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 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:
- 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 terminal after doing so? ?What operating system are you running? ?You might try using c-shell instead of bash. -Louis
On Fri, 24 May 2013, clelia pellicano wrote: Hi Louis, thank you for your answer.? I sourced freesurfer again, but I still ?get 'command notfound'. What can I try? Thank you,
Clelia On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinkevinke@nmr.mgh.harvard.edu wrote: ? ? ? Hi Clelia, ? ? ? If this is in a new terminal then you'll have to source freesurfer again. See here for details: ? ? ? https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration ? ? ? -Louis
? ? ? On Wed, 22 May 2013, clelia pellicano wrote: ? ? ? ? ? ? Hi, ? ? ? ? ? ? I have run recon-all -s bert -all to try myinstallation and it worked. ? ? ? ? ? ? Now, when I try to use other command (and also again?recon-all -s bert -all) I always get this:
? ? ? ? ? ? dyn1097-8:subjects cpellica$ tkmedit bertorig.mgz ? ? ? ? ? ? -bash: tkmedit: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz ? ? ? ? ? ? -bash: tkmedit: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial ? ? ? ? ? ? -bash: tksurfer: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ qdec ? ? ? ? ? ? -bash: qdec: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ recon-all help ? ? ? ? ? ? -bash: recon-all: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ recon-all -s bert -all ? ? ? ? ? ? -bash: recon-all: command not found
? ? ? ? ? ? I don't know how to do. Please, could you helpme?
? ? ? ? ? ? Thanks ? ? ? ? ? ? Clelia The information in this e-mail is intended only for the personto whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Message: 2 Date: Fri, 24 May 2013 12:14:51 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A question of running fsfast in mac To: freesurfer@nmr.mgh.harvard.edu Message-ID: 519F91FB.8070709@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Sharon, you have to specify an analysis (as created by mkanalysis-sess) as the argument to -analysis doug
On 05/24/2013 10:35 AM, Yongxia Zhou wrote:
Dear Freesurfer experts: hi, I'm one of the attendees of the multi-modality training program. I had tried running fsfast in the mac and got an error message. Below is the detail information. Any of your suggestions is highly appreciated and thank you very much. -Sharon
OS: Mac OS X 10.5.6
[YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% pwd /Users/Young/Desktop/DICOM/13051914 [YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% selxavg3-sess -s sess01 -analysis /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/001/test01.sm05.lh
-no-preproc -c music_silence.mat
selxavg3-sess logfile is /Users/Young/Desktop/DICOM/13051914/log/selxavg3-sess-bold-test01.sm05.lh-130524090501.log
/Users/Young/Desktop/DICOM/13051914/sess01 Fri May 24 09:05:02 EDT 2013 anadir = /Users/Young/Desktop/DICOM/13051914/sess01/bold/test01.sm05.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1
------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen.
< M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007Warning: Duplicate directory name: /Users/Young/matlab. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com http://www.mathworks.com/. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
In hgrc at 132
In matlabrc at 105 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
In path at 110
In startup at 5 In matlabrc at 255 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
In path at 110
In startup at 14 In matlabrc at 255
>> >> >> >> >> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
#@# sess01 ############################### /Users/Young/Desktop/DICOM/13051914/sess01
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Applications/freesurfer/matlab/MRIread.m
outtop = /Users/Young/Desktop/DICOM/13051914 Extension format = nii.gz 1 music_silence.mat ??? Error using ==> MRIread at 76 ERROR: cannot determine format of /Users/Young/Desktop/DICOM/13051914/sess01/bold/001/fmc.siemens.sm5 (MRIread)
Error in ==> flac_customize at 87 mri = MRIread(fstem,1);
Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0);
2013-05-24 09:05:32.710 MATLAB[65661:60b] Process manager already
initialized -- can't fully enable headless mode.
