Thanks Markus. Doug, Bruce, any 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 4:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question 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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Markus Gschwind [markus.gschw...@gmail.com<mailto: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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Markus Gschwind [markus.gschw...@gmail.com<mailto: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<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Markus Gschwind [markus.gschw...@gmail.com<mailto: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<mailto: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/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.edu<mailto: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<mailto: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<mailto: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<mailto: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.
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