Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

QDEC and Freesurfer version compatibility
by Paul Greenberg 13 Jan '08

13 Jan '08

Hi all, Will the QDEC program and the associated preprocessing steps (recon-all / -qcache) run correctly with data from Freesurfer version 3.0.5, or do all data sets first need to be reprocessed with version 4.0.2? I downloaded stable version 4.0.2, ran recon-all /- qcache on my previous data, and wanted to know if this approach was correct. Thanks much, 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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create segmentation...
by Cameron Ellis 13 Jan '08

13 Jan '08

Hi All, Does anyone have any information on whether it is possible to create a segmentation based on custom volumetric labels one has created, and then extract functional values from that segmentation using mri_segstats? If so, how would one go about making the segmentation? Thanks, Cameron

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Hardware
by Thomas Doering 11 Jan '08

11 Jan '08

Hi, we are buying a new Computer for running Freesurfer, FSL etc. After my experience, that a 3 GHz xeon 5050 was running slower than a 1.6 GHz Xeon 5110, due to older processor architecture, i wanna be sure to buy the right one. Does somebody has an experience with a Xeon E 5345, 2.66 GHz ? If so, how long does a Freesurfer recon-all process run? Thanks for any suggestions, Thomas

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recon-all Flirt Error
by özlem özmen okur 11 Jan '08

