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-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 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 <eiranh@tlvmc.gov.il>:

Hi Markus,

Thanks, it's is in FSL_DIR           /usr/local/fsl.

Is MATLAB necessary to run FSL?

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 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 <eiranh@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-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.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

_______________________________________________
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.