On Sunday, May 26, 2013, wrote:

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When replying, please edit your Subject line so it is more specific
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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 (stdp82@virgilio.it)
12. contrast selection and group analyses (Damien MARIE)

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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
> >
> > 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-request@nmr.mgh.harvard.edu
> >
> > 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:
> >
> > 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
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Message: 2
Date: Sat, 25 May 2013 12:14:18 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Digest, Vol 111, Issue 34
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <51A0E35A.505@nmr.mgh.harvard.edu>
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
>>