Hi Doug,
I changed the file permissions to be executable and it passed this stage.
It then gets stuck when looking for bet.fsl:

# ---------- Using FSL's BET to Extract Brain------------------ #
/applications/freesurfer/BSMT_project/bsmt103/bold
bet.fsl /tmp/mkbrainmask_76128/in.nii /tmp/mkbrainmask_76128/brain -m -f 0.1
bet.fsl: Command not found.
ERROR: bet failed

Was there something wrong in the insatallation that it is missing those files?
Thanks!
Eiran

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]

Sent: Wednesday, April 02, 2014 5:21 PM

To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] preprocessing question

a couple of thiings to check: make sure it is exectuable and make sure
that you rehash your path. Make sure that if you type fslmaths.fsl that
it runs something

On 04/02/2014 03:23 AM, Eiran Harel wrote:
> Thanks Doug, i downloaded it and now the file exists:
>
> $FREESURFER_HOME/bin/fslmaths.fsl
>
> Unfortuantely it is still not running and gives the same error when running preproc-sess:
>
> mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0
> ERROR: cannot find either fslmaths for avwmaths
>
> How can i proceed?
> Thanks,
> Eiran
> ________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]
> Sent: Wednesday, April 02, 2014 12:41 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] preprocessing question
>
> thanks, it must be something in our distribution script affecting mac
>
> On 04/01/2014 05:13 PM, Markus Gschwind wrote:
>> Thanks Doug,
>>
>> I notice that on my Mac
>> build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>>
>> ...I don't have fslmaths.fsl neither. There are only
>>
>>      $ which $FREESURFER_HOME/bin/fsl*
>>      /Applications/freesurfer/bin/fsl_label2voxel
>>      /Applications/freesurfer/bin/fsl_rigid_register
>>      /Applications/freesurfer/bin/fsl_sub_mgh
>>      /Applications/freesurfer/bin/fslregister
>>
>>      $ which $FREESURFER_HOME/bin/*.fsl
>>      /Applications/freesurfer/bin/epidewarp.fsl
>>      /Applications/freesurfer/bin/fscalc.fsl
>>      /Applications/freesurfer/bin/mri_motion_correct.fsl
>>
>> (I never executed the above mentioned process of Eiran thoug...)
>>
>> Best,
>> Markus
>>
>>
>>
>>
>>
>> 2014-04-01 18:36 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu
>> <mailto:greve@nmr.mgh.harvard.edu>>:
>>
>>      That is weird. You can get a copy from here
>>
>>      ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac
>>
>>      copy it to
>>
>>      $FREESURFER_HOME/bin/fslmaths.fsl
>>
>>
>>      On 04/01/2014 12:25 PM, Eiran Harel wrote:
>>      > Hi Doug,
>>      > No, it does not exist.
>>      > What should i do?
>>      > Thanks,
>>      > Eiran
>>      > ________________________________________
>>      > From: freesurfer-bounces@nmr.mgh.harvard.edu
>>      <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
>>      [freesurfer-bounces@nmr.mgh.harvard.edu
>>      <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of
>>      Douglas N Greve [greve@nmr.mgh.harvard.edu
>>      <mailto:greve@nmr.mgh.harvard.edu>]
>>      > Sent: Tuesday, April 01, 2014 7:16 PM
>>      > To: freesurfer@nmr.mgh.harvard.edu
>>      <mailto:freesurfer@nmr.mgh.harvard.edu>
>>      > Subject: Re: [Freesurfer] preprocessing question
>>      >
>>      > does $FREESURFER_HOME/bin/fslmaths.fsl exist?
>>      >
>>      > On 04/01/2014 03:59 AM, Eiran Harel wrote:
>>      >> 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
>>      <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>      >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>      > --
>>      > Douglas N. Greve, Ph.D.
>>      > MGH-NMR Center
>>      > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>      > Phone Number: 617-724-2358 <tel:617-724-2358>
>>      > Fax: 617-726-7422 <tel:617-726-7422>
>>      >
>>      > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>      <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>      > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>      > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>      <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>      > Outgoing:
>>      ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>      >
>>      > _______________________________________________
>>      > 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
>>      >
>>      >
>>
>>      --
>>      Douglas N. Greve, Ph.D.
>>      MGH-NMR Center
>>      greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>>      Phone Number: 617-724-2358 <tel:617-724-2358>
>>      Fax: 617-726-7422 <tel:617-726-7422>
>>
>>      Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>      <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>      FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>      www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>      <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>      Outgoing:
>>      ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>>      _______________________________________________
>>      Freesurfer mailing list
>>      Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>      https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer