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-requ...@nmr.mgh.harvard.edu >> <freesurfer-requ...@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-requ...@nmr.mgh.harvard.edu >>> >>> You can reach the person managing the list at >>> freesurfer-ow...@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 <vi...@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] command not found >>> To: clelia pellicano <pellica...@gmail.com> >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: <alpine.lrh.2.03.1305241206080.43...@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 >>>> <vi...@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 not >>>> found'. >>>> What can I try? >>>> Thank you, >>>> >>>> Clelia >>>> >>>> >>>> On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke >>>> <vi...@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 my >>>> installation 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 bert >>>> orig.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 >>>> help >>>> me? >>>> >>>> ? ? ? ? ? ? Thanks >>>> >>>> ? ? ? ? ? ? Clelia >>>> >>>> >>>> >>>> >>>> The information in this e-mail is intended only for >>>> the 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 <gr...@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] A question of running fsfast in mac >>> To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: <519f91fb.8070...@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, 2007 >>>> >>>> Warning: 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 >>> gr...@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 <gr...@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] p-value visualization >>> To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: <519f923b.20...@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 >>> gr...@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 <pellica...@gmail.com> >>> Subject: Re: [Freesurfer] command not found >>> To: Louis Nicholas Vinke <vi...@nmr.mgh.harvard.edu> >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: >>> <CAENN+0=nzuJnq+eSEVuYagRX+mPVd8D2DR=xksfsez4xdwv...@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 < >>> vi...@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 < >>>>> vi...@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 >>>>> not >>>>> found'. >>>>> What can I try? >>>>> Thank you, >>>>> >>>>> Clelia >>>>> >>>>> >>>>> On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke < >>>>> vi...@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<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 my >>>>> installation 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 bert >>>>> orig.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 >>>>> help >>>>> me? >>>>> >>>>> Thanks >>>>> >>>>> Clelia >>>>> >>>>> >>>>> >>>>> >>>>> The information in this e-mail is intended only for the >>>>> 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<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. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130524/35ef35dd/attachment-0001.html >>> >>> >>> >>> >>> ------------------------------ >>> >>> Message: 5 >>> Date: Fri, 24 May 2013 12:23:36 -0400 >>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] problem with alignment of labeling files >>> generated from the rh.area file >>> To: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: <519f9408.1080...@nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> >>> Hi Tina, I don't really understand what you mean by offset. Do you mean >>> when you visualize on the surface? The placement is completely dictated >>> by the index you assign in that case. If you are doing this in matlab, >>> make sure you account for the fact that the vertex numbers are 0 based >>> not 1-based >>> doug >>> >>> >>> >>> On 05/24/2013 11:12 AM, Tina Jeon wrote: >>>> Doug can you answer this? >>>> >>>> The vertex indices can be fixed with matlab but more importantly I >>>> need to >>>> know why there is a slight offset in vertex coordinates. >>>> >>>> Thank you! >>>> Tina Jeon >>>> >>>> -----Original Message----- >>>> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] >>>> Sent: Thursday, May 23, 2013 10:57 AM >>>> To: Tina Jeon >>>> Cc: freesurfer@nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] problem with alignment of labeling files >>>> generated from the rh.area file >>>> >>>> hmmm, then I would have thought that they would have vertex indices >>>> >=0. >>>> Maybe Doug knows? >>>> On Thu, 23 May 2013, Tina Jeon wrote: >>>> >>>>> I generated the labeling file from the corresponding numbers in base >>>>> file. The ctx-rh-bankssts was generated from mris_annotation2label >>>>> with >>>>> input -a2005. This is the file with -1 vertex numbers. >>>>> >>>>> In theory these files should be the same. >>>>> >>>>> On May 23, 2013, at 10:28 AM, "Bruce Fischl" >>>>> <fis...