David,

Hi, I'd be happy to try to help you with learning the Freesurfer tools.

First off, to get a sense of what you have learned so far, have you read the FreeSurfer Manual that is available at:

http://surfer.nmr.mgh.harvard.edu/docs/index.html

Click on the Guide icon (PDF format).

Note: This guide is a bit out of date, and a new tutorial is forth- coming very soon, but for now, much in this guide is applicable to first-time users.

Per this guide, have you created subject directories, and placed your converted structural files in the <subject-name>/mri/orig directory? For instance, if you have three structural scans for a subject, you would put each of them in directories named 001, 002, and 003 in the <subject-name>/mri/orig directory.

Once these are in place, you will want to use the Setup Structural Scans function in csurf (for each directory, highlight and click Read Header. then once all directories have their headers read, click Convert/Average). Following this, the reconstruction steps can follow.

Another note. In general, we recommend using the command-line tools. While csurf is fine for most common tasks, inevitably, users who rely on the Freesurfer tools need to change tool options, and doing this on the command-line is simplest. Also, in the case of problems, it is easier to copy-and-paste the run-time error, so that we can see the command-line, and its output.

Hope this is enough to start. I can try to answer more specific questions when I have a sense of your setup.

Nick

On Fri, 2005-06-24 at 11:28 -0400, David Soscia wrote:

I am just getting acquianted with the program, and I am running into some difficulties. I have a CD filled with MRI scans in AFNI format (.img, .mat, .BRIK, etc.) and I managed after some time to convert one of my .BRIK files to the .cor extention for Freesurfer. Now I am having trouble opening it. When I go to "open subjects" and try to get to where the file is, is lists a "T1" folder where the folder I have the file in should be, and it will not open. Where can I find this file to open it?...it is still on the CD (that is the location I gave when I converted the file), and also I copied all of the files to another folder on the computer, but when I tried to convert the file from that folder, it did not work. The files that I copied over all now have a pen with a cross through it next to the icon (read only maybe that means?)...I'm not sure because I'm very new with Linux. If anyone can help me, let me know.

Thanks, Dave

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