Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

analysis.cfg for retinotopy analysis
by romain valabregue 27 Nov '07

27 Nov '07

Hello I am trying to analyze retiontopy data using the indication found : http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I first created the analysis with the comand : mkanalysis-sess -a rtopy -TR 2.8 -designtype retinotopy -paradigm rtopy.par -ncycles But then when I try to run the anlysis with the comand : sfa-sess -a rtopy -s ../Sujet5_retino I get the folowing error --- Parsing Config File: /homenasFC1/romdat/data/freesurfer_DB/Sujet5_retino/rtopy/analysis.cfg ---- -ncycles 7 -delay 0 -acfbins 10 -nskip 0 -fwhm 0 -noautostimdur ERROR: Flag -acfbins unrecognized. -ncycles 7 -delay 0 -acfbins 10 -nskip 0 -fwhm 0 -noautostimdur -TR 2.8 -o rtopy/polar/h -i 001/f -i 002/f -cfg /homenasFC1/romdat/data/freesurfer_DB/Sujet5_retino/rtopy/analysis.cfg -parname rtopy.par ERROR: selfreqavg failed So I remove from the rtopy/analysis.cfg file the line -acfbins 10 I get an other error : ERROR: Flag -noautostimdur unrecognized. So I remove the line -noautostimdur So I change from -ncycles 7 -delay 0 -acfbins 10 -nskip 0 -fwhm 0 -noautostimdur to -ncycles 7 -delay 0 -nskip 0 -fwhm 0 Why it does not recognize thoses option, what are the diference on the model build ? Thank for your help Romain

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Qdec parcelation display
by Pratap Kunwar 27 Nov '07

27 Nov '07

Hi Nick, Regarding the parcellation display in Qdec; Is it possible to load aparc.a2005.annot instead of aparc.annot? "Parcellation Display: The cortical parcellation is loaded into Qdec upon opening. On the Display tab you can adjust the annotation opacity. " thanks pratap

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Problem launching qdec.
by zheng.hui＠singhealth.com.sg 27 Nov '07

27 Nov '07

Hi, I have two questions: 1) I just upgrade our intel Mac OS from Tiger to Leopard, and now are having problem using qdec. I am using version 4.0.0. When I type qdec in xterm, it outputs the following error msg: dyld: Library not loaded: /usr/X11R6/lib/libexpat.0.dylib Referenced from: /Applications/freesurfer/lib/KWWidgets/lib/KWWidgets/libKWWidgets.dylib Reason: image not found Trace/BPT trap Any idea how to fix this? 2) We have done the editing on 300 subjects (pial, wm and control point) and re-generated all the surfaces. One thing I realized is that the aseg.mgz does not follow the surfaces as it is processed before the surface reconstruction. Is there any way to re-generate the aseg.mgz using ?h.pial, ?h.white? Thanks, Zheng Hui

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recon-all Flirt Error
by Anil Roy 26 Nov '07

26 Nov '07

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. [root@wonglinux1 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 #-------------------------------------------- #@# 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 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

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RE: [Freesurfer] recon-all Flirt Error
by Pedro Paulo Oliveira Jr 26 Nov '07

26 Nov '07

The FSL library or the path to FSL is missing. regards, Pedro Paulo Oliveira Jr. -- mens. original -- Assunto: [Freesurfer] recon-all Flirt Error De: "Anil Roy" <aroy85(a)gmail.com> Data: 26/11/2007 22:38 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. [root@wonglinux1 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 #-------------------------------------------- #@# 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 - - - Selecione 'Recuperar' no menu de opções para recuperar todo o e-mail - - -

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About Gaussian Random Field Theory on fsaverage
by jorge luis 26 Nov '07

26 Nov '07

Thank you Bruce and Moo Chung I will try with those tools I have another question: If I want to use GRFT on smooth thickness spms over the fsaverage subject , should I use the fsaverage white matter total surface area which is 70394.7 mm2 or the group average surface area which is 86444.7 mm2? In advance thank you Jorge ______________________________________________ ¿Chef por primera vez? Sé un mejor Cocinillas. http://es.answers.yahoo.com/info/welcome

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Make_average_subject
by Alexander Fornito 26 Nov '07

