Hi all, below is my information.

rhinal

cat $FREESURFER_HOME/build-stamp.txt
source /usr/local/freesurfer/nmr-dev-env
setenv SUBJECTS_DIR /space/rhinal/2/users/gopal/lynch_data

which tkmedit

cd /space/rhinal/2/users/gopal/lynch_data


tkmedit lynch filled.mgz

error: loading volume filled.mgz
couldn't read the anatomical volume.

TKMedit couldn't read the file you specified.  This could be because the image format wasn't recognized,

or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size.


Again, to clarify, I ran the 'recon-all' command on the lynch data, per the tutorial.  However, as you can see from above, I did not create the ' filled.mgz' file, nor other files which I thought would have been created (e.g. .white, .pial, and .thickness files).  How do I create these files?  I thought that by running recon-all I would have created them.  Please let me know what you think; I believe that this is a very basic question.

Thanks
Abi

On 11/13/06, Doug Greve <greve@nmr.mgh.harvard.edu> wrote:
Hi Abi,

in general, we need more info than what you have supplied. As a new user, you are probably what is  helpful info and what is not. To assist you, we have prepared the following web site: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting. Please look over that and supply all the information is asks for.

thanks!

doug



Abi Gopal wrote:
Hello all

Hello all

I am trying to view my outputted images from reconstruction in tksurfer.  However, there are no files in the 'surf' folder in my subject.  The 'mri' folder only has the orig.mgz file.  How do I get the other files, such as .wm, .filled, etc, that result from the 'tesselating' and 'smoothing and inflating' steps?

To clarify, I performed the 'recon-all' command on my data set, but I only see the orig.mgz file.  I consulted the tutorial, and using the example 'bert,' it showed all the outputted files in the surf folder.  However, it does not state what actions I need to perform in order to get these files.  In fact, it seems to suggest that the recon-all command would take care of all these steps.  I'm a little confused.

Please let me know if you can answer my questions.

Thanks!
Abi

--
Abilash A. Gopal
Doris Duke Research Fellow, Harvard Medical School
MD Candidate 2008, Tufts Medical School 

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



--
Abilash A. Gopal
Doris Duke Research Fellow, Harvard Medical School
MD Candidate 2008, Tufts Medical School