Hi David, it is not a problem if you're not going to run FS-FAST. If it bugs you, you can setenv NO_FSFAST 1 in your cshrc file prior to sourcing the FS env

doug

On 06/10/2013 03:35 PM, David Dalton wrote:

Hello FreeSurfer experts,

I recently downloaded and installed FreeSurfer on my Mac computer, but I have a few questions about the startup.

1. When I run FreeSurfer, I get the following. I know the Wiki says

to ignore the warning, and FreeSurfer does run normally after this, but I wanted to be sure it really was not a problem.

[SiriasBook:/] csirias% setenv FREESURFER_HOME Applications/freesurfer/ [SiriasBook:/] csirias% source Applications/freesurfer/SetUpFreeSurfer.csh -------- freesurfer-Darwin-lion-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

WARNING: The /Users/csirias/matlab/startup.m file does not appear to be configured correctly. You may not be able to run the FS-FAST programs Try adding the following lines to /Users/csirias/matlab/startup.m -----------------cut--------------------- fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; -----------------cut---------------------

MNI_DIR Applications/freesurfer//mni [SiriasBook:/] csirias%

2. When I type in 'freeview' to the command line, I get several other

messages as the program opens. I am not sure if they are a problem, but here they are. I seem to be able to run freeview despite these messages, but some others have told me that these messages do not appear on their computers, so I am wondering why they appear.

[SiriasBook:/] csirias% freeview 2013-06-10 12:22:57.739 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.740 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.754 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.755 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.768 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.769 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.781 Freeview[1200:303] invalid drawable 2013-06-10 12:22:57.782 Freeview[1200:303] invalid drawable

3. And my last question. How do I run FreeSurfer automatically when I

open the terminal window? I would like to just type 'freeview' into the command line to have the program run, but I currently have to type

setenv FREESURFER_HOME Applications/freesurfer/

followed by

source Applications/freesurfer/SetUpFreeSurfer.csh

in order for the program to run.

Thank you so much for any help you can give! Like I said, the program appears to run normally despite the messages, but I just want to know why they are appearing. The last question is more of a convenience issue.

Thanks, David

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