11 Jan '08

Hi, I have got the same error with freesurfer-Linux-rh9-stable-pub-v4.0.2-full.tar.gz that I have downloaded yesterday. Thanks Ozlem ---------------------------------------------------------------------- Sarah, Indeed you are correct! The rh9 freesurfer v4.0.1 distribution is missing the fsl tools. I don't know how this happened, as the other dists have it, but I have re-posted freesurfer-Linux-rh9-stable-pub-v4.0.1.tar.gz, containing the fsl tools (actually, a subset of the full fsl distribution). recon-all will work without the fsl tool 'flirt' if there is just one structural scan. flirt is used to motion correct two or more scans. Also, the FS-FAST tools use some of the fsl tools. Apologies again, and also to Anil, Nick On Wed, 2007-11-28 at 14:03 -0600, [EMAIL PROTECTED] wrote: > i have installed version freesurfer-Linux-rh9-stable-pub-v4.0.1 > > and i do not see a dir for fsl, only fsafd and fsfast. i tend > to get the flirt error but this does not seem to affect the > completion of recon-all so i've ignored it 'til now. but just > wondering why i don't see an fsl directory if there is meant > to be one in the distribution package... > > thanks > sarah > > ---- Original message ---- > >Date: Mon, 26 Nov 2007 19:38:45 -0500 > >From: Nick Schmansky <[EMAIL PROTECTED]> > >Subject: Re: [Freesurfer] recon-all Flirt Error > >To: Anil Roy <[EMAIL PROTECTED]> > >Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > > > >Anil, > > > >flirt is an FSL utility that is included in the freesurfer > distribution > >in the $FREESURFER_HOME/fsl directory (in bin). Normally, > freesurfer > >will setup a path to it. Make sure it is in your path. > > > >Nick > > > >On Mon, 2007-11-26 at 16:26 -0600, Anil Roy wrote: > >> Hello All, > >> > >> I wanted to test the Freesurfer installation by running > recon-all but > >> I received an error saying flirt no found. Can someone > point me to the > >> cause of this problem, is it a missing library or some > other issue? > >> > >> I have posted the output from running recon-all on bert below. > >> > >> Thanks, > >> > >> Anil. > >> > >> [EMAIL PROTECTED] freesurfer]# recon-all -s bert -autorecon1 > >> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > >> Actual FREESURFER_HOME /usr/local/freesurfer > >> -rw-rw-rw- 1 root root 657949 Aug 18 > >> 23:25 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log > >> Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 > i686 i686 > >> i386 GNU/Linux > >> flirt: Command not found. > >> INFO: current FREESURFER_HOME does not match that of previous > >> processing. > >> Current: /usr/local/freesurfer > >> Previous: /space/freesurfer/build/pub-releases/freesurfer > >> #-------------------------------------------- > >> [EMAIL PROTECTED] MotionCor Mon Nov 26 16:17:47 CST 2007 > >> Found 3 runs > >> /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz > >> /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz > >> /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz > >> #----------------------------------------------- > >> /usr/local/freesurfer/subjects/bert > >> > > >> mri_motion_correct.fsl - > >> o /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz - > >> wild /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz > /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz > /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz > >> > > >> tmpdir is /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009 > >> -------------------------------------------------------------- > >> mri_motion_correct.fsl logfile > >> is > /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz.mri_motion_correct.fsl.log > >> -------------------------------------------------------------- > >> ----------------------------------------- > >> Converting /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz > >> Mon Nov 26 16:18:28 CST 2007 > >> /usr/local/freesurfer/subjects/bert > >> mri_convert > /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz > /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- > 1.img -odt float > >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ > >> reading from > /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz... > >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > >> i_ras = (-1, -0, -0) > >> j_ras = (0, 0, -1) > >> k_ras = (-0, 1, -0) > >> changing data type from 0 to 3 (noscale = 0)... > >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-1.img... > >> Analyze Output Matrix > >> - 1.000 0.000 -0.000 134.400; > >> -0.000 0.000 1.000 -111.000; > >> -0.000 -1.000 -0.000 129.000; > >> 0.000 0.000 0.000 1.000; > >> -------------------- > >> INFO: set hdr.hist.orient to -1 > >> ----------------------------------------- > >> Converting /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz > >> Mon Nov 26 16:18:33 CST 2007 > >> /usr/local/freesurfer/subjects/bert > >> mri_convert > /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz > /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- > 2.img -odt float > >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ > >> reading from > /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz... > >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > >> i_ras = (-1, -0, -0) > >> j_ras = (0, 0, -1) > >> k_ras = (-0, 1, -0) > >> changing data type from 0 to 3 (noscale = 0)... > >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-2.img... > >> Analyze Output Matrix > >> - 1.000 0.000 -0.000 134.400; > >> -0.000 0.000 1.000 -111.000; > >> -0.000 -1.000 -0.000 129.000; > >> 0.000 0.000 0.000 1.000; > >> -------------------- > >> INFO: set hdr.hist.orient to -1 > >> ----------------------------------------- > >> Converting /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz > >> Mon Nov 26 16:18:40 CST 2007 > >> /usr/local/freesurfer/subjects/bert > >> mri_convert > /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz > /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- > 3.img -odt float > >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ > >> reading from > /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz... > >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > >> i_ras = (-1, -0, -0) > >> j_ras = (0, 0, -1) > >> k_ras = (-0, 1, -0) > >> changing data type from 0 to 3 (noscale = 