The 'make_average_surface' script is in Dos format. You can use the
'dos2unix' application to remove the offending characters from it
(dos2unix comes with all linux dist and you can use fink to download
it for mac os x).
Cheers,
Itamar
-------------------------
[EMAIL PROTECTED] kahn]$ dos2unix --help
dos2unix Copyright (c) 1994-1995 Benjamin Lin
Copyright (c) 1998 Bernd Johannes Wuebben (Version 3.0)
Copyright (c) 1998 Christian Wurll (Version 3.1)
Usage: dos2unix [-hkqV] [-c convmode] [-o file ...] [-n infile
outfile ...]
-h --help give this help
-k --keepdate keep output file date
-q --quiet quiet mode, suppress all warnings
always on in stdin->stdout mode
-V --version display version number
-c --convmode conversion mode
convmode ASCII, 7bit, ISO, Mac, default to ASCII
-l --newline add additional newline in all but Mac convmode
-o --oldfile write to old file
file ... files to convert in old file mode
-n --newfile write to new file
infile original file in new file mode
outfile output file in new file mode
On Jun 27, 2005, at 4:39 PM, Fornito, Alexander wrote:
Hi Nick,
I copied the script into
the bin dir, but when I type make_average_surface, I get the
following:
make_average_surface
'nknown option: `-
Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
Is this normal?
Thanks,
Alex
-----Original Message-----
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Tue 6/21/2005 11:00 PM
To: Fornito, Alexander
Cc: Freesurfer Mailing List; Bruce Fischl
Subject: RE: [Freesurfer] mris_glm
Alex,
Attached is the make_average_surface script. Copy it to the
freesurfer/bin directory, and be sure to make it executable (run
'chmod
755 make_average_surface' in the freesurfer/bin directory).
Type 'make_average_surface' to get help. Basically, just the subject
names are required. By default, a 'subject' named 'average' will be
created from your set of subjects (a name instead of 'average' can be
specified on the command line).
Nick
ps. I am working on the mris_surface seg-fault problem using the
rh.orig
file that you sent.
On Tue, 2005-06-21 at 08:23 -0400, Bruce Fischl wrote:
Hi Alex,
you're better off using the make_average_surfaces.csh script to
make an
average of your subjects. Nick: can you send Alex a copy?
thanks,
Bruce
On Tue, 21 Jun
2005, Fornito, Alexander wrote:
Def. sounds worth doing then! I'll give it a try.
My other question is, where can I get my hands on the average7? It's
used as the target in the mris_glm examples, but I haven't been
able to
find the actual average7 surface in any of the freesurfer
directories.
Am I missing something?
Thanks again,
Alex
-----Original Message-----
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Tuesday, June 21, 2005 4:11 PM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_glm
You can run with just the design matrix, but you won't be able to
use
the cool fsgdf stuff in tksurfer (Load->FSGDF). The fsgdf is a
way to
specify how to build the des mtx. The fsgdf keeps track of what the
regressors mean (eg, Age, Class, IQ, etc). When you save the
preprocessed data with --y, you'll see that there will be an fsgdf
file saved with it. Load this in tksurfer, click on a point, and you
will be able to make a scatter plot of, say, thickness vs age, with
each class (eg, Male, Female) having a different color dot in the
scatter plot. When you mouse-over the dot, it tells you the subject
name. Click on a new point and you'll see the scatter plot for that
point. If you use --xmat, you can save the design matrix (in
matlab-4
format).
doug
On Tue, 21 Jun 2005, Fornito, Alexander wrote:
Hi,
I was seeking some clarification re: the relationship between the
fsgdf
and design matrix file for use with mris_glm. It seems to me
that the
two contain very similar info, the examples in the -help don't
use the
fsdf at all. Is it necessary to create one, or can you just run an
analysis with the desmtx?
Thanks,
Alex
Alexander Fornito
M.psych (Clin. Neuro.)/PhD candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
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_________________________________________________
Itamar Kahn
Department of Psychology
Stanford University
Jordan Hall, Bldg 420
Mail Code 2130
Stanford, CA 94305
office: 650-724-9515 fax: 650-725-5699
url: http://web.mit.edu/kahn/www
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