Hello Zeke, Thanks for you valuable reply! I will go with option first of reinstalling freesurfer for 64bit version. I have a quick question though: my fsl binaries already have fslswapdim in it. If I go with an option second (just in case), do I still need to download fsl binaries?
Thanks and regards, Sampada On Wed, Mar 18, 2015 at 5:30 PM, Z K <zkauf...@nmr.mgh.harvard.edu> wrote: > Hello Sampada, > > It appears you are running the 32bit version of freesurfer on your 64bit > Mac machine. Which is fine, but you would probably get better performance > if you installed the 64bit bit version of freesurfer onto your machine. > > In regard to the error you are experiencing, you have 2 options: > > 1) Delete the version of freesurfer you have on your machine and install > the 64bit version from the following page: > (https://surfer.nmr.mgh.harvard.edu/fswiki/Download) > > 2) Keep the version of freesurfer you currently have on your machine and > download the the fsl binaries from here (ftp://surfer.nmr.mgh.harvard. > edu/pub/dist/freesurfer/patches/freesurfer_fsl.tar.gz). Extract the > contents of the tar file into the $FREESURFER_HOME/bin directory. This > should result in 6 new files with a .fsl extension in the > $FREESURFER_HOME/bin directory. > > Both options are valid. > > -Zeke > > > > On 03/18/2015 06:20 PM, Dr Sampada Sinha wrote: > >> I hope you are looking for this: >> >> Last login: Tue Mar 17 15:48:52 on ttys009 >> rmbp:~ Sampada$ export FREESURFER_HOME=/Applications/freesurfer >> rmbp:~ Sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh >> -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- >> Setting up environment for FreeSurfer/FS-FAST (and FSL) >> FREESURFER_HOME /Applications/freesurfer >> FSFAST_HOME /Applications/freesurfer/fsfast >> FSF_OUTPUT_FORMAT nii.gz >> SUBJECTS_DIR /Applications/freesurfer/subjects >> MNI_DIR /Applications/freesurfer/mni >> FSL_DIR /Applications/fsl >> rmbp:~ Sampada$ tcsh >> [rmbp:~] Sampada% setenv dtimartinos /Users/Sampada/Desktop/dtimartinos >> [rmbp:~] Sampada% setenv SUBJECTS_DIR $dtimartinos/diffusion_recons/ >> [rmbp:~] Sampada% setenv TUTORIAL_DIR $dtimartinos/diffusion_tutorial/ >> [rmbp:~] Sampada% set subj = Diff001 >> [rmbp:~] Sampada% dt_recon --i $TUTORIAL_DIR/$subj/orig/*-1.dcm --s >> $subj --o $TUTORIAL_DIR/$subj/dtrecon >> INFO: SUBJECTS_DIR is /Users/Sampada/Desktop/ >> dtimartinos/diffusion_recons/ >> dt_recon logfile >> Wed Mar 18 16:38:49 CDT 2015 >> VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $ >> setenv SUBJECTS_DIR /Users/Sampada/Desktop/dtimartinos/diffusion_recons/ >> cd /Users/Sampada >> /Applications/freesurfer/bin/dt_recon --i >> /Users/Sampada/Desktop/dtimartinos/diffusion_ >> tutorial//Diff001/orig/6-1.dcm >> --s Diff001 --o >> /Users/Sampada/Desktop/dtimartinos/diffusion_tutorial//Diff001/dtrecon >> rmbp.home >> Sampada >> /Applications/fsl/bin/eddy_correct >> ECRefTP 0 >> #@#------------------------------- >> Converting input >> Wed Mar 18 16:38:49 CDT 2015 >> cd /Users/Sampada >> mri_convert >> /Users/Sampada/Desktop/dtimartinos/diffusion_ >> tutorial/Diff001/orig/6-1.dcm >> /Users/Sampada/Desktop/dtimartinos/diffusion_ >> tutorial/Diff001/dtrecon/dwi.nii >> mri_convert >> /Users/Sampada/Desktop/dtimartinos/diffusion_ >> tutorial/Diff001/orig/6-1.dcm >> /Users/Sampada/Desktop/dtimartinos/diffusion_ >> tutorial/Diff001/dtrecon/dwi.nii >> >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from >> /Users/Sampada/Desktop/dtimartinos/diffusion_ >> tutorial/Diff001/orig/6-1.dcm... >> Getting Series No >> INFO: Found 72 files in >> /Users/Sampada/Desktop/dtimartinos/diffusion_tutorial/Diff001/orig >> INFO: Scanning for Series Number 6 >> Scanning Directory >> INFO: found 70 files in series >> INFO: loading series header info. >> >> >> (Sorry about the typos: I meant martinos and not martinis) >> >> Thanks and regards, >> >> Sampada >> >> >> >> On Wed, Mar 18, 2015 at 5:18 PM, Z K <zkauf...