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:
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Today's Topics:
- Re: Freesurfer Digest, Vol 111, Issue 34 (Yongxia Zhou)
- Re: Freesurfer Digest, Vol 111, Issue 34 (Douglas Greve)
- Re: possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences (Douglas Greve)
- Re: possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences (Salil Soman)
- Re: possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences (Douglas Greve)
- Correction for multiple comparisons error (Fotiadis, Panagiotis)
- minor bug report (Joseph Dien)
- Fwd: BBR Register failing (Salil Soman)
- Re: BBR Register failing (Salil Soman)
- Re: BBR Register failing (Salil Soman)
- very slow analysis with recon-all (stdp82@virgilio.it)
- contrast selection and group analyses (Damien MARIE)
Message: 1 Date: Sat, 25 May 2013 12:05:10 -0400 From: Yongxia Zhou yongxiazhou@gmail.com Subject: Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 34 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: <CAMYv_=v0mvsPYnyS-TTXNhxYfPj9nyPyz3sjhiT1AE7Ra2m= rA@mail.gmail.com> 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, freesurfer-request@nmr.mgh.harvard.edu javascript:; freesurfer-request@nmr.mgh.harvard.edu wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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You can reach the person managing the list at freesurfer-owner@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:
- Re: command not found (Louis Nicholas Vinke)
- Re: A question of running fsfast in mac (Douglas N Greve)
- Re: p-value visualization (Douglas N Greve)
- Re: command not found (clelia pellicano)
- Re: problem with alignment of labeling files generated from the rh.area file (Douglas N Greve)
- Re: FreeSurfer v 5.3.0 compatibility with Mac OS X 10.4.11
(Z
K)
- Re: mri_concat --conjunct (Caspar M. Schwiedrzik)
- Re: p-value visualization (MCLAREN, Donald)
Message: 1 Date: Fri, 24 May 2013 12:09:59 -0400 (EDT) From: Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] command not found To: clelia pellicano pellicanoc@gmail.com Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1305241206080.43202@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 vinke@nmr.mgh.harvard.edu wrote: Hi Clelia, What do you run to source FS and do you get any output in your ter