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 > > > > > > > > */ > /* > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