0)... > >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-3.img... > >> Analyze Output Matrix > >> - 1.000 0.000 -0.000 134.400; > >> -0.000 0.000 1.000 -111.000; > >> -0.000 -1.000 -0.000 129.000; > >> 0.000 0.000 0.000 1.000; > >> -------------------- > >> INFO: set hdr.hist.orient to -1 > >> ----------------------------------------- > >> Motion Correcting /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-2.img > >> Mon Nov 26 16:18:45 CST 2007 > >> /usr/local/freesurfer/subjects/bert > >> fsl_rigid_register -maxangle 90 - > >> r /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor- 1.img - > >> i /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-2.img - > >> o /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/resampled.img - > >> tmpdir /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009 -cleanup > >> > >> > >> > >> $Id: fsl_rigid_register,v 1.26 2007/06/12 15:11:07 greve Exp $ > >> Mon Nov 26 16:18:46 CST 2007 > >> /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/resampled.img > >> -------------------------------------- > >> /usr/local/freesurfer/subjects/bert > >> mri_convert /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-1.img > /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.nii > > >> mri_convert /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-1.img > /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.nii > >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ > >> reading from /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-1.img... > >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > >> i_ras = (-1, 0, 0) > >> j_ras = (0, 0, -1) > >> k_ras = (0, 1, 0) > >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.nii... > >> -------------------------------------- > >> /usr/local/freesurfer/subjects/bert > >> mri_convert /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-2.img > /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/invol.fsl_rigid_register.nii > >> mri_convert /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor- > >> 2.img /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/invol.fsl_rigid_register.nii > >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ > >> reading from /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor- 2.img... > >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > >> i_ras = (-1, 0, 0) > >> j_ras = (0, 0, -1) > >> k_ras = (0, 1, 0) > >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/invol.fsl_rigid_register.nii... > >> -------------------------------------- > >> /usr/local/freesurfer/subjects/bert > >> tkregister2_cmdl --targ > /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-1.img -- > >> mov /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor- 2.img -- > >> reg /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/tkregister.dat -- > >> fslregout /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/initxfm.fslmat --regheader > --noedit --s > >> doesnotmatter > >> target volume /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-1.img > >> movable volume /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor-2.img > >> reg file /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/tkregister.dat > >> LoadVol 0 > >> ZeroCRAS 0 > >> $Id: tkregister2.c,v MailScanner has detected a possible > fraud attempt > >> from "1.86.2.1" claiming to beMailScanner warning: > numerical links are > >> often malicious: 1.86.2.1 2007/08/15 15:39:42 nicks Exp $ > >> Diagnostic Level -1 > >> INFO: loading target > /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor- 1.img > >> Ttarg: -------------------- > >> -1.000 0.000 0.000 128.000; > >> 0.000 0.000 1.000 -128.000; > >> 0.000 -1.000 0.000 128.000; > >> 0.000 0.000 0.000 1.000; > >> INFO: loading movable > /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/cor- 2.img > >> Tmov: -------------------- > >> -1.000 0.000 0.000 128.000; > >> 0.000 0.000 1.000 -128.000; > >> 0.000 -1.000 0.000 128.000; > >> 0.000 0.000 0.000 1.000; > >> mkheaderreg = 1, float2int = 0 > >> Computing reg from header (and possibly input matrix) > >> ---- Input registration matrix (computed) -------- > >> 1.000 0.000 0.000 0.000; > >> 0.000 1.000 0.000 0.000; > >> 0.000 0.000 1.000 0.000; > >> 0.000 0.000 0.000 1.000; > >> --------------------------------------- > >> ---- Input registration matrix -------- > >> 1.000 0.000 0.000 0.000; > >> 0.000 1.000 0.000 0.000; > >> 0.000 0.000 1.000 0.000; > >> 0.000 0.000 0.000 1.000; > >> subject = doesnotmatter > >> RegMat --------------------------- > >> 1.000 0.000 0.000 0.000; > >> 0.000 1.000 0.000 0.000; > >> 0.000 0.000 1.000 0.000; > >> 0.000 0.000 0.000 1.000; > >> register: file /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/tkregister.dat written > >> FSLOUTPUTTYPE NIFTI > >> tkreg2FSL: mov det = -1, ref det = -1 > >> Init FSL Mat based on geometry ------------------- > >> 1.00000000 -0.00000000 -0.00000000 -0.00000000 > >> -0.00000000 1.00000000 -0.00000000 -0.00000000 > >> -0.00000000 -0.00000000 1.00000000 -0.00000000 > >> 0.00000000 0.00000000 0.00000000 1.00000000 > >> ------------------------------------------------- > >> -------------------------------------- > >> /usr/local/freesurfer/subjects/bert > >> calling eval flirt -in > /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/invol.fsl_rigid_register.hdr - > >> out /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/outvol.fsl_rigid_register.hdr > -bins 256 - > >> cost corratio -searchrx -90 90 -searchry -90 90 -searchrz > -90 90 - > >> interp trilinear -dof 6 - > >> ref /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.hdr - > >> init /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/initxfm.fslmat - > >> omat /usr/local/freesurfer/subjects/bert/mri/tmp- > >> mri_motion_correct.fsl-9009/outvol.fsl_rigid_register.fslmat > >> flirt: Command not found. > >> ERROR: running flirt > >> Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 > i686 i686 > >> i386 GNU/Linux > >> > >> recon-all exited with ERRORS at Mon Nov 26 16:18:55 CST 2007 > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >_______________________________________________ > >Freesurfer mailing list > >Freesurfer(a)nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Analysis question
by Corey Keller 10 Jan '08

