Hi Bruce,
              I just realised that the cropping at the posterior aspect is similar to the
cropping usually done for the inferior aspect in a saggital view (to get rid of the
neck etc..) . Could it be (remotely) possible that the cropping was done in a different
orientation (nose pointing up in the sagittal view), and then oriented to the views
that we see now? I have only used the basic commands "make_average_subject"
with no special flags except --force
sid.


On Fri, Jan 23, 2009 at 10:33 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
I'm not really sure. Doug or Nick: any ideas?


On Fri, 23 Jan 2009, Siddharth Srivastava wrote:

Hi Bruce,
            please find attached a tiff file generated by mri_concat
--mean on the original mprages.
Here i can see the full view, and i think no registration has been performed
as yet on these
images...  Regarding exploring the dataset for 1 image, is it possible that
just 1 rouge image
can cause this problem? The clipping has a sharp border, almost as if the
bounding box
itself has been cropped at that level. the intensity in these posterior
slices is zero.
thanks,
sid.

On Fri, Jan 23, 2009 at 9:51 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:

if you can find a small set (1?) of subjects that generate the same image,
then maybe you can just send us that subject and your commandline

On Fri, 23 Jan 2009, Siddharth Srivastava wrote:

 ok.. i will try that and let you know... what other image/logs can i
provide
for
localizing the source of the error?
sid.

On Fri, Jan 23, 2009 at 9:04 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:

 not really, it seems like there is a bug. If you can localize it to just
one or a  few subjects it would a lot easier to track down

On Fri, 23 Jan 2009, Siddharth Srivastava wrote:

 Hi Bruce,

         These are about 28 images. I have not tried fewer...do you
think there
are some images with incorrect orientation in the cohort? That would
show
up
in the other location in the average i think...
sid.
On Fri, Jan 23, 2009 at 8:46 AM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu

wrote:


 I don't think so. How many subjects? Have you tried fewer?


On Fri, 23 Jan 2009, Siddharth Srivastava wrote:

 The surfaces look all right. It happens only to T1. It cant be a
display

 problem, can it??
sid.

On Fri, Jan 23, 2009 at 5:58 AM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu

 wrote:


 that is strange. Do the surfaces look ok? How many subjects are you

 averaging? Does this happen if you only average one or a few?

On Thu, 22 Jan 2009, Siddharth Srivastava wrote:

 Hi everyone,

              I am attaching a tiff file showing the tkmedit view of

the average
T1 that freesurfer created during make_average_subject. I am a bit
concerned

about the cropping that is evident at the posterior aspect of the
brain.
The

individual T1's are complete and ok, so i am guessing that something
went
wrong during the transform of the individual brain during the
process.
Can
anyone help me find out the problem ? The average surfaces also look
all
right.
            thanks,
            sid.