26 Nov '07

Hi all, I've been having problems with make_average_subject. The command and error are below. Below this is the same command with the output generated by the --debug flag. I am running version 4.0 (redhat) on Linux Debian. I'd appreciate any help on this. Thanks, Alex make_average_surface --subjects cann01 cann02 cann04 cann05 cann06 cann07 cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19 cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30 cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40 cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52 cann53 cann54 cann55 cann56 --out testavg $Id: make_average_surface,v 1.39 2007/08/13 20:54:29 greve Exp $ Fri Oct 26 11:03:31 EST 2007 /data/kang/work/struct/alex/freesurfer/subjects_cann setenv SUBJECTS_DIR /data/kang/work/struct/alex/freesurfer/subjects_cann output ddir is /data/kang/work/struct/alex/freesurfer/subjects_cann uid=1003(alex) gid=1003 groups=200(mnc),201(fmri),1003 make_average_subject --subjects cann01 cann02 cann04 cann05 cann06 cann07 cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19 cann20 cann21 cann22 cann23 cann24 cann25 cann27 cann28 cann29 cann30 cann31 cann32 cann33 cann34 cann35 cann36 cann37 cann38 cann39 cann40 cann41 cann43 cann44 cann46 cann47 cann48 cann49 cann50 cann51 cann52 cann53 cann54 cann55 cann56 --out testavg --debug set verbose = 1 breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( ! $?SUBJECTS_DIR ) then if ( ! 1 ) then if ( ! -e $SUBJECTS_DIR ) then if ( ! -e /data/kang/work/struct/alex/freesurfer/subjects_cann ) then if ( ! $?FREESURFER_HOME ) then if ( ! 1 ) then if ( ! -e $FREESURFER_HOME ) then if ( ! -e /usr/local/freesurfer_4.0 ) then if ( $#sdout == 0 ) set sdout = $SUBJECTS_DIR if ( 0 == 0 ) set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann set sdout = /data/kang/work/struct/alex/freesurfer/subjects_cann set outdir = $sdout/$average_subject set outdir = /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg if ( -e $outdir && ! $Force ) then if ( -e /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg && ! 0 ) then echo "ERROR: $outdir already exists, select a new average subject name" echo ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg already exists, select a new average subject name ERROR: /data/kang/work/struct/alex/freesurfer/subjects_cann/testavg already exists, select a new average subject name echo " or delete and rerun" echo or delete and rerun or delete and rerun exit 1 ; exit 1

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Re: [Freesurfer] loading data to matlab?
by Maryam Vaziri 26 Nov '07