10 Jan '08

> > Hi, > > I have a quick and hopefully simple question. The picture on the left > is an individual fmri mean functional display. To get it I used > > Tksurfer-sess -hemi rh -aparc -s PROZ06004 -analysis simple_v_complex -c > simple_v_complex while in /space/multnomah/3/users/gow/PROZ06/fMRI > > The picture is "splotchy" whereas the second picture which is the average > of all subjects for this same analysis and contrast is smooth and cleaner. > In order to display the averaged data I used > > Tksurfer fsaverage rh inflated -annot aparc -overlay > group-analysis/simple_v_complex/rh.meanfunc.nii -fthresh 2 while in the > same directory > I'm trying to get the individual subjects to look like the smooth averaged output. Can you help me with this? Thanks so much. > Best, > Corey > > -------------------- > Corey Keller > Epilepsy Unit > Clinical Research Coordinator > Massachusetts General Hospital > Wang 735, 55 Fruit Street > Boston, MA 02114 > Phone 802.578.6292 > Email cjkeller(a)partners.org > ckeller(a)nmr.mgh.harvard.edu >

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evaluating schedules with optseq2
by rhdesai＠mcw.edu 10 Jan '08

10 Jan '08

Hello, I am trying to find the cost for a schedule with optseq2. As a start, I am just using a .par file generated by optseq2 itself (from a previous search). There are two problems: (1) The --i option does not seem to work at all. It always gives the error that --nosearch option requires an input file (no matter which file you specify with --i) (2) the --in option takes the input file, but gives a bus error, as shown below. Version: $Id: optseq2.c,v 2.12 2006/12/29 02:09:11 nicks Exp $ MacOSX Tiger 10.4.11 thanks, Rutvik --------- % ./optseq2 --in optseq_out_run1-001.par --ntp 160 --tr 2 --psdwin 0 12 --polyfit 2 --nosearch --ev M 2 9 --ev L 2 9 --ev A 2 9 --ev P 2 9 --ev N 2 9 --ev F 2 6 --evc 1 -1 0 0 0 0 --evc 1 0 -1 0 0 0 --evc 0 1 -1 0 0 0 --cost vrfavg --o optseq_eval optseq2 $Id: optseq2.c,v 2.12 2006/12/29 02:09:11 nicks Exp $ NoSearch = 1 nKeep = 1 PctUpdate = 10.000000 nCB1Opt = 0 seed = -1 Ntp = 160 TR = 2 TPreScan = 0 PSD Window = 0 12 2 nEvTypes = 6 EvNo Label Duration nRepsNom 1 M 2.000 9 2 L 2.000 9 3 A 2.000 9 4 P 2.000 9 5 N 2.000 9 6 F 2.000 6 PctVarEvReps = 0 VarEvRepsPerCond = 0 PolyOrder = 2 tNullMax = -1 tNullMin = 0 outstem = optseq_eval nInFiles: 1 0 infile = optseq_out_run1-001.par AR1 = 0 No refractory penalty Cost = vrfavg OutStem = optseq_eval Summary File = optseq_eval.sum nTaskAvgs = 36 C Contrast Matrix ---------------------- 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000; ================== ---------------------- 0 0 0.0 3.83588 0.639127 0.5103 3.83588 0.0714353 3.72409 3.93012 0.206034 0 0 outstem = optseq_eval Bus error

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Re: [Freesurfer] Memory problems
by Juergen Haenggi 10 Jan '08