ERROR: fast_selxavg3() failed\n
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Message: 3 Date: Fri, 24 May 2013 12:15:55 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] p-value visualization To: freesurfer@nmr.mgh.harvard.edu Message-ID: 519F923B.20300@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
We don't have a binary that does it. You can do it in matlab, but it will take a bit of programming. doug
On 05/24/2013 10:54 AM, Ludovici, Katharine (NIH/NIMH) [F] wrote:
Hello,
We are attempting to compare surface area for 46 regions of interest in subjects versus controls. We've created a list of p-values for each ROI using R Studio to compare the two groups. Is there any way to visualize these p-values mapped on to the ROI's?
Thanks very much,
Katie Ludovici Postbaccalaureate IRTA National Institute of Mental Health Child Psychiatry Branch 301-435-5557
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Message: 4 Date: Fri, 24 May 2013 17:15:57 +0100 From: clelia pellicano pellicanoc@gmail.com Subject: Re: [Freesurfer] command not found To: Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: CAENN+0=nzuJnq+eSEVuYagRX+mPVd8D2DR=XkSFSEz4XDWVaYg@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hi Louise,
yes, teh FreeSurfer related commands are still not found. The other thing is that I had problem with license file. I have created a file in Applications/Freesurfer named .license and tried to copy inside le license key but I'm not sure that it worked beacuse if I write cd .license I get 'it is not a file not a directory'. Thanks
Clelia
On Fri, May 24, 2013 at 5:09 PM, Louis Nicholas Vinke < vinke@nmr.mgh.harvard.edu> wrote:
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 terminal after doing so? What operating system are you running? You might try using c-shell instead of bash. -Louis
On Fri, 24 May 2013, clelia pellicano wrote: Hi Louis, thank you for your answer. I sourced freesurfer again, but I still get 'command notfound'. What can I try? Thank you,
Clelia On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu> wrote: Hi Clelia, If this is in a new terminal then you'll have to source freesurfer again. See here for details: https://surfer.nmr.mgh.**harvard.edu/fswiki/** SetupConfigurationhttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis
On Wed, 22 May 2013, clelia pellicano wrote: Hi, I have run recon-all -s bert -all to try myinstallation and it worked. Now, when I try to use other command (and also again recon-all -s bert -all) I always get this:
dyn1097-8:subjects cpellica$ tkmedit bertorig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial -bash: tksurfer: command not found dyn1097-8:subjects cpellica$ qdec -bash: qdec: command not found dyn1097-8:subjects cpellica$ recon-all help -bash: recon-all: command not found dyn1097-8:subjects cpellica$ recon-all -s bert -all -bash: recon-all: command not found
I don't know how to do. Please, could you helpme?
Thanks Clelia The information in this e-mail is intended only for theperson to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 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:
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 terminal after doing so? ?What operating system are you running? ?You might try using c-shell instead of bash. -Louis
On Fri, 24 May 2013, clelia pellicano wrote: Hi Louis, thank you for your answer.? I sourced freesurfer again, but I still ?get 'command notfound'. What can I try? Thank you,
Clelia On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinkevinke@nmr.mgh.harvard.edu wrote: ? ? ? Hi Clelia, ? ? ? If this is in a new terminal then you'll have to source freesurfer again. See here for details: ? ? ? https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration ? ? ? -Louis
? ? ? On Wed, 22 May 2013, clelia pellicano wrote: ? ? ? ? ? ? Hi, ? ? ? ? ? ? I have run recon-all -s bert -all to try myinstallation and it worked. ? ? ? ? ? ? Now, when I try to use other command (and also again?recon-all -s bert -all) I always get this:
? ? ? ? ? ? dyn1097-8:subjects cpellica$ tkmedit bertorig.mgz ? ? ? ? ? ? -bash: tkmedit: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz ? ? ? ? ? ? -bash: tkmedit: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial ? ? ? ? ? ? -bash: tksurfer: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ qdec ? ? ? ? ? ? -bash: qdec: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ recon-all help ? ? ? ? ? ? -bash: recon-all: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ recon-all -s bert -all ? ? ? ? ? ? -bash: recon-all: command not found
? ? ? ? ? ? I don't know how to do. Please, could you helpme?
