recon-all -i asl_12slices_180/1024.dcm -s lynch
it outputted 001.mgz
what are the steps i need to follow in order to create the 'filled.mgz' file and the other files (e.g. .white, .pial, and .thickness files)? I thought that recon-all would have taken care of the remaining steps and created these files.
Thanks
abi
On 11/14/06, Bruce Fischl <[EMAIL PROTECTED]> wrote:
but how did you reun recon-all and what did it output?
On Tue, 14 Nov 2006,
Abi Gopal wrote:
> 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 <[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
>> [EMAIL PROTECTED]://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
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