@nmr.mgh.harvard.edu >> <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: >> >> Hello Sampada, >> >> Can you please tell me the contents of the "build-stamp.txt" file in >> your FREESURFER_HOME directory? >> >> -Zeke >> >> >> On 03/18/2015 06:06 PM, Dr Sampada Sinha wrote: >> >> Hello Freesurfer experts, >> >> I am trying to learn dti using data downloaded from the martinis >> and >> everything was running fine till I got this message: >> >> Wed Mar 18 16:54:54 CDT 2015 >> --s Diff001 --mov >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/template.nii >> --reg >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/reg.init.dat >> --niters 1 --maxangle 90 --nobetmov --tmp >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/fslregister >> --dof 6 --fsvol brainmask.mgz >> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ >> rmbp.home >> Darwin rmbp.home 12.5.0 Darwin Kernel Version 12.5.0: Sun Sep 29 >> 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE___X86_64 x86_64 >> nIters 1 >> ------------------------------__-------- >> /Users/Sampada >> mri_convert >> /Users/Sampada/Desktop/__dtimartinos/diffusion_recons// >> __Diff001/mri/brainmask.mgz >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/fslregister/ >> __refvol.fslregister.nii >> mri_convert >> /Users/Sampada/Desktop/__dtimartinos/diffusion_recons// >> __Diff001/mri/brainmask.mgz >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/fslregister/ >> __refvol.fslregister.nii >> >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from >> /Users/Sampada/Desktop/__dtimartinos/diffusion_recons// >> __Diff001/mri/brainmask.mgz... >> TR=12.00, TE=4.76, TI=4.76, flip angle=20.00 >> i_ras = (-1, 3.72529e-09, 2.09548e-09) >> j_ras = (6.75209e-09, -1.93715e-07, -1) >> k_ras = (1.11759e-08, 1, -3.72529e-08) >> writing to >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/fslregister/ >> __refvol.fslregister.nii... >> ------------------------------__-------- >> /Users/Sampada >> mri_convert >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/template.nii >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/fslregister/ >> __movvol.fslregister.nii >> --frame 0 >> mri_convert >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/template.nii >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/fslregister/ >> __movvol.fslregister.nii >> --frame 0 >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/template.nii.__.. >> TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-0.998075, -0.0596198, -0.0170599) >> j_ras = (0.0587821, -0.997211, 0.0459901) >> k_ras = (-0.0197543, 0.0448988, 0.998796) >> keeping frame 0 >> writing to >> /Users/Sampada/Desktop/__dtimartinos/diffusion___ >> tutorial/Diff001/dtrecon/tmp.__bbregister.49197/fslregister/ >> __movvol.fslregister.nii... >> Mov determinant is 8 >> Swapping dims for pos det >> fslswapdim.fsl: Command not found. >> >> >> Will you please let me know if the error is a part of the >> processing >> for non-martinis site users? >> >> Appreciate all your help! >> >> Thanks and regards, >> >> Sampada >> >> -- >> Sampada Sinha >> Post-Doctoral Associate >> University of Minnesota (East Bank) >> Molecular and neuroimaging laboratory >> Department of Psychiatry >> Minneapolis-55415 >> Phone number: 718-913-0636 <tel:718-913-0636> >> email: sin...@umn.edu <mailto:sin...@umn.edu> >> <mailto:email%3asin...@umn.edu <mailto:email%253asin...@umn.edu >> >__> >> drsampadasi...@gmail.com <mailto:drsampadasi...@gmail.com> >> <mailto:drsampadasinha@gmail.__com >> <mailto:drsampadasi...@gmail.com>> >> >> >> >> >> >> >> */ >> /* >> >> >> >> _________________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer >> <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 >> <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. >> >> >> >> >> -- >> Sampada Sinha >> Post-Doctoral Associate >> University of Minnesota (East Bank) >> Molecular and neuroimaging laboratory >> Department of Psychiatry >> Minneapolis-55415 >> >> >> >> >> >> >> >> */ >> /* >> >> -- Sampada Sinha Post-Doctoral Associate University of Minnesota (East Bank) Molecular and neuroimaging laboratory Department of Psychiatry Minneapolis-55415 Phone number: 718-913-0636 email: sin...@umn.edu <email%3asin...@umn.edu> drsampadasi...@gmail.com
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