Hi Mark,
Thanks for your email. Its good to know that you think the initial registration is good.
With regards to viewing the thresholded zstat images - I have tried using applywarp just as you suggested. Unfortunately I am still getting activation blobs outside of the standard brain on all the images. After reading the applywarp information on the website, I tried adding a premat file (example_func2highres.mat in this case), but that made it much worse! I used the verbose option in case any errors came up: this is the command and output:
[psech@adara mando_opt2A.feat]$ applywarp --in=thresh_zstat4.nii.gz --ref=reg/standard.nii.gz --warp=reg/example_func2standard_warp.nii.gz --out=thresh_zstat4_standard_warp.nii.gz --verbose
Automatically determining absolute/relative warp convention
Assuming warps was relative
superflag = 0
ssvec = 0 0 0
I would be really grateful for any further ideas for me to try to register these images!
With thanks
Ella
********
Hi,
The registrations look good to me, and I can definitely see the difference in applying the fieldmap, so I'm surprised to say that you thought that changing the sign didn't make a difference. I would double-check that.
I didn't spot an obvious issue in your previous email (and please keep copying them in the thread as it helps in answering them). You previously said that you used the command:
flirt -in thresh_zstat1.nii.gz -ref reg/standard.nii.gz -applyxfm -init reg/example_func2standard.mat -interp trilinear -out thresh_zstat1_standard.nii.gz
but this is only good if you have just done linear registration. If you have done nonlinear registration then you need to use applywarp with the example_func2standard_warp.nii.gz image with a command like:
applywarp --ref=reg/standard --in= thresh_zstat1 --warp=reg/example_func2standard_warp --out=thresh_zstat1_standard
All the best,
Mark
On 15 Aug 2013, at 22:38, Ella Hinton <[log in to unmask]> wrote:
> Hi Mark
>
> Many thanks for your email. I have uploaded the reg folder and design.fsf file as requested. Let me know if the upload hasn't worked ([log in to unmask]). I really appreciate you taking a look.
>
> The uploaded data are from the Feat we ran with the default unwarp direction of -y. We also ran it with unwarp direction of y, but it didn't appear to make any difference.
>
> Thanks in advance
> Ella
>
> (Research Associate, CRICBristol)
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