Re: [Freesurfer] Mac OSX installations incomplete? What to do?

2014-04-08 Thread Eiran Harel
Thank you Zeke and Markus! From: Z K [zkauf...@nmr.mgh.harvard.edu] Sent: Tuesday, April 08, 2014 10:17 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Markus Gschwind; Eiran Harel Subject: Re: [Freesurfer] Mac OSX installations incomplete? What to do? Markus

Re: [Freesurfer] preprocessing question

2014-04-03 Thread Eiran Harel
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

Re: [Freesurfer] preprocessing question

2014-04-03 Thread Eiran Harel
g 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 m

Re: [Freesurfer] preprocessing question

2014-04-02 Thread Eiran Harel
ve/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 > >

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
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 >

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
: 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-snowl

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
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 mailto:eir...@tlvmc.gov.il>>: Hi Markus, [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_P

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
R/etc/fslversion and echo $FSLDIR #(without the _ between FSL and DIR!) Best, Markus 2014-04-01 12:13 GMT+02:00 Eiran Harel 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:

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
arkus 2014-04-01 10:25 GMT+02:00 Eiran Harel 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.

Re: [Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
Eiran Harel 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 FSFAS

[Freesurfer] preprocessing question

2014-04-01 Thread Eiran Harel
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_F