Dear Derek,
It seems to me that FNIRT is doing a pretty reasonable job given the scope of the lesion.
The areas away from the lesion are well registered.
What particular areas are you concerned about?
It is certainly true that in the regions where the lesion is that the brain edge gets stretched, but as far as I can see this is really contained to the areas within the lesion. As there is no strong and reliable brain edge in the FA images, this is doing what it can given the lesion mask.
If you have more specific queries or problems with the registration, let me know.
All the best,
Mark
On 6 Mar 2014, at 03:36, "Archer,Derek B" <[log in to unmask]> wrote:
> Hello Mark,
>
> I have uploaded all the relevant images and matrices to the link provided. The code I used, with the exact file names, is below:
>
> flirt -in native_FA.nii.gz -ref FMRIB_FA_1mm.nii.gz -out flirted_FA.mat -bins 256 -cost corratio -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -inweight native_lesionmask.nii.gz -interp trilinear
>
> fnirt --ref=FMRIB_FA_1mm.nii.gz --aff=flirted_FA.mat --inmask=native_lesionmask.nii.gz --in=native_FA.nii.gz --config=FA_2_FMRIB58_1mm.cnf --iout=fnirted_FA.nii.gz --jout=jac_sub_to_FMRIB --cout=coef_sub_to_FMRIB
>
> Let me know if I have missed something. I really appreciate all of your help!
>
> Derek
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Mark Jenkinson
> Sent: Thursday, February 27, 2014 1:35 AM
> To: [log in to unmask]
> Subject: Re: [FSL] FNIRT Distortions
>
> Hi,
>
> Yes, I could see the illustrations that you provided but it wasn't enough to know what was really happening.
> This is why I asked you to upload the relevant nifti data (input image, output image and lesion mask) to the following:
> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=68312615463381F4C
>
> All the best,
> Mark
>
> On 26 Feb 2014, at 16:32, "Archer,Derek B" <[log in to unmask]> wrote:
>
>> Hello Mark,
>>
>> I was wondering if you noticed the distortions I have been seeing in my fnirt results. Do you have any ideas of what could be causing this?
>>
>> Thanks as always,
>> Derek
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Derek Archer
>> Sent: Thursday, February 13, 2014 10:33 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] FNIRT Distortions
>>
>> Hi Mark,
>>
>> Sorry about that! It is working now. Here is the link: http://archerdb.imgur.com/
>>
>> Thanks,
>> Derek
|