know if it has been implemented a tool based on permutation test to compare thickness and volume of different regions. we know that there are similar tools for voxels scale, but we did not know anything of similar for regional anlaysis.(and if this could be useful ) Thank you Massimiliano Calabrese Multiple Sclerosis Centre University of Padova Italy Marco Battaglini Quantitative Neuroimaging Laboratory University of Siena _________________________________________________________________ Stanco della solita finestra? Personalizza la tua Hotmail! http://www.messenger.it/personalizza.html#sfondi

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convert point from anatomical- to functional space
by Steinmann, Iris 01 Sep '08

01 Sep '08

Dear Freesurfers, I have a question concerning the register.dat. In Freesurfer-Wiki I found that sentence: 'The last four lines of register.dat have the values of the registration matrix that converts a location in anatomical space to a location in functional space' I want convert one special point from my high resolution anatomical space (256x256) to my low resolution functional space (64x64). So I want apply the register.dat-Matrix to the Vektor from this point in anatomical space. But why is it an 4x4 Matrix? I supposed that I need an 3x3-matrix for an translation in x,y,z-direction. How can I get this anatomical point in my functional space? Thanks for your answer

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definition of metric distortion
by Patrick Schikowski 31 Aug '08

31 Aug '08

I am wondering how the percent distance error you present in fig.11 in "Cortical Surface-Based Analysis - II: Inflation, Flattening, and a Surface-Based Coordinate System" [Fischl et al, 1998] was exactly determined? In "6. ERROR ANALYSIS" you just mentioned "Finally, we present the errors of the flattening and spherical transformation on a set of 10 human hemispheres.All percentages in this section are computed using an L1 norm as it is less sensitive to outliers than the L2 norm." Could you please give me some details about the process of measuring the errors, maybe an equation? thanks a lot, patrick

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mri_glmfit error while following tutorial
by N. Eiji Nawa 31 Aug '08

31 Aug '08

Hi: I am doing the freesurfer tutorial (http://surfer.nmr.mgh.harvard.edu/ fswiki/FsFastTutorial), but got an error while running the Random Effects Surface-based Group Analysis section. The command line was: mri_glmfit --y lh.ces.nii --osgm --mask ../lh.mask.nii --glmdir lh.rfx.osgm --nii --surf fsaverage lh and this is the terminal output: Reading source surface /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial//fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /Applications/freesurfer/subjects/ buckner_data/tutorial_subjs/fsfast-tutorial//fsaverage/surf/ lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/ fsfast-tutorial/fb1-analysis-study/group-analysis-tut/sm-gamma-fwhm5/ odd-v-0 cmdline mri_glmfit --y lh.ces.nii --osgm --mask ../lh.mask.nii -- glmdir lh.rfx.osgm --nii --surf fsaverage lh sysname Darwin hostname cerezo.cis.atr.jp machine Power Macintosh user eiji FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/ fsfast-tutorial/fb1-analysis-study/group-analysis-tut/sm-gamma-fwhm5/ odd-v-0/lh.ces.nii logyflag 0 usedti 0 mask ../lh.mask.nii maskinv 0 glmdir lh.rfx.osgm DoFFx 0 Creating output directory lh.rfx.osgm Loading y from /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group-analysis-tut/ sm-gamma-fwhm5/odd-v-0/lh.ces.nii ERROR: Read 819210, expected 41943552 niiRead(): error reading from /Applications/freesurfer/subjects/ buckner_data/tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group- analysis-tut/sm-gamma-fwhm5/odd-v-0/lh.ces.nii ERROR: loading y /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group-analysis-tut/ sm-gamma-fwhm5/odd-v-0/lh.ces.nii I am not quite sure what is in 'lh.ces.nii' - from the file's time stamp it looks like it was not generated during the tutorial (Jun 19 2007). Any help or comment will be very helpful - I am basically clueless... Thanks a lot in advance!!! Eiji (below is the summary of my environment and problem) -- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5 Kernel info: Darwin 8.11.0 Power Macintosh (Mac OS 10.4.11 on a G5) SUBJECTS_DIR: /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/ which mri_glmfit: /Applications/freesurfer/bin/mri_glmfit pwd: /Applications/freesurfer/subjects/buckner_data/tutorial_subjs/ fsfast-tutorial/fb1-analysis-study/group-analysis-tut/sm-gamma-fwhm5/ odd-v-0 command line: /Applications/freesurfer/subjects/buckner_data/ tutorial_subjs/fsfast-tutorial/fb1-analysis-study/group-analysis-tut/ sm-gamma-fwhm5/odd-v-0 error message: ERROR: Read 819210, expected 41943552

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optseq2- bus error?
by Audrey Nath 29 Aug '08

29 Aug '08

Hello I am running optseq2 on Mac OS X, v.10.5.4. Over the past 2 days, Optseq2 has been crashing after running for a few minutes. It will run along smoothly, and then suddenly: optseq2(22653) malloc: *** error for object 0x3be83b0: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug Bus error Even if I run a simple script like /Applications/freesurfer/bin/optseq2 \ --tsearch .5 \ --psdwin 0 16 2 \ --nkeep 3 --o test_0.5hr \ --ntp 100 --tr 2 \ --polyfit 2 --focb 1 \ --ev evt1 2 30 \ --ev evt2 2 30 it still crashes after running for a while. The log file doesn't give any indication as to why it stops running. When I entered 'bugr', it output the following: --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5 Kernel info: Darwin 9.4.0 i386 --------------------------------------------------------------------- Thank you! Audrey Nath

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RE: Freesurfer Digest, Vol 54, Issue 34
by Prapti Gautam 29 Aug '08

29 Aug '08

Hi, Is it possible to run recon-all so that both control point edits and brain volumes can be processed with a single command? Currently I use recon-all -autorecon2-cp -autorecon3 -subjid for corrections to control points and recon-all -autorecon2-pial -autorecon3 -subjid for corrections to brain volume but is there another way so that when a brain needs corrections with both control points and brain volume, both can be edited with a single command at the same time so that I save on processing times?? Thanks, Prapti

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tkmedit error
by Jing Wu 29 Aug '08

29 Aug '08

> From: wuj3040(a)hotmail.com> To: analysis-bugs(a)nmr.mgh.harvard.edu> Subject: > Date: Thu, 28 Aug 2008 16:14:21 +0000> > > Dear Expert,> I am new user to FreeSuefer. I have tried the reconstruction work flow for our Cor 3D SPGR images from 3T MRI scanner. I have imported dicom images to the directory, the volume dimension/voxel were as 256x256x216/0.9375x0.9375x1. The steps autorecon1 and autorecon2 were completely without error. When I tried to load the rh_volume, the tkmedit was crashed down and indicated to send the error message to you. > The aseg.stats was shown the excited segmentation data. Do you think that we could use Cor 3D SPGR images instead of MPRAGE images?> How to rotate the brainmask image as attached for good looking?> Thank you very much!> > Jing> > _________________________________________________________________> Talk to your Yahoo! Friends via Windows Live Messenger. Find out how.> http://www.windowslive.com/explore/messenger?ocid=TXT_TAGLM_WL_messenger_ya… _________________________________________________________________ Get thousands of games on your PC, your mobile phone, and the web with Windows®. http://clk.atdmt.com/MRT/go/108588800/direct/01/

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