Here are the details of the acquisitions:

Images acquired on a 3T Signa scanner with a standard GE head coil. 3D T1-weighted spiral volume scan (120 slices, 1.4875-mm thick, TR = 20 msec, TE = 6 msec, 40 degrees flip angle, 256 * 192 matrix)

The machine has 4 gigs of RAM. Also, AFNI is able to talairach and skull strip. Is there a way I can input the files from AFNI to Freesurfer to resume the recon-all pipeline.

Nick, is there a way for me to see your reg so that I can be sure that its not my created xfm that is  causing this problem.

Thanks,

Anil.

On 2/14/07, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
why is the background so high? Also, what field strength was this at? There
looks to be dielectric-like center brightening. The contrast isn't terrible
though.

On Wed, 14 Feb 2007, Nick
Schmansky wrote:

> Bruce,
>
> the orig.mgz can be downloaded via the filedrop, see link in email
> below.
>
> or i have copied it to:
>
>  /autofs/space/minerva_001/users/nicks/subjects/anil/mri
>
> N.
>
>
> On Wed, 2007-02-14 at 17:02 -0500, Bruce Fischl wrote:
>> put the .mgz somewhere and I'll take a look. And make sure it's the
>> orig.mgz, which is un-normalized
>>
>>
>> On Wed, 14 Feb 2007, Nick Schmansky wrote:
>>
>>> Anil,
>>>
>>> The image has almost no contrast.  I've attached a TIFF of one slice.
>>> How was this acquired?  Bruce, any idea why it would be so white?
>>>
>>> Nick
>>>
>>>
>>> On Wed, 2007-02-14 at 16:10 -0500, aroy85@gmail.com wrote:
>>>> The following files have been uploaded to the Martinos Center FileDrop site
>>>> by Anil Roy for you to download:
>>>>
>>>> (1) orig.mgz
>>>>
>>>>
>>>>
>>>> These files will expire in 30 days.
>>>>
>>>> To view or download these files, go in your web browser to:
>>>>
>>>> https://www.nmr.mgh.harvard.edu/facility/filedrop/showgroup/5010/426/7389dc72a7ad03d19b7736c8a7adff69
>>>>
>>>> DO NOT SHARE this web address with anyone else.  It is your personal access key to the files.
>>>>
>>>> Overall Comment about files from Anil Roy:
>>>>
>>>> Hi,
>>>>
>>>> Attached is the orig.mgz file for the subject that quits at the watershed step.
>>>>
>>>> Thanks,
>>>>
>>>> Anil.
>>>>
>>>>
>>>
>>
>>
>
>
>