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
<fis...@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 <fis...@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 <
>>>> fis...@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 <
>>>>>> fis...@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 <
>>>>>>>> fis...@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.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>
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