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 > > -- 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