10 Jan '08

Hi Doug I tried to make that file executable (as root I typed chmod a+x make_average_volume) but it did not work. The file I found under the URL you send me is a text file and it is not compiled. Please can you give me any hint to make the new version of make_average_volume executable. Is there a compiled version that is already executable? Thanks a lot in advance Best regards Juergen On 4.1.2008 23:06 Uhr, "Doug Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > You may have to make it executable > > Juergen Haenggi wrote: >> >> Hi Doug >> >> Thanks for the new version, but the following error occurred: >> >> Cleaning up >> ----------------------- >> rm -r ./tmp.mris_preproc.9682 >> Fri Jan 4 21:36:04 CET 2008 >> mris_preproc done >> --------------------------------------------------- >> >> >> >> Fri Jan 4 21:36:04 CET 2008 >> make_average_surface done >> >> make_average_volume --subjects SNPs_Vp01 SNPs_Vp02 SNPs_Vp03 SNPs_Vp04 >> SNPs_Vp05 SNPs_Vp06 SNPs_Vp07 SNPs_Vp08 SNPs_Vp09 SNPs_Vp10 SNPs_Vp11 >> SNPs_Vp12 SNPs_Vp13 SNPs_Vp14 SNPs_Vp15 SNPs_Vp16 SNPs_Vp17 SNPs_Vp18 >> SNPs_Vp19 SNPs_Vp20 SNPs_Vp21 SNPs_Vp22 SNPs_Vp23 SNPs_Vp24 SNPs_Vp25 >> SNPs_Vp26 SNPs_Vp27 SNPs_Vp28 SNPs_Vp29 SNPs_Vp30 SNPs_Vp31 SNPs_Vp32 >> SNPs_Vp33 SNPs_Vp34 SNPs_Vp35 SNPs_Vp36 SNPs_Vp37 SNPs_Vp38 SNPs_Vp39 >> SNPs_Vp40 SNPs_Vp41 SNPs_Vp42 SNPs_Vp43 SNPs_Vp44 SNPs_Vp45 SNPs_Vp46 >> SNPs_Vp47 SNPs_Vp48 SNPs_Vp49 SNPs_Vp50 SNPs_Vp51 SNPs_Vp52 SNPs_Vp53 >> SNPs_Vp54 SNPs_Vp55 SNPs_Vp56 SNPs_Vp57 SNPs_Vp58 SNPs_Vp59 SNPs_Vp60 >> SNPs_Vp61 SNPs_Vp62 SNPs_Vp63 SNPs_Vp64 SNPs_Vp65 SNPs_Vp66 SNPs_Vp67 >> SNPs_Vp68 SNPs_Vp69 SNPs_Vp70 SNPs_Vp71 SNPs_Vp72 SNPs_Vp73 SNPs_Vp74 >> SNPs_Vp75 SNPs_Vp76 SNPs_Vp77 SNPs_Vp78 SNPs_Vp79 SNPs_Vp80 SNPs_Vp81 >> SNPs_Vp82 SNPs_Vp83 SNPs_Vp84 SNPs_Vp85 SNPs_Vp86 SNPs_Vp87 SNPs_Vp88 >> SNPs_Vp89 SNPs_Vp90 SNPs_Vp91 SNPs_Vp92 >> 'csh: Unknown option: `- >> Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ]. >> [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] >> juergenh% >> >> >> Best regards >> Juergen >> >> >> On 3.1.2008 21:03 Uhr, "Doug Greve" <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu> wrote: >> >> >> >>> >>> >>> This is a problem when it attempts to create an "average" aseg. As a >>> stop-gap measure, I've created a new version that will not stop the >>> execution if this stage fails. You can get it from here: >>> >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_v >>> ol >>> ume >>> >>> doug >>> >>> Juergen Haenggi, Psychological Institute wrote: >>> >>> >>> >>>> >>>> Dear FS experts >>>> >>>> I tried to average the brains of 92 subjects. We used a MacPro Quad >>>> with 5 GB RAM and about 10 GB virtual memory. When running >>>> make_average_subject the following error occurred: >>>> >>>> Checking 91 >>>> /Applications/freesurfer/subjects/average/tmp/make_average_vol-tmp/seg-SNPs >>>> _V >>>> p92.mgh >>>> >>>> nframestot = 92 >>>> Allocing output >>>> mri_concat(13587) malloc: *** vm_allocate(size=262144) failed (error >>>> code=3) >>>> mri_concat(13587) malloc: *** error: can't allocate region >>>> mri_concat(13587) malloc: *** set a breakpoint in szone_error to debug >>>> MRIalloc(256, 256, 256): could not allocate 262144 bytes for 14117th >>>> slice >>>> >>>> Cannot allocate memory >>>> [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] >>>> juergenh% >>>> >>>> Does it really mean there is too less memory or is it a similar >>>> problem occurred in other software, i.e. memory acquisition >>>> restriction by the Java Runtime Environment? >>>> Is there any possibility, beside buying more RAM, to run >>>> make_average_subject with the available 5 GB RAM? >>>> >>>> Thanks in advance and Happy New Year >>>> Best regards >>>> Juergen >>>> >>>> >>>> ------------------------------------------------- >>>> Juergen Haenggi >>>> Ph.D. (Dr. des.) >>>> Division of Neuropsychology >>>> Institute of Psychology >>>> University of Zurich >>>> Binzmuehlestrasse 14, PO Box 25 >>>> 8050 Zurich, Switzerland >>>> 0041 44 635 73 97 (phone office) >>>> 0041 76 445 86 84 (phone mobile) >>>> 0041 44 635 74 09 (fax office) >>>> BIN 4.D.04 (office room number) >>>> j.haenggi(a)psychologie.uzh.ch (email) >>>> http://www.psychologie.uzh.ch/neuropsy/ (website) >>>> http://www.juergenhaenggi.ch (private website) >>>> ------------------------------------------------- >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> >>> >> >> >> >> ----------------------------------------------------------- >> Juergen Haenggi >> Ph.D. (Dr. des.) >> Division of Neuropsychology >> Institute of Psychology >> University of Zurich >> Binzmuehlestrasse 14, PO Box 25 >> 8050 Zurich, Switzerland >> 0041 44 635 73 97 (phone office) >> 0041 76 445 86 84 (phone mobile) >> 0041 44 635 74 09 (fax office) >> BIN 4.D.04 (office room number) >> j.haenggi(a)psychologie.uzh.ch (email) >> http://www.psychologie.uzh.ch/neuropsy/ (website) >> http://www.juergenhaenggi.ch (private website) >> ----------------------------------------------------------- >> >> >> >> ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