26 Nov '07

Hi Cameron, I want to run a classification analysis on my functional data from all of the cortex using matlab. It is not something complicated but the very fist step is to run a PCA on all the data from all the voxels in the cortex. I am trying to reduce my data set as much as I can as the computation will b every extensive if I have huge files and Hardware-wise impossible to do. So vertex based data the way it is in the surfaces is very big for my purpose. I need volume data. I read my functional volumes to matlab using MRIread and reading the bhdr files in my BOLD directory (I can also read it using fmri_ldbvolume). But the problem with these files is that It is still too big. For reducing it I have to get rid of everything but the cortex. The problem is that I want the whole cortex data, and thus I cannot read just a label. I also need volume data so I cannot read a surface. Moreover I need to reduce my data set so I cannot read the whole brain volume. I also need all the time points so I cannot read the w files from a contrast analysis. What I finaly want is a N*T*4 matrix, containing x,y,z coordinates and values of all (N) voxels in the cortex, in all(T) time points. I figured that if I can somehow relate the voxels in the ribbon.mgz to the functional volumes I will be all set. But is this impossible? What does the contents of register.dat mean? Is there anyway that I can relate the two files using register.dat? Or maybe somebody has a totally different suggestion? Bests, Maryam. On Nov 20, 2007, at 10:32 AM, Cameron Ellis wrote: > Hi Maryam, > What type of analysis are you trying to do? It sounds like you are > trying > to do something unique and not simply follow the fs-fast surface based > analysis. Were you able to read the entire functional volume into > matlab? > It will be hard to limit this matrix to "active" voxels (not 0) > because it > is unlikely that any voxel in your functional will have a value of > 0. I > think you should be able to restrict the functional volume to the > cortex > but I am not sure how to do this. The register.dat file contains the > matrix used to relate the anatomic volume to the functional volume > but I > am also unsure if how to apply this to the ribbon.mgz or the raw > functional data and I am not sure that this is the best way to > obtain the > information you want. I wish I could be more help. I am just not > sure of > how that data is organized when it is read into matlab (according to > scanner coordinates/tal coordinates etc.) Are you sure there is not > a way > to do what you would like to do without reading the data into matlab? > Cameron > >> Hi again, >> >> I found a file named ?h.ribbon.mgz among the structural files which >> contains the cortical part of the volume that I want. But I do not >> know how to relate this structural volume to my functional volumes to >> get only cortical voxels from my functional volumes. I think that I >> should use the file register.dat, but I do not know what does the >> information inside the register.dat mean. What I basically want to do >> is to read voxels in my functional data, which their corresponding >> voxel in the ribbon.mgz is not zero and get rid of the voxels that >> their corresponding voxels in ribbon,mgz is zero. >> >> Bests, >> Maryam. >> >> On Nov 16, 2007, at 12:28 AM, Cameron Ellis wrote: >> >>> Hi Maryam, >>> do you know about the matlab toolbox for freesurfer? it is >>> located at: >>> $FREESURFER_HOME/matlab. all of these scripts are intended to read >>> fmri >>> data into matlab. I think the script you are looking for is >>> MRIread.m or >>> maybe load_analyze.m, load_cor.m or load_dicom.m I think you may be >>> able >>> to load a surface volume using cortical_labeling_tabel.m I actually >>> haven't used these so i could be completely off the mark that these >>> would >>> be useful. Hope this helps. >>> Cameron >>> >>>> Hi, >>>> >>>> I am a newbie in using freesurfer so sorry if this is a very >>>> trivial >>>> question. I want to load my fMRI data into matlab. I want to make a >>>> matrix containing coordinates and values of all the voxels in the >>>> brain at all timepoints. I also only want the voxels that are in >>>> the >>>> gray matter and not the voxels that are in the white matter or >>>> outside the brain. Where can I get this data and how can I load >>>> it to >>>> matlab? I have already managed to import all the voxels using MRI- >>>> ldbvolume, but this includes white matter and skull. How can I get >>>> rid of the rest of the brain and just get the surface? >>>> >>>> Bests, >>>> Maryam. >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >> >> >>

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Re: [Freesurfer] Error with mc-sess
by lreddy＠MIT.EDU 26 Nov '07

26 Nov '07

Hi, I've tried a few more things since posting my last message but have still not been able to solve the problem with mc-sess where it hangs. I got rid of the Matlab process manager error by using Matlab 6, but the motion correction process still hangs after opening Matlab and printing >> >>INFO: northog = 6, pct=100. I also tried to use the bert dataset and had the same output and then it hanged. The exact command I used was mc-sess -sf sessid -df sesspar I use the PowerPC version of freesurferv4.0.1. Any help would be appreciated. I attach the log file generated by mc-sess with this email. Leila --------------------------------------------------------------------- FREESURFER_HOME: /Software/freesurfer Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1 Kernel info: Darwin 8.10.0 Power Macintosh --------------------------------------------------------------------- ------------------------------ Message: 3 Date: Tue, 13 Nov 2007 22:08:45 -0500 From: Leila Reddy <lreddy(a)MIT.EDU> Subject: [Freesurfer] Error with mc-sess To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <20071113220845.pkqf8xeylhs8ggg8(a)webmail.mit.edu> Content-Type: text/plain; charset=ISO-8859-1 Hi, I recently installed freesurfer, AFNI etc but am having problems with mc-sess. The script runs and gets to the stage in each run where it calls up matlab, enters the MRIwrite command but then gives the message below. It then hangs. >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2007-11-13 18:44:51.464 MATLAB[6569] Process manager already initialized -- can't fully enable headless mode. I can kill the process (e.g.6569 in the example above) and it moves on to the next run, but without saving anything for the current run. Does anyone know what I can do to fix it? Thanks, Leila ------------------------------

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DODS or DOSS?
by Juergen Haenggi 26 Nov '07

26 Nov '07

Dear FS experts We have done a group analysis with FS, but we are not absolutely sure which is the most adequate design matrix to describe our data. We compared two groups and used one covariate of no interest (mean thickness, total area, etc.). Because there are two different options to create the design matrix (dods and doss), we run the analysis twice, one time with dods and the other time with doss, and unfortunately, we got two quite different patterns of structural brain differences. Is there any theoretical and/or empirical recommendation/clues in order to decide which type of design matrix is more appropriate for our data? Thanks in advance 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) -----------------------------------------------------------

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