Freesurfer January 2008

freesurfer@nmr.mgh.harvard.edu

54 participants
69 discussions

recon-all error
by fpolli＠nmr.mgh.harvard.edu 17 Jan '08

17 Jan '08

hi in /space/nexlin3/3/users/kahn/fpolli, i ran reconall -i RECONS_DIR/pol001/003/001.mgz -all i got the following error: ERROR: wrong talsrcimg.4dfp.ifh orientation ERROR: mpr2mni305 failed, see transforms/talairach_avi.log this is data collected at MIT, so does it have to do with something in the DICOM being different here? thanks, frida

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apple leopard 64 bit
by Kirk, Gregory 17 Jan '08

17 Jan '08

Hi all, Are there plans to release binaries for the Mac Leopard 64 bit Greg.

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Zen of label editing in tksurfer
by Graham Wideman 17 Jan '08

17 Jan '08

Folks: We notice that when we try editing labels in tksurfer (eg: draw an outline, fill with new label value), this results in tksurfer's control panel showing two labels everywhere (even where we didn't edit), with the second one saying "1 additional label" (or something like that... don't have it running at the moment). Further exploration has us puzzled about deletion, saving and so on. What is the model that tksurfer is following here? If you load one label file, and then start editing, is that like tksurfer introduces another "layer" (ie: a second label slot for every vertex?). How do you load a label file and explicitly edit that data instead of creating new data? Thanks, Graham

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error: libexpat.so.0
by Woo Suk, Tae 17 Jan '08

17 Jan '08

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } How are you?When I run recon-all -s subjid -all with Fressurfer 4.02,the process was terminated with the error message of" mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory"And, when I ran 'qdec' , the same error "qdec.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file:No such file or directory" was occured.But, "libexpat.so.0" was already installed.How can I correct it?Woo Suk, Tae Ph.D

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-autorecon2 FILL
by bell0368＠umn.edu 15 Jan '08

15 Jan '08

Freesurfers, I have a subject that exits with errors from autorecon2 FILL with the following message "mri_fill: could not find any points where lh and rh wm are nbr s" Has anyone come across a similar problem? Thanks Chris Bell

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Custom color scale for overlays in tksurfer
by Hans Johnson 15 Jan '08

15 Jan '08

Hello, Is there a way to apply a custom color scale to overlays in tksurfer. It seems that the the only options are "Green Red; Heat; "Blue Red". I would really like to make my own colors. Any suggestions would be greatly appreciated. Thanks, Hans -- Hans J. Johnson, Ph.D. Hans-johnson(a)uiowa.edu 278 GH The University of Iowa Iowa City, IA 52241 (319) 353 8587

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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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Freesurfer January 2008