Dear Freesurfer experts, > thank you very much for your suggestion. This is the error message > when I specify the -analysis folder. It seems coming from the > preprocessing registration step.
Any of your advice will be greatly appreciated. > best regards > yongxia > > fslregister --s andrew_fsaverage --mov > bold/tmp.bbregister.65172/template.nii --reg > bold/tmp.bbregister.65172/reg.init.dat --niters 1 --maxangle 90 > --nobetmov --tmp bold/tmp.bbregister.65172/fslregister --dof 6 > > Log file is bold/tmp.bbregister.65172/reg.init.dat.fslregister.log > > Fri May 24 08:40:39 EDT 2013 > --s andrew_fsaverage --mov bold/tmp.bbregister.65172/template.nii > --reg bold/tmp.bbregister.65172/reg.init.dat --niters 1 --maxangle 90 > --nobetmov --tmp bold/tmp.bbregister.65172/fslregister --dof 6 > $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ > YongxiaZhous-MacBook.local > Darwin YongxiaZhous-MacBook.local 9.6.1 Darwin Kernel Version 9.6.1: > Sun Dec 21 19:45:33 PST 2008; root:xnu-1228.9.75~4/RELEASE_I386 i386 > nIters 1 > -------------------------------------- > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/sess02 > mri_convert > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/brainmask.mgz > bold/tmp.bbregister.65172/fslregister/refvol.fslregister.nii > mri_convert > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/brainmask.mgz > bold/tmp.bbregister.65172/fslregister/refvol.fslregister.nii > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/brainmask.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) > writing to bold/tmp.bbregister.65172/fslregister/refvol.fslregister.nii... > -------------------------------------- > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/sess02 > mri_convert bold/tmp.bbregister.65172/template.nii > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii --frame 0 > mri_convert bold/tmp.bbregister.65172/template.nii > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii --frame 0 > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from bold/tmp.bbregister.65172/template.nii... > TR=7.00, TE=0.00, TI=0.00, flip angle=0.00 > warning: input volume axes are not orthogonal:i_dot_j = 0.000000, > i_dot_k = 1.000000, j_dot_k = 0.000000 > i_ras = (-1, -0, 0) > j_ras = (-0, -0, -1) > k_ras = (-1, -0, 0) > warning: output volume axes are not orthogonal:i_dot_j = 0.000000, > i_dot_k = 1.000000, j_dot_k = 0.000000 > i_ras = (-1, -0, 0) > j_ras = (-0, -0, -1) > k_ras = (-1, -0, 0) > keeping frame 0 > writing to bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii... > WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... > ... continuing. > Mov determinant is 0 > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/sess02 > tkregister2_cmdl --mov > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii --reg > bold/tmp.bbregister.65172/fslregister/reg0.65212.dat --regheader > --fslregout bold/tmp.bbregister.65172/reg.init.dat.fsl.mat0 --s > andrew_fsaverage --noedit > tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl > INFO: no target volume specified, assuming FreeSurfer orig volume. > target volume orig > movable volume bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii > reg file bold/tmp.bbregister.65172/fslregister/reg0.65212.dat > LoadVol 0 > ZeroCRAS 0 > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > Diagnostic Level -1 > INFO: loading target > > /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/andrew_fsaverage/mri/orig.mgz > 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 > bold/tmp.bbregister.65172/fslregister/movvol.fslregister.nii > Tmov: -------------------- > -0.508 0.000 0.000 130.000; > 0.000 0.000 9.600 -14.400; > 0.000 -0.508 0.000 130.000; > 0.000 0.000 0.000 1.000; > MatrixMultiply: m2 is null! > > mkheaderreg = 1, float2int = 0 > Computing reg from header (and possibly input matrix) > ERROR: tkregister2_cmdl > if ( $status ) exit 1 ; > if ( 1 ) exit 1 > exit 1 > > > On 5/24/13, freesurfer-requ...@nmr.mgh.harvard.edu <javascript:;> > <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > > Send Freesurfer mailing list submissions to > > freesurfer@nmr.mgh.harvard.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > or, via email, send a message with subject or body 'help' to > > freesurfer-requ...@nmr.mgh.harvard.edu > > > > You can reach the person managing the list at > > freesurfer-ow...@nmr.mgh.harvard.edu > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Freesurfer digest..." > > > > > > Today's Topics: > > > > 1. Re: command not found (Louis Nicholas Vinke) > > 2. Re: A question of running fsfast in mac (Douglas N Greve) > > 3. Re: p-value visualization (Douglas N Greve) > > 4. Re: command not found (clelia pellicano) > > 5. Re: problem with alignment of labeling files generated from > > the rh.area file (Douglas N Greve) > > 6. Re: FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11 (Z > K) > > 7. Re: mri_concat --conjunct (Caspar M. Schwiedrzik) > > 8. Re: p-value visualization (MCLAREN, Donald) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 24 May 2013 12:09:59 -0400 (EDT) > > From: Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] command not found > > To: clelia pellicano <pellica...@gmail.com> > > Cc: freesurfer@nmr.mgh.harvard.edu > > Message-ID: <alpine.lrh.2.03.1305241206080.43...@nmr.mgh.harvard.edu> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi Clelia, > > That mv command is failing presumably because SetUpFreeSurfer.txt does > not > > exist in that directory. What are you trying to do with the mv command? > > > > It does look like freesurfer was sourced successfully. Are the > FreeSurfer > > related commands still not found? > > > > Don't forget to cc the freesurfer mailing list. > > -Louis > > > > On Fri, 24 May 2013, clelia pellicano wrote: > > > >> Hi Louise, > >> I'm now using tcsh. Here what I did > >> > >> [dyn1097-8:~] cpellica% setenv FREESURFER_HOME > >> /Applications/freesurfer > >> [dyn1097-8:~] cpellica% source > >> /Applications/freesurfer/SetUpFreesurfer.csh > >> -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- > >> Setting up environment for FreeSurfer/FS-FAST (and FSL) > >> FREESURFER_HOME ? /Applications/freesurfer > >> FSFAST_HOME ? ? ? /Applications/freesurfer/fsfast > >> FSF_OUTPUT_FORMAT nii.gz > >> SUBJECTS_DIR ? ? ?/Applications/freesurfer/subjects > >> MNI_DIR ? ? ? ? ? /Applications/freesurfer/mni > >> FSL_DIR ? ? ? ? ? /usr/local/fsl > >> [dyn1097-8:~] cpellica% mv ?SetUpFreeSurfer.txt SetUpFreeSurfer.csh? > >> mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such file or > >> directory > >> > >> Do you have any advice? > >> > >> Thanks > >> > >> Clelia > >> > >> > >> > >> > >> > >> On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke > >> <vi...@nmr.mgh.harvard.edu> wrote: > >> Hi Clelia, > >> What do you run to source FS and do you get any output in your > >> ter
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