Well, Eiran, That seems all fine.
Maybe Bruce or Doug can jump in and help? Sorry! Markus 2014-04-01 15:25 GMT+02:00 Eiran Harel <eir...@tlvmc.gov.il>: > Hi Markus, > > [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% > more $FSL_DIR/etc/fslversion > 5.0.6 > [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran% > echo $FSLDIR > /usr/local/fsl > > Thanks! > Eiran > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ > freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ > markus.gschw...@gmail.com] > *Sent:* Tuesday, April 01, 2014 2:48 PM > > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] preprocessing question > > Hi, > > Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that > can be used in FSL, I think it is not necessary to have matlab working for > FSL to work. > > There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab). > > The error message tells you that freesurfer doesn't find fslmaths in the > fsl directory... > > Can you post here the exact result of > > more $FSL_DIR/etc/fslversion > > and > > echo $FSLDIR #(without the _ between FSL and DIR!) > > Best, > Markus > > > > > > > > > > > > 2014-04-01 12:13 GMT+02:00 Eiran Harel <eir...@tlvmc.gov.il>: > >> Hi Markus, >> Thanks, it's is in FSL_DIR /usr/local/fsl. >> Is MATLAB necessary to run FSL? >> EIran >> >> >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ >> markus.gschw...@gmail.com] >> *Sent:* Tuesday, April 01, 2014 12:55 PM >> >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] preprocessing question >> >> Hi, >> what does it say when you type >> which fsl >> which fslmath >> ? >> >> It mud be the same thing as >> FSL_DIR /usr/local/fsl >> >> It is possible that the FSL_DIR specified in the freesurfersetup is not >> the good one... >> >> Best, >> Markus >> >> >> 2014-04-01 10:25 GMT+02:00 Eiran Harel <eir...@tlvmc.gov.il>: >> >>> Hi Markus, >>> Thanks, i did install fsl and when i type fslmaths it gives me the help >>> for that command. >>> Any other suggestions? >>> Eiran >>> ------------------------------ >>> >>> >>> >>> >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [ >>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [ >>> markus.gschw...@gmail.com] >>> *Sent:* Tuesday, April 01, 2014 11:11 AM >>> *To:* Freesurfer support list >>> *Subject:* Re: [Freesurfer] preprocessing question >>> >>> Hi! >>> >>> Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/) >>> What happens if you type in your terminal >>> fslmaths >>> ? >>> >>> Best, >>> Markus >>> 2014-04-01 9:59 GMT+02:00 Eiran Harel <eir...@tlvmc.gov.il>: >>> >>>> Dear freesurfers, >>>> I have installed freesurfer and fsl on my Mac: >>>> >>>> *-------- 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 /usr/local/fsl* >>>> >>>> I am trying to run Preproc-sess command: >>>> >>>> *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm 5 -fsd >>>> bold -stc odd -per-run -force* >>>> >>>> and get this error: >>>> >>>> *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 >>>> -ndil 1 -nerode 0* >>>> *ERROR: cannot find either fslmaths for avwmaths* >>>> >>>> Any suggestions? >>>> Thanks! >>>> Eiran >>>> >>>> >>>> >>>> >>>> <http://www.tasmc.org.il/be-well/Pages/default.aspx> >>>> <https://www.facebook.com/ichilov.medical> <http://twitter.com/tasmc1> >>>> <http://www.youtube.com/tasmc1> >>>> <http://www.tasmc.org.il/sites/en/Pages/default.aspx> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> 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 >> >> >> 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 > > > 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 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.
