Thanks for getting back to me, and you are absolutely correct. My mistake
was that I was only including one structural image in the same folder as my
EPI data. I was clearly confused in my reading of the fnirt instructions,
and this email chain clarified it for me. I now have much better
registration.
Thanks for your help!
Ben
On Sun, Jun 6, 2010 at 12:08 PM, Jesper Andersson <[log in to unmask]>wrote:
> Dear Ben,
>
> hope you are fine with me CC'ing the mailbase. It may be useful for others
> too.
>
> I had a look at your data, and it registers acceptably well. Both the
> functional->structural and the structural->standard. The
> structural->standard is not perfect in the topmost slices. It is made
> difficult by signal from the meningies (I think it is) that has almost
> identical intensity as the grey matter. But it is still acceptable.
>
> I notice that the structural scan you sent me was
> named CNMC0194-msr1_brain.nii.gz, but that is still contained the scalp. If
> you want to use fnirt in feat you need to supply two versions of your
> structural scan.
>
> 1. A betted version whos name ends in _brain
> 2. A non-betted version with an identical name to the one above but which
> does not end in _brain
>
> I suspect your non-betted scan with the ending _brain might have been used
> by flirt as if it was betted, giving very poor results. These will then be
> fed into fnirt which will then also fail.
>
> So try that and let me know how it goes.
>
> Good Luck Jesper
>
>
>
>
> On 6/3/10, Jesper Andersson <[log in to unmask]> wrote:
>>
>> Dear Ben,
>>
>> I would need to properly see your data to be able to help you with this.
>> Could you please upload the structural scan you are using as well as the
>> example_func file to
>>
>> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>>
>> and then send the six-digit number to my mail address (not the mailbase).
>>
>> Jesper
>>
>>
>>
>> On 2 Jun 2010, at 20:19, Ben Yerys wrote:
>>
>> Hi FSLers--
>>>
>>> Thanks to Jesper and others for input on my registration woes. Removing
>>> the neck from the MPRAGE was one of several big problems in registering the
>>> High Res image to the Standard. However, I'm still having significant
>>> problems with registration. I do have a fair amount of ghosting in my
>>> images, because Fat Sat was turned off in order to have a sequence with
>>> TR=2000. At least I was told that Fat Sat had to be turned off for the
>>> sequence to be this fast.
>>>
>>> I've attached one picture which highlights my problem. It appears as
>>> though the EPI image is highly distorted in the right hemisphere (left side
>>> of display) and my thought is that this is driving all of my registration
>>> problems. I ran BET ("apply to 4D") with the default fractional intensity
>>> threshold of 0.5 to my 4D data and this removed almost all of the ghosting
>>> except for the two most superior slices and the distortion was reduced but
>>> still a problem. My other pre-processing steps include:
>>> MCFLIRT
>>> Slicetiming *I've taken this out in case I made a mistake in my
>>> slicetiming file
>>> Smooth FWHM
>>> Registration - Main structural image - Linear: Normal search with 6 DOF
>>> Registration - Standard Space - Linear+Nonlinear with MNI152_T1_2mm_brain
>>> Warp Res=10mm
>>>
>>> The participant is a typically developing 12-yr-old who had a max
>>> translation movement of 0.5mm. I ran this data through SPM5 and from what I
>>> can see by eye using check reg, the registration looks acceptable and my
>>> activation map is in line with predictions for my set-shifting task. What
>>> am I missing?
>>>
>>> Thanks for the help!
>>> Ben
>>> <highres_to_standard_neck removed3.jpg>
>>>
>>
>
>
> --
> Benjamin Yerys, PhD
> Assistant Professor
> Center for Autism Spectrum Disorders
> Children's Research Institute - Neuroscience
> Children's National Medical Center
> 111 Michigan Ave, NW
> Washington DC, 20010
> 202-476-5358 (office)
> 301-765-5425 (lab)
>
>
>
--
Benjamin Yerys, PhD
Assistant Professor
Center for Autism Spectrum Disorders
Children's Research Institute - Neuroscience
Children's National Medical Center
111 Michigan Ave, NW
Washington DC, 20010
202-476-5358 (office)
301-765-5425 (lab)
