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
<freesurfer-request@nmr.mgh.harvard.edu> wrote:
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> 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 <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