I'll defer to Doug/Zeke/Nick on this one
Bruce
On Tue, 1 Apr 2014, Eiran Harel
wrote:
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>:
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
[sign_smallHE_01.jpg]
[sign_smallHE_02.jpg]
[sign_smallHE_03.jpg]
[sign_smallHE_04.jpg]
[sign_smallEN_05.jpg]
[sign_smallHE_06.jpg]
_______________________________________________
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.