Input parameters
by SANCHEZ BENAVIDES, GONZALO 10 Jan '08

10 Jan '08

Hello, I'm new with FreeSurfer and I need some help. We want to run cortical thickness analysis in batch on a big computer system and the technician asked me for the "input parameters" to run automatically several studies. Where can I find information about this, please? Thank you. -------- Abans d'imprimir aquest missatge, si us plau, comprova que és realment necessari. El medi ambient és cosa de tots. Antes de imprimir este mensaje, por favor, comprueba que es realmente necesario. El medio ambiente es cosa de todos. Before printing this e-mail, please make certain it is absolutely necessary. The environment is everybody's business. -------- La informació continguda en aquest missatge i en qualsevol fitxer adjunt és confidencial, privada i d'ús exclusiu per al destinatari. Si no és la persona a la qual anava dirigida aquesta informació, si us plau, notifiqui immediatament l'enviament erroni al remitent i esborri el missatge. Qualsevol còpia, divulgació, distribució o utilització no autoritzada d'aquest correu electrònic i dels seus adjunts està prohibida en virtut de la legislació vigent. La información contenida en este mensaje y en cualquier fichero adjunto es confidencial, privada y de uso exclusivo para el destinatario. Si usted no es la persona a la cual iba dirigida esta información, por favor, notifique inmediatamente el envío erróneo al remitente y borre el mensaje. Cualquier copia, divulgación, distribución o utilización no autorizada de este correo electrónico y de sus adjuntos está prohibida en virtud de la legislación vigente. The information included in this e-mail and any attached files is confidential and private. If you are not the intended recipient, please notify the sender and delete this message immediately. Dissemination, forwarding or copying of this e-mail and its associated attachments is strictly prohibited in accordance with current legislation. --------

1 0

segmentation of brain of age 8-13
by BumSeok Jeong 09 Jan '08

09 Jan '08

Dear freesurfer experts, I got uncorrected segmentation results, especially occipital cortex, from brain of age 8-13. I found similar problem in adult brain in freesurfer mailing list and the resolving answer like below. "use the control points with the mri_ca_normalize flag as part of the aseg. I've not used the command much, but you should be able to add the flag '-f tmp/control.dat' to the normal mri_ca_normalize command to run this step" Do I have to do any procedure for brain of age 8-13 in addition to suggestion like above? Thanks, bsjeong

2 1

Gray Matter Mask - twist on previous post
by Emily Trittschuh 09 Jan '08

09 Jan '08

Dear Group, Back in April, Anil Roy posted a question about methods to generate a gray matter mask that can be fed into AFNI . . . I'm wondering if the opposite can be done? Can a functional mask made in AFNI be fed easily into Freesurfer? Currently this mask is saved as a NIFTI dataset. Thank you. Emily Emily Trittschuh, PhD Neuropsychology Post-doctoral Fellow Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11-579 Chicago, IL 60611 phone 312/503-1155 fax 312/908-8789

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