@nmr.mgh.harvard.edu> >>>>> wrote: >>>>> >>>>>> Hi Tina >>>>>> >>>>>> how did you create it? If the vertex indices are -1 it means they >>>>>> are >>>>>> not assigned, and when you load it into tksurfer it will sample them >>>>>> onto the surface. You can then save it it will write the new vertex >>>>>> numbers into the label file. >>>>>> >>>>>> Not sure about the offset though. >>>>>> Bruce >>>>>> >>>>>> On Thu, 23 May 2013, Tina Jeon wrote: >>>>>> >>>>>>> Hello Freesurfers, >>>>>>> >>>>>>> I have created labeling files from a subject using the area file >>>>>>> (previously named base). The label file corresponds to the >>>>>>> freesurfer generated cortical label, ctx-rh-bankssts, which I have >>>>>>> attached in this email. The labeling files should be the same, >>>>>>> however, there are some discrepancies in the files: >>>>>>> 1). There is a slight offset in the vertices. >>>>>>> 2). A reduced number of vertices in the .label file created from >>>>>>> the >>>>>>> area file. >>>>>>> 3). The vertex numbers are numbered -1. >>>>>>> >>>>>>> Our goal is to overlay a custom atlas onto a cortical surface >>>>>>> generated from amira in freesurfer. Can you please tell how to >>>>>>> transform the labeling files so that I can successfully overlay >>>>>>> them? >>>>>>> >>>>>>> I have attached all three files for you. rh.rh_label_2001.label is >>>>>>> the labeling file created from the base file, >>>>>>> rh.ctx-rh-bankssts.label is the label from freesurfer and the >>>>>>> rh.base file I have sent to Bruce the file is too large. When I >>>>>>> overlay the rh.rh_label_2001.label and other labels generated >>>>>>> from the >>>>>>> base file, only parts of the temporal lobe are overlayed. >>>>>>> >>>>>>> Thank you in advance, >>>>>>> >>>>>>> Tina Jeon >>>>>>> UT Southwestern Medical Center '14 >>>>>>> >>>>>>> ____________________________________________________________________ >>>>>>> >>>>>>> ________ >>>>>>> UT Southwestern Medical Center >>>>>>> The future of medicine, today. >>>>>>> >>>>>> The information in this e-mail is intended only for the 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. >>>>> >>>> _______________________________________________ >>>> 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 >>> gr...@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: 6 >>> Date: Fri, 24 May 2013 12:37:27 -0400 >>> From: Z K <zkauf...@nmr.mgh.harvard.edu> >>> Subject: Re: [Freesurfer] FreeSurfer v 5.3.0 compatibility with Mac OS >>> X 10.4.11 >>> To: "Swartz, Max" <swart...@miamioh.edu> >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Message-ID: <519f9747.6070...@nmr.mgh.harvard.edu> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> Max, >>> >>> All of Sebastian's answers below are accurate. Unfortunately their are >>> no no immediate plans to build a PowerPC compatible version of >>> freesurfer. You choice is to either use a different Mac with an intel >>> chip or download freesurfer v5.1 which is PowerPC compatible from this >>> link: >>> >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz >>> >>> >>> >>> -Zeke >>> >>> On 05/24/2013 10:04 AM, Sebastian Moeller wrote: >>>> Hi Max, >>>> >>>> not speaking for the fressurfer developers, just as a user like >>>> yourself... >>>> >>>> On May 24, 2013, at 00:58 , Swartz, Max wrote: >>>> >>>>> Hello, >>>>> >>>>> I am working as a research assistant for the summer with the >>>>> University >>>>> of Cincinnati's Psychiatry department in the Division of Bipolar >>>>> Disorders Research under Cal Adler and Melissa DelBello. We are >>>>> looking >>>>> to start utilizing FreeSurfer; however, I am getting some error >>>>> messages >>>>> when trying to perform most of the tasks on the "Testing your >>>>> FreeSurfer >>>>> installation" page in the wiki ( >>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer ). >>>>> >>>>> >>>>> The most common of the error messages I am receiving is "Exec format >>>>> error. Binary file not executable." >>>>> >>>>> The Mac I am trying to run FreeSurfer on has a dual 2 GHz PowerPC G5 >>>>> processor and 4 GB DDR SDRAM, and is running Mac OS X 10.4.11 >>>>> (Tiger). >>>> Ah, unfortunatelly all modern fressufer macosx versions are for >>>> intel x86 >>>> processors only, and will not work on powerPCs at all. So either >>>> the free >>>> surfer developers can compile a powerPC version of 5.3 for you, or >>>> you get >>>> a newer x86 based computer. (Freesurfer will for great on x86 linux >>>> machines and on x86 macosx machines) It seems free surfer 5.1 was >>>> the last >>>> version for powerPCs >>>> (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer//5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz). >>>> >>>> >>>> >>>> >>>>> >>>>> I have been trying to use FreeSurfer v5.3.0 for SnowLeopard OS X 10.6 >>>>> (32b Intel). Should this version compatible with my computer? >>>> As hinted at above, this will not work on your G5. Either use the old >>>> version from the ftp link above or switch to a x86 linux or macosx >>>> based >>>> computer. >>>> >>>>> We are thinking that our error messages are the result of either >>>>> operating system incompatibility or not having all of the necessary >>>>> privileges on our account (which can be fixed through IT). >>>>> >>>>> >>>>> Any insight you can provide regarding the compatibility of FreeSurfer >>>>> v5.3.0 on Mac OS X 10.4 Tiger systems would be incredibly helpful. >>>> Currently not supported, but maybe the friendly and competent >>>> free surfer >>>> developers might be able to compile a version of 5.3? >>>> >>>> >>>> best regards >>>> Sebastian >>>> >>>>> Thanks so much, >>>>> >>>>> >>>>> Max Swartz >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> The information in this e-mail is intended only for the 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. >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> >>> ------------------------------ >>> >>> Message: 7 >>> Date: Fri, 24 May 2013 14:10:00 -0400 >>> From: "Caspar M. Schwiedrzik" <cschwie...