Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30083 discussions

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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fsl ROIs become smaller after registered to freesurfer
by Wang, Xin 28 Aug '08

28 Aug '08

Hello, Group, I tried to registered the fsl average of one subject .gfeat to his freesurfer surface. After manual correction of register files, the ROIs of ,gfeat become much smaller on the freesufer surface (including less cortical areas). please help me with this problem. Thank in advance, Xin

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Recommended workflow
by Martin Kavec 28 Aug '08

28 Aug '08

Greetings to all, I have several pathological subjects, which need substantial editing involving removing of dura reminders, filling WM due to the lesions, and adding control points due to the WM atrophy. I ran "recon-all -all" first to have initial reconstruction, which helps me to focus on correcting the earlier mentions problems. I have corrected brainmask, wm, and created control points, and now I wonder if re-running "recon-all -autorecon2-cp -autorecon3" would be sufficient to get correct results, or should better run separately "recon-all -autorecon2-cp" followed by "recon-all -autorecon2-wm -autorecon3"? Thanks in advance, Martin

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Classifying cortical thickness
by Sebastian Gluth 28 Aug '08

28 Aug '08

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

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mri_glmfit full Monte Carlo simulation run time on tutorial data
by Silviu Podariu 28 Aug '08

28 Aug '08

Hello! I was running the full Monte Carlo simulation on the 40 subjects tutorial data (following the Group Analysis tutorial, with mri_glmfit from command line) and I see the simulation is still running after 10 days... I was wondering if this was normal or something is wrong. (using a single 2GHz dual-core Intel Xeon processor on an 8GB Mac workstation). What would be an expected time for that simulation, with exactly the same options/parameters as given in the tutorial command (shown below)? mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 10000 2 lh.gender_age.glmdir/csd1Thank you very much, Silviu Podariu U.Nebr.Med.Cent. Omaha, NE

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Configure Overlay display
by Nicola Hobbs 28 Aug '08

28 Aug '08

Hi all, We've noticed that the min threshold value in the configure overlay display toolbar doesn't correpond to the value displayed on the scale bar. Could someone explain this difference please? Thanks for your help. Nicola -- Nicola Hobbs Dementia Research Centre National Hospital for Neurology and Neurosurgery Queen Square London WC1N 3BG +44 (0)845 155 5000 ext. 723839

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