Hi,
This sounds unusual.
Can you send us data from an example subject so that we can see the problem ourselves?
You can send the data to:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
All the best,
Mark
On 28 Apr 2014, at 14:16, [log in to unmask] <[log in to unmask]> wrote:
> Hello Mark,
>
> Thank you for the reply and for your insight.
>
> I have checked the highres2standard_linear images and compared these with
> the oriented highres and the non-linear images. I also doubled checked my
> naming convention/directory structure and confirmed that that was not a
> contributing factor.
>
> It seems that the registrations are distorting/dropping out the wide sulci
> areas during the non-linear transformation. Any ideas on why this may be
> happening and how I may be able to fix these registrations?
>
> Please let me know if you would like me to send you additional screenshots
> of these different registration step comparisons.
>
> Thank you again for the help.
>
> Jacob
>
>
>
>> Hi,
>>
>> The first thing to check is if the problem arises from the linear or the
>> non-linear registration steps.
>> Have a look at the highres2standard_linear images and see if these are OK
>> or not.
>>
>> If these are fine then the problem is in the non-linear stage (FNIRT) and
>> may be due to it being unable to find the non-brain extracted image (as
>> both images should be in the same directory and follow the naming
>> convention: aname.nii.gz and aname_brain.nii.gz, where the "aname" part
>> can be anything you want).
>>
>> If the linear step is problematic then it might be due to bias field
>> (which can be reduced/removed with FAST), or large initial orientation
>> difference (which can be solved by running fslreorient2std on all images
>> first).
>>
>> There are other possibilities too, but these are the things I would look
>> at first.
>>
>> All the best,
>> Mark
>>
>>
>>
>>
>> On 25 Apr 2014, at 13:53, [log in to unmask]
>> <[log in to unmask]> wrote:
>>
>>> Hello FSL Experts,
>>>
>>> In reviewing structural and functional registrations from within
>>> subjects'
>>> higher-level FEAT directories, I have come across two subjects where
>>> FLIRT/FNIRT seems to have made an error in determining the brain
>>> outline.
>>> I make this assumption based on the way the images seem to be distorted
>>> relative to native space folding patterns that contain a large amount of
>>> space.
>>>
>>> I have attached screenshots of the two subjects' structural images in
>>> native and MNI space and am interested to hear what you may think is
>>> going
>>> on, and of course, how best to fix the registration.
>>>
>>> Please let me know if you would like me to send additional information
>>> or
>>> images and I would be happy to do so.
>>>
>>> Thank you for the help and insight.
>>>
>>> Jacob
>>>
>>>
>>>
>>>
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>>
>>
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