Freesurfer November 2007

freesurfer@nmr.mgh.harvard.edu

54 participants
74 discussions

FS & group feat
by oxro03＠yahoo.com 29 Nov '07

29 Nov '07

Hi, I have a 3 level feat analysis with 2 runs in each subject on the first level. At the second level these two get combined with a fixed effect analysis to produce a mean for each subject. At the third level, the second level results are combined with FLAME to produce group maps. I was able to paint the first and second level results onto the individual subjects' surface by following the excellent instructions on the FS wiki. But how do I paint the 3rdlevel FLAME results onto the fsaverage brain? (Without using group analysis in surface space). Thanks a lot, Sandy --------------------------------- Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how.

2 1

flat map issue
by romain valabregue 29 Nov '07

29 Nov '07

Hello, I define a patch of the occipital lob flat_patch and run the comand mris_flatten lh.occip.patch.3d lh.occip.flat.patch.3d why do I end up with a 'closed' flattened surface flatten result points around the cutting line stay close and not far away like in classical view like this one : flat clasic What's wrong ? Thank for your help Romain

2 4

Cluster thresholding
by Alex Fornito 28 Nov '07

28 Nov '07

Hi, I have run qdec for a simple contrast comparing thickness across the cortical surface between a patient and control group. Not much survives vertex-wise FDR correction, and I would like to try cluster- based thresholding. I would like to make sure I understand the inputs to the command. Am I correct on the following? --in = the signifcance values (i.e., contrast_name.sig.mgh file) --thmin = the vertexwise threshold for determining clusters, where 2 corresponds to p=.01 --minarea = the cluster extent threshold - Am I correct in assuming this should not be smaller than the smoothing kernel? When I run the command below, I get the following output. Only one (whole hemi) cluster is identified. I'm not sure if its a problem in my command line, or with my data. Also, I seem to have the --cwsig flag wrong, but can't figure out the error (appending .w or .label to the end of the output filename does not change the error). I greatly appreciate your help. mri_surfcluster --in qdec/MF_group_lh/contrasts.sig.mgh --subject fsaverage --hemi lh --surf white --annot aparc --sign abs --thmin 2 -- minarea 25 --sum stats/qdec_run/cluster/summary.txt --o stats/ qdec_run/cluster/cluster_output --cwsig stats/qdec_run/cluster/cwsig --olab stats/qdec_run/cluster/MF_group_lh_thk thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = lh srcid = qdec/MF_group_lh/contrasts.sig.mgh paint srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr = -1 minarea = 25 xfmfile = talairach.xfm nth = -1 outid = stats/qdec_run/cluster/cluster_output paint sumfile = stats/run2/cluster/summary.txt subjectsdir = /data/kang/work/struct/alex/freesurfer/subjects_cann FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/mri/ transforms/talairach.xfm 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; ---------------------------------------------------- Reading source surface /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/lh.white.avg.area.mgh Done reading source surface Reading annotation /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/ buckner_cortical_atlas/scripts/colortable_final.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 43.1907 at vertex 101931 overall min = 7.66111 at vertex 28089 surface nvertices 163842 surface area 65416.985991 surface area 65416.985976 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, minarea=25.000000 Found 1 clusters Max cluster size 103339.460938 INFO: fixing MNI talairach coordinates Saving thresholded output to stats/qdec_run/cluster/cluster_output avg = 35.029, stdev = 4.669, min = 7.661, max = 43.191 Saving cluster pval stats/qdec_run/cluster/cwsig unknown file type for file (stats/qdec_run/cluster/cwsig) LabelWrite: saving to stats/qdec_run/cluster/MF_group_lh_thk-0001.label Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 fornitoa(a)unimelb.edu.au

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Re: [Freesurfer] recon-all Flirt Error
by skenny＠uchicago.edu 28 Nov '07

28 Nov '07

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 <nicks(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] recon-all Flirt Error >To: Anil Roy <aroy85(a)gmail.com> >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. >> >> [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 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

2 1

BrainMaskVol vs BrainSegVol
by Akram Bakkour 28 Nov '07

28 Nov '07

Hi all, I want to pull the measure of whole brain volume. In the aseg.stats there is a BrainMaskVol and a BrainSegVol. Which one do I want? As I understand it, BrainMaskVol is the volume of the brainmask (including the ventricles) whereas BrainSegVol is the volume of brain matter and not including the ventricles, so I think this is the one I want, but I want to make sure and I couldn't find a straight answer on the wiki. Thanks! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

3 3

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

2 1

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

2 1

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

3 2

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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Freesurfer November 2007