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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschwind@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 <eiranh@tlvmc.gov.ilmailto:eiranh@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/DocLib/SIGN/sign_smallHE_01.jpg]http://www.tasmc.org.il/be-well/Pages/default.aspx [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_02.jpg] https://www.facebook.com/ichilov.medical [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_03.jpg] http://twitter.com/tasmc1 [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_04.jpg] http://www.youtube.com/tasmc1 [http://www.tasmc.org.il/DocLib/SIGN/sign_smallEN_05.jpg] http://www.tasmc.org.il/sites/en/Pages/default.aspx
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.