@mail.rockefeller.edu> >>> Subject: Re: [Freesurfer] mri_concat --conjunct >>> To: Douglas N Greve <gr...@nmr.mgh.harvard.edu>, >>> "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: >>> <CA+bX-38N8rj5TpxMpFB9U5-K7D1+91HoU=7VkKFSUx=eytt...@mail.gmail.com> >>> >>> Content-Type: text/plain; charset=ISO-8859-1 >>> >>> Hi Doug, >>> I am trying to implement something like the MS/CN conjunction >>> suggested by Nichols. >>> For that, I am finding the voxels that show a significant effect at a >>> given threshold in both contrast maps. >>> I have one question about the resulting p-value. >>> In principle, I would tend to think that the conjunction p-value is >>> p-value of contrast1 x p-value of contrast 2, e.g., 0.05*0.05=0.0025. >>> However, one could also think that it is the max of the two p-values. >>> Which one is correct? >>> Thanks, Caspar >>> >>> >>> >>> 2013/5/23 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>>> Hi Caspar, I think the 4.x should be the same as 5.x. I'm not sure >>>> about >>>> your fsfast question. There is nothing to automatically do it (ie, >>>> you'll need to run mri_concat) >>>> doug >>>> On 05/23/2013 03:06 PM, Caspar M. Schwiedrzik wrote: >>>>> Hi! >>>>> I am trying to do a conjunction analysis using mri_concat --conjunct >>>>> with 2 to three sig.nii as input. >>>>> It seems to me that the resulting map is what Nichols et al. refer to >>>>> as MS/GN, i.e., a test against the global null (at least one effect). >>>>> Is that correct, and does that depends on v4.5 / 5.x? >>>>> Is there something in FSFAST that would allow me to do a "real" >>>>> conjunction, that is, all effects significant in a given voxel? >>>>> Thanks, Caspar >>>>> _______________________________________________ >>>>> 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 >>>> gr...@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/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the 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: 8 >>> Date: Fri, 24 May 2013 14:08:49 -0400 >>> From: "MCLAREN, Donald" <mclaren.don...@gmail.com> >>> Subject: Re: [Freesurfer] p-value visualization >>> To: "Ludovici, Katharine (NIH/NIMH) [F]" <katharine.ludov...@nih.gov> >>> Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: >>> <CAKwrF_WXmT=cnqs1une4b9ltw2a3fu0p9t-apunvv3k7fbt...@mail.gmail.com> >>> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Katharine, >>> >>> Here is some code to do what you want, I think. You need to create >>> regionaldata structure variable. >>> >>> This has 2 fields, label (label names, which must match the annot file >>> label names) and data (the values you want to project). >>> >>> I've included the script and the base nifti file. If you look at the >>> script, there are setup instructions and full details of how to run it. >>> >>> Hope this helps. >>> >>> Best Regards, Donald McLaren >>> ================= >>> D.G. McLaren, Ph.D. >>> Research Fellow, Department of Neurology, Massachusetts General >>> Hospital >>> and >>> Harvard Medical School >>> Postdoctoral Research Fellow, GRECC, Bedford VA >>> Website: http://www.martinos.org/~mclaren >>> Office: (773) 406-2464 >>> ===================== >>> This e-mail contains CONFIDENTIAL INFORMATION which may contain >>> PROTECTED >>> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >>> intended only for the use of the individual or entity named above. >>> If the >>> reader of the e-mail is not the intended recipient or the employee >>> or agent >>> responsible for delivering it to the intended recipient, you are hereby >>> notified that you are in possession of confidential and privileged >>> information. Any unauthorized use, disclosure, copying or the taking >>> of any >>> action in reliance on the contents of this information is strictly >>> prohibited and may be unlawful. If you have received this e-mail >>> unintentionally, please immediately notify the sender via telephone at >>> (773) >>> 406-2464 or email. >>> >>> >>> On Fri, May 24, 2013 at 10:54 AM, Ludovici, Katharine (NIH/NIMH) [F] < >>> katharine.ludov...@nih.gov> 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 >>>> >>>> >>>> The information in this e-mail is intended only for the 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. >>>> >>>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130524/bd91ba6e/attachment.html >>> >>> >>> >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: ProjectRegionalValues_public.m >>> Type: application/octet-stream >>> Size: 3306 bytes >>> Desc: not available >>> Url : >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130524/bd91ba6e/attachment.obj >>> >>> >>> >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: fsaverageprojection.nii >>> Type: application/octet-stream >>> Size: 655720 bytes >>> Desc: not available >>> Url : >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130524/bd91ba6e/attachment-0001.obj >>> >>> >>> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> End of Freesurfer Digest, Vol 111, Issue 34 >>> ******************************************* >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >
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