? ? ? ? ? ? Thanks ? ? ? ? ? ? Clelia The information in this e-mail is intended only for the personto whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Message: 2 Date: Fri, 24 May 2013 12:14:51 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A question of running fsfast in mac To: freesurfer@nmr.mgh.harvard.edu Message-ID: 519F91FB.8070709@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Sharon, you have to specify an analysis (as created by mkanalysis-sess) as the argument to -analysis doug
On 05/24/2013 10:35 AM, Yongxia Zhou wrote:
Dear Freesurfer experts: hi, I'm one of the attendees of the multi-modality training program. I had tried running fsfast in the mac and got an error message. Below is the detail information. Any of your suggestions is highly appreciated and thank you very much. -Sharon
OS: Mac OS X 10.5.6
[YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% pwd /Users/Young/Desktop/DICOM/13051914 [YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% selxavg3-sess -s sess01 -analysis /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/001/test01.sm05.lh
-no-preproc -c music_silence.mat
selxavg3-sess logfile is /Users/Young/Desktop/DICOM/13051914/log/selxavg3-sess-bold-test01.sm05.lh-130524090501.log
/Users/Young/Desktop/DICOM/13051914/sess01 Fri May 24 09:05:02 EDT 2013 anadir = /Users/Young/Desktop/DICOM/13051914/sess01/bold/test01.sm05.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1
------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen.
< M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007Warning: Duplicate directory name: /Users/Young/matlab. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com http://www.mathworks.com/. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
In hgrc at 132
In matlabrc at 105 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
In path at 110
In startup at 5 In matlabrc at 255 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
In path at 110
In startup at 14 In matlabrc at 255
>>>>>>>>>>> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
#@# sess01 ############################### /Users/Young/Desktop/DICOM/13051914/sess01
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Applications/freesurfer/matlab/MRIread.m
outtop = /Users/Young/Desktop/DICOM/13051914 Extension format = nii.gz 1 music_silence.mat ??? Error using ==> MRIread at 76 ERROR: cannot determine format of /Users/Young/Desktop/DICOM/13051914/sess01/bold/001/fmc.siemens.sm5 (MRIread)
Error in ==> flac_customize at 87 mri = MRIread(fstem,1);
Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0);
2013-05-24 09:05:32.710 MATLAB[65661:60b] Process manager already
initialized -- can't fully enable headless mode.
ERROR: fast_selxavg3() failed\n
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Message: 3 Date: Fri, 24 May 2013 12:15:55 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] p-value visualization To: freesurfer@nmr.mgh.harvard.edu Message-ID: 519F923B.20300@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
We don't have a binary that does it. You can do it in matlab, but it will take a bit of programming. doug
On 05/24/2013 10:54 AM, Ludovici, Katharine (NIH/NIMH) [F] wrote:
Hello,
We are attempting to compare surface area for 46 regions of interest in subjects versus controls. We've created a list of p-values for each ROI using R Studio to compare the two groups. Is there any way to visualize these p-values mapped on to the ROI's?
Thanks very much,
Katie Ludovici Postbaccalaureate IRTA National Institute of Mental Health Child Psychiatry Branch 301-435-5557
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Message: 4 Date: Fri, 24 May 2013 17:15:57 +0100 From: clelia pellicano pellicanoc@gmail.com Subject: Re: [Freesurfer] command not found To: Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: CAENN+0=nzuJnq+eSEVuYagRX+mPVd8D2DR=XkSFSEz4XDWVaYg@mail.gmail.com Content-Type: text/plain; charset="iso-8859-1"
Hi Louise,
yes, teh FreeSurfer related commands are still not found. The other thing is that I had problem with license file. I have created a file in Applications/Freesurfer named .license and tried to copy inside le license key but I'm not sure that it worked beacuse if I write cd .license I get 'it is not a file not a directory'. Thanks
Clelia
On Fri, May 24, 2013 at 5:09 PM, Louis Nicholas Vinke < vinke@nmr.mgh.harvard.edu> wrote:
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 terminal after doing so? What operating system are you running? You might try using c-shell instead of bash. -Louis
On Fri, 24 May 2013, clelia pellicano wrote: Hi Louis, thank you for your answer. I sourced freesurfer again, but I still get 'command notfound'. What can I try? Thank you,
Clelia On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu> wrote: Hi Clelia, If this is in a new terminal then you'll have to source freesurfer again. See here for details: https://surfer.nmr.mgh.**harvard.edu/fswiki/** SetupConfigurationhttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration -Louis
On Wed, 22 May 2013, clelia pellicano wrote: Hi, I have run recon-all -s bert -all to try myinstallation and it worked. Now, when I try to use other command (and also again recon-all -s bert -all) I always get this:
dyn1097-8:subjects cpellica$ tkmedit bertorig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial -bash: tksurfer: command not found dyn1097-8:subjects cpellica$ qdec -bash: qdec: command not found dyn1097-8:subjects cpellica$ recon-all help -bash: recon-all: command not found dyn1097-8:subjects cpellica$ recon-all -s bert -all -bash: recon-all: command not found
I don't know how to do. Please, could you helpme?
