Dear Dr. Greve, Thank you very much for your information. I double checked the data, and realizes that the anatomical volume linked to fsaverage subject, which should be induvidual subject. Sorry that I missed your reply yesterday. I will try to run everything again to make sure data format and processing are all done correct. Thanks very much again. Best regards Yongxia
On Sunday, May 26, 2013, wrote: > Send Freesurfer mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Freesurfer Digest, Vol 111, Issue 34 (Yongxia Zhou) > 2. Re: Freesurfer Digest, Vol 111, Issue 34 (Douglas Greve) > 3. Re: possible to use freesurfer segmentations to get mean > values for anatomic structures from other sequences (Douglas Greve) > 4. Re: possible to use freesurfer segmentations to get mean > values for anatomic structures from other sequences (Salil Soman) > 5. Re: possible to use freesurfer segmentations to get mean > values for anatomic structures from other sequences (Douglas Greve) > 6. Correction for multiple comparisons error (Fotiadis, Panagiotis) > 7. minor bug report (Joseph Dien) > 8. Fwd: BBR Register failing (Salil Soman) > 9. Re: BBR Register failing (Salil Soman) > 10. Re: BBR Register failing (Salil Soman) > 11. very slow analysis with recon-all ([email protected]) > 12. contrast selection and group analyses (Damien MARIE) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 25 May 2013 12:05:10 -0400 > From: Yongxia Zhou <[email protected]> > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 34 > To: "[email protected]" <[email protected]> > Message-ID: > <CAMYv_=v0mvsPYnyS-TTXNhxYfPj9nyPyz3sjhiT1AE7Ra2m= > [email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > 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, [email protected] <javascript:;> > > <[email protected]> wrote: > > > Send Freesurfer mailing list submissions to > > > [email protected] > > > > > > 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 > > > [email protected] > > > > > > You can reach the person managing the list at > > > [email protected] > > > > > > 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 <[email protected]> > > > Subject: Re: [Freesurfer] command not found > > > To: clelia pellicano <[email protected]> > > > Cc: [email protected] > > > Message-ID: <[email protected]> > > > 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 > > >> <[email protected]> wrote: > > >> Hi Clelia, > > >> What do you run to source FS and do you get any output in your > > >> ter > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130525/2166bf9b/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Sat, 25 May 2013 12:14:18 -0400 > From: Douglas Greve <[email protected]> > Subject: Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 34 > To: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > yongxia, did you see my reply from yesterday? > > On 5/24/13 6:08 PM, Douglas N Greve wrote: > > where did your raw data come from? Specifically, how were the nifti > > files created? There is a warning in there that indicates that there > > is some problem with them. > > doug > > > > > > On 05/24/2013 05:56 PM, Yongxia Zhou wrote: > >> Dear Dr. Greve, > >> 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. > >> 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 > >>
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