Hi Francesca,

the spot in the map is the point measure, possibly smoothed over an area. The ROI thicknesses are average over a specified anatomical region (e.g. precentral gyrus).

cheers, Bruce

On Sun, 18 Feb 2007, Bagnato, Francesca (NIH/NINDS) [E] wrote:

Hi there: I would like to ask you the difference between the number produced as assessing cortical thickness of a given region and the spots of reduced in thickness of part of regions. Do those spots represent areas with reduced signal intensity within voxels or areas where a less number of voxels with GM signal intensity is contained?

Thanks, Francesca

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Vinny,

I'm stumped on this one. Sorry! You could try the centos x86_64 distribution of freesurfer. Maybe it is a library problem (although I don't understand why 'ldd' is not working for you, as that is a Unix utility). Others have gotten Freesurfer to work under Ubuntu, so in theory it should work.

If you do get past this problem, then another known problem with Ubuntu concerns tkmedit and tksurfer. They will not work with the default NVidia drivers (assuming you have an NVidia graphics card). You will need to update to the most recent NVidia driver to fix the problem (consult NVidia website).

Nick

On Sun, 2007-02-18 at 23:12 -0500, Vincent Costa wrote:

Nick,

Here is the output from the commands you suggested:

CostaAMDX2:~/freesurfer/bin> ./mri_convert

./mri_convert: Command not found.

CostaAMDX2:~/freesurfer/bin> ldd ./mri_convert

/usr/bin/ldd: line 171: /lib/ld-linux.so.2: No such file or directory ldd: /lib/ld-linux.so.2 exited with unknown exit code (127)

Any diagnostic suggestions?

Vinny

On Sun, 2007-02-18 at 19:56 -0500, Nick Schmansky wrote:

...

Vinny,

What happens if you type the following:

cd $FREESURFER_HOME/bin ./mri_convert

And what is the output of this:

cd $FREESURFER_HOME/bin ldd ./mri_convert

The rh9 build should work on the x86_64 architecture, but of course you can try the x86_64 build of freesurfer.

Nick

On Sun, 2007-02-18 at 14:04 -0500, Vincent Costa wrote:

...

Hi,

I am attempting to install Freesurfer on a system running Ubuntu 6.10 with x86_64 architecture.

On the Freesurfer Wiki it states that Debian users should install the Red Hat 9 package. I went ahead and did this, setting up and configuring Freesurfer following the directions listed on the Wiki.

When I enter the tcsh shell I get the following output as expected:

% tcsh -------- freesurfer-Linux-rh9-stable-pub-v3.0.5 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/vdcosta/freesurfer FSFAST_HOME /home/vdcosta/freesurfer/fsfast SUBJECTS_DIR /home/vdcosta/freesurfer/subjects MNI_DIR /home/vdcosta/freesurfer/mni GSL_DIR /home/vdcosta/freesurfer/lib/gsl FSL_DIR /home/vdcosta/freesurfer/fsl

However when I attempt to test my install, all commands result in the following error:

/home/vdcosta/freesurfer/bin/tkmedit.bin: Command not found.

tkmedit can be replaced by other commands to generate the same error message.

If I enter on the command line:

recon-all --help | less

: the returned ouput is what appears to be a full manual on all Freesurfer processing steps.

Do I need to install the x86_64 package?

The following is my .tcshrc file:

setenv AFNI_PATH ~/afni set path = ($path .) set path = ($path $AFNI_PATH .) set path = ($path ~/bin) set history = 100 alias copy cp alias del rm alias dir ls alias find 'find . -name !^ -print' alias dir/p 'ls . | more' alias type 'cat !^ | more' alias xterm 'xterm -sb &' alias h history alias m more= setenv FREESURFER_HOME /home/vdcosta/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh

Any help in getting Freesurfer running would be greatly appreciated.

Thanks,

Vinny Costa

vdcosta at ufl dot edu

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