Thanks Clelia The information in this e-mail is intended only for theperson to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 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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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 terminal after doing so? ?What operating system are you running? ?You might try using c-shell instead of bash. -Louis
On Fri, 24 May 2013, clelia pellicano wrote: Hi Louis, thank you for your answer.? I sourced freesurfer again, but I still ?get 'command notfound'. What can I try? Thank you,
Clelia On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinkevinke@nmr.mgh.harvard.edu wrote: ? ? ? Hi Clelia, ? ? ? If this is in a new terminal then you'll have to source freesurfer again. See here for details: ? ? ? https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration ? ? ? -Louis
? ? ? On Wed, 22 May 2013, clelia pellicano wrote: ? ? ? ? ? ? Hi, ? ? ? ? ? ? I have run recon-all -s bert -all to try myinstallation and it worked. ? ? ? ? ? ? Now, when I try to use other command (and also again?recon-all -s bert -all) I always get this:
? ? ? ? ? ? dyn1097-8:subjects cpellica$ tkmedit bertorig.mgz ? ? ? ? ? ? -bash: tkmedit: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz ? ? ? ? ? ? -bash: tkmedit: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial ? ? ? ? ? ? -bash: tksurfer: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ qdec ? ? ? ? ? ? -bash: qdec: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ recon-all help ? ? ? ? ? ? -bash: recon-all: command not found ? ? ? ? ? ? dyn1097-8:subjects cpellica$ recon-all -s bert -all ? ? ? ? ? ? -bash: recon-all: command not found
? ? ? ? ? ? I don't know how to do. Please, could youhelp me?
? ? ? ? ? ? Thanks ? ? ? ? ? ? Clelia The information in this e-mail is intended only forthe person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Message: 2 Date: Fri, 24 May 2013 12:14:51 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A question of running fsfast in mac To: freesurfer@nmr.mgh.harvard.edu Message-ID: 519F91FB.8070709@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Sharon, you have to specify an analysis (as created by mkanalysis-sess) as the argument to -analysis doug
On 05/24/2013 10:35 AM, Yongxia Zhou wrote:
Dear Freesurfer experts: hi, I'm one of the attendees of the multi-modality training program. I had tried running fsfast in the mac and got an error message. Below is the detail information. Any of your suggestions is highly appreciated and thank you very much. -Sharon
OS: Mac OS X 10.5.6
[YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% pwd /Users/Young/Desktop/DICOM/13051914 [YongxiaZhous-MacBook:~/Desktop/DICOM/13051914] Young% selxavg3-sess -s sess01 -analysis /Users/Young/Desktop/DICOM/13051914/sess01/bold/raw/001/test01.sm05.lh
-no-preproc -c music_silence.mat
selxavg3-sess logfile is /Users/Young/Desktop/DICOM/13051914/log/selxavg3-sess-bold-test01.sm05.lh-130524090501.log
/Users/Young/Desktop/DICOM/13051914/sess01 Fri May 24 09:05:02 EDT 2013 anadir = /Users/Young/Desktop/DICOM/13051914/sess01/bold/test01.sm05.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1
------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen.
