Freesurfer August 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
82 discussions

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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design matrix : inter-run effetcs
by Andersson Frederic 02 Dec '08

02 Dec '08

Hi, Computing individual fMRI analysis (several runs) and looking at the design matrix (X.mat), I saw that only one regressor represents each condition. I was expecting that the number of regressors concerning a condition would be the number of runs (as SPM). There are "inter-run effect" regressors but is this better if I affect a different value for each of run and each condition (see examples below). Other question concerning design matrix : only 3 movement parameters included in the design matrix. Why 3 rather than the 6 computed during movement correction? Concerning inter-run effects and movement parameters, is there any advantage of reducing the number of regressors but having a less ideal model? >>> 1 condition = 1regressor 0 = rest 1=conditionA 2=conditionB Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 1 15 1 18 1 18 1 18 1 21 1 21 1 21 1 24 1 24 1 24 1 27 1 27 1 27 1 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 2 42 2 45 2 45 2 45 2 48 2 48 2 48 2 51 2 51 2 51 2 54 2 54 2 54 2 57 0 57 0 57 0 >>> 1 condition = 1regressor / run 0=rest 1=conditionA run#1 2=conditionB run#1 3=conditionA run#2 4=conditionB run#2 5=conditionA run#3 6=conditionB run#3 Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 3 15 5 18 1 18 3 18 5 21 1 21 3 21 5 24 1 24 3 24 5 27 1 27 3 27 5 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 4 42 6 45 2 45 4 45 6 48 2 48 4 48 6 51 2 51 4 51 6 54 2 54 4 54 6 57 0 57 0 57 0 Frédéric ANDERSSON.

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Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats
by bell0368＠umn.edu 08 Oct '08

08 Oct '08

I was wondering how the calculations of the wm volume were performed as well. The six values below are volume values from aseg I believe. I assume mris_wm_volume does more than sub-divide these regions into the wm parcellations, but probably also includes partial volume estimations along the wm/gm surface, is this correct? I basically have the same question for the gm volume values in aparc.stats; do they include partial volume calculations from the gm/pial and gm/white borders? Which binary is used to create these values for gm in aparc.stats... is it mri_segstats (with --pv)? I was assuming it would be an mris (surface) calculation as well. I am asking because if you use tkmedit to view the ?h.surface files and load the aparc+aseg or wmparc segmentation volumes in also, the surfaces and the segmentations don't seem to line up. Is there a way to create a segmentation volume that includes partial-volumed voxels at the gray/white and gray/pial boundries? Thanks for your help. Chris Bell the interior voxels are only included in the volume if they are one of the following in the aseg.mgz: case Left_Cerebral_Cortex: case Right_Cerebral_Cortex: case Left_Cerebral_White_Matter: case Right_Cerebral_White_Matter: case Left_WM_hypointensities: case Right_WM_hypointensities: cheers, Bruce On Tue, 15 Jul 2008, Marin Richardson wrote: OK, so aparc.stats is better for cortical gray matter. I want to look at the parcellated white matter volumes as well - is the only/best option to use the wm volumes from wmparc.stats? Also, when using mris_wm_volume to calculate total white matter, I saw the result defined as the volume within the white matter surface minus non-WM structures? Can you tell me which regions are and are not included? Marin Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>> It is better to use the aparc as it is derived from surface measurements, which have sub-voxel resolution. The wmparc.stats are generated by counting 1mm^3 voxels. doug Marin Richardson wrote: Hi all, I noticed that the gray volumes for parcellated cortical regions in wmparc.stats are different from those for the same region in aparc.stats (e.g. ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = 9466 in lh.aparc.stats). Why are the values different and which one is a better measure to use? Thanks, Marin

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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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Re: FDR correction
by d.g.lawyer＠medisin.uio.no 28 Aug '08

28 Aug '08

Dear Manja, It is statistically valid for the threshold suggested by FDR to vary in the different hemispheres. The reason is that FDR defines a proportion, not an absolute. The FDR procedure suggests a p-value threshold with the property that of all positive results at that threshold, one can expect that no more than X percent are false positives (where X is the desired FDR rate). It is very possible that the threshold with this property would be different in the right compared to the left hemisphere. More informally, one is claiming that of all results declared "significant", X% are probably B.S. Since X is presumably small and the number of results large enough to be interesting, one can safely conclude that the experimental condition explains cortical variation at (most of) the locations indicated. Now divide the brain into subregions (perhaps right and left hemisphere, or perhaps something else) in each of which X% of the significant results are probably false. Then the claim that "X% of the overall results are probably false" is valid. +glenn ------------------------------------ Here miracles become marvels, and marvels recurring wonders. -- William Beebe Dr. Glenn Lawyer +352 661 967 244 Instituttgruppe for psykiatri Seksjon Vinderen PB 85 Vinderen 0319 Oslo http://folk.uio.no/davidgl

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Re: [Freesurfer] Classifying cortical thickness
by Sebastian Gluth 28 Aug '08

28 Aug '08

Quoting Polina Golland <polina(a)csail.mit.edu>: > http://www.na-mic.org/Wiki/index.php/Mbirn:_Machine_Learning_Tools > > If you scroll down to the middle of the page, there is a link to > download the classification scripts. > > Polina. > > > > > > On Thu, Aug 28, 2008 at 04:02:09PM -0400, Bruce Fischl wrote: >> Hi Sebastian, >> >> I think Polina might have packaged something up for either ITK or mBIRN. >> Polina? >> >> Bruce >> >> On Thu, 28 Aug 2008, Sebastian Gluth wrote: >> >> >Hi, >> >I'm planning to analyze cortical thickness data and read about this >> >classification and permutation approach by Golland et al. (2002) and >> >Golland & >> >Fischl (2003) in order to account for multivariate effects. >> > >> >Is this classification procedure included in FreeSurfer (in form of a tool >> >or a >> >Matlab script or so)? >> > >> >Thanks, >> >Sebastian >> >_______________________________________________ >> >Freesurfer mailing list >> >Freesurfer(a)nmr.mgh.harvard.edu >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> > >> > > > -- > Polina Golland > MIT CSAIL > 32 Vassar Street D470 > Cambridge, MA 02139 > > polina(a)csail.mit.edu > http://people.csail.mit.edu/polina > > Office: 32-D470 > Phone: (617) 253-8005 > Fax: (617) 253-4640 > > Hi Polina and Bruce, many thanks for this (very rapid) help! Best, Sebastian

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Freesurfer August 2008