If I understand your question correctly, your saying you already have fsl installed and have the fslswapdim binary. If this is the case, I suppose it would be possible to copy the fslswapdim into the FREESURFER_HOME/bin directory. But you would also have to append a ".bin" at the end.
This is slightly risky because the fslswapdim bianry that you have might be different than the one that ships with freesurfer. But I suppose its worth a try. -Zeke On 03/18/2015 08:18 PM, Dr Sampada Sinha wrote: > 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 <[email protected] > <mailto:[email protected]>> 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 > <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 > > <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 > <[email protected] <mailto:[email protected]> > <mailto:[email protected].__harvard.edu > <mailto:[email protected]>>> 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> > <tel:718-913-0636 <tel:718-913-0636>> > email: [email protected] <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>> > <mailto:email%[email protected] > <mailto:email%[email protected]> > <mailto:email%253Asinhas@umn.__edu > <mailto:email%[email protected]>>__> > [email protected] <mailto:[email protected]> > <mailto:drsampadasinha@gmail.__com > <mailto:[email protected]>> > <mailto:drsampadasinha@gmail. > <mailto:drsampadasinha@gmail.>____com > <mailto:drsampadasinha@gmail.__com > <mailto:[email protected]>>> > > > > > > > */ > /* > > > > ___________________________________________________ > Freesurfer mailing list > [email protected] > <mailto:[email protected]> > <mailto:[email protected].__harvard.edu > <mailto:[email protected]>> > https://mail.nmr.mgh.harvard.____edu/mailman/listinfo/____freesurfer > > <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> > <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: [email protected] <mailto:email%[email protected]> > [email protected] <mailto:[email protected]> > > > > > > > */ > /* > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