< M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.4.0.287 (R2007a) January 29, 2007Warning: Duplicate directory name: /Users/Young/matlab. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com http://www.mathworks.com/. Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
In hgrc at 132
In matlabrc at 105 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
In path at 110
In startup at 5 In matlabrc at 255 Warning: Function /Users/Young/Downloads/matlab_bgl/test/assert.m has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict.
In path at 110
In startup at 14 In matlabrc at 255
>>>>>>>>>>>> /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m
#@# sess01 ############################### /Users/Young/Desktop/DICOM/13051914/sess01
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m /Applications/freesurfer/fsfast/toolbox/fast_ldanaflac.m /Applications/freesurfer/matlab/MRIread.m
outtop = /Users/Young/Desktop/DICOM/13051914 Extension format = nii.gz 1 music_silence.mat ??? Error using ==> MRIread at 76 ERROR: cannot determine format of /Users/Young/Desktop/DICOM/13051914/sess01/bold/001/fmc.siemens.sm5 (MRIread)
Error in ==> flac_customize at 87 mri = MRIread(fstem,1);
Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0);
2013-05-24 09:05:32.710 MATLAB[65661:60b] Process manager already
initialized -- can't fully enable headless mode.
ERROR: fast_selxavg3() failed\n
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Message: 3 Date: Fri, 24 May 2013 12:15:55 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] p-value visualization To: freesurfer@nmr.mgh.harvard.edu Message-ID: 519F923B.20300@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed
We don't have a binary that does it. You can do it in matlab, but it will take a bit of programming. doug
On 05/24/2013 10:54 AM, Ludovici, Katharine (NIH/NIMH) [F] wrote:
Hello,
We are attempting to compare surface area for 46 regions of interest in subjects versus controls. We've created a list of p-values for each ROI using R Studio to compare the two groups. Is there any way to visualize these p-values mapped on to the ROI's?
Thanks very much,
Katie Ludovici Postbaccalaureate IRTA National Institute of Mental Health Child Psychiatry Branch 301-435-5557
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Message: 4 Date: Fri, 24 May 2013 17:15:57 +0100 From: clelia pellicano pellicanoc@gmail.com Subject: Re: [Freesurfer] command not found To: Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: CAENN+0=nzuJnq+eSEVuYagRX+mPVd8D2DR=XkSFSEz4XDWVaYg@mail.gmail.com
Content-Type: text/plain; charset="iso-8859-1"
Hi Louise,
yes, teh FreeSurfer related commands are still not found. The other thing is that I had problem with license file. I have created a file in Applications/Freesurfer named .license and tried to copy inside le license key but I'm not sure that it worked beacuse if I write cd .license I get 'it is not a file not a directory'. Thanks
Clelia
On Fri, May 24, 2013 at 5:09 PM, Louis Nicholas Vinke < vinke@nmr.mgh.harvard.edu> wrote:
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 terminal after doing so? What operating system are you running? You might try using c-shell instead of bash. -Louis
On Fri, 24 May 2013, clelia pellicano wrote: Hi Louis, thank you for your answer. I sourced freesurfer again, but I still get 'commandnot found'. What can I try? Thank you,
Clelia On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu> wrote: Hi Clelia, If this is in a new terminal then you'll have to source freesurfer again. See here for details: https://surfer.nmr.mgh.**harvard.edu/fswiki/** SetupConfigurationhttps://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration
-Louis On Wed, 22 May 2013, clelia pellicano wrote: Hi, I have run recon-all -s bert -all to try myinstallation and it worked. Now, when I try to use other command (and also again recon-all -s bert -all) I always get this:
dyn1097-8:subjects cpellica$ tkmedit bertorig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial -bash: tksurfer: command not found dyn1097-8:subjects cpellica$ qdec -bash: qdec: command not found dyn1097-8:subjects cpellica$ recon-all help -bash: recon-all: command not found dyn1097-8:subjects cpellica$ recon-all -s bert -all -bash: recon-all: command not found
I don't know how to do. Please, could youhelp me?
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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:
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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
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Yongxia Zhou