rhinal
cat $FREESURFER_HOME/build-stamp.txt
source /usr/local/freesurfer/nmr-dev-envAgain, 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.
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.
Thanks
Abi
On 11/13/06, Doug Greve <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED] 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
