Thank you for your response. I am pasting the command lines below, and attaching the images that correspond to each command line after tkregister2 is run.
command line for registration using all echos:
bbregister --s T1subject2 --mov [path]/T2star.nii.gz --reg [path]/registerT2allechos.dat --init-fsl --t2 --o [path]/T2starallechos_registeredtocorticalsurfacesubject2.nii
command line for registration using fourth echo only (as instructed):
bbregister --s T1subject2 --mov [path]/T2starecho4.nii.gz --reg [path]/registerT2starecho4.dat --init-reg [path]/registerT2allechos.dat --t2 --o [path]/T2starecho4_registeredtocorticalsurfacesubject2.nii
On 2013-07-23 23:45, Douglas Greve wrote:
What is your command line? This is surely an initialization error. Try running tkregister2 with --regheader to see where it starts. If that is close, then use --init-header on bbregister
doug
On 7/23/13 4:13 PM, Smian wrote:
Thank you for your reponse. The registration has turned out quite strangely (please see attached). I checked the first value in the mincost file and it is quite high (~0.95). I'm assuming that means that the initialization was bad. I tried changing the initialization from fsl to spm and header, but that failed too. Would you know why this could be occurring and how I might be able to fix it?
Thank you!
On 2013-07-23 16:07, Bruce Fischl wrote: you can use bbregister to register your T2* volumes to the surface, then mri_vol2surf to sample and display it.
cheers Bruce On Tue, 23 Jul 2013, Smian wrote:
Hi everyone,
To put things into context, I am trying to follow the four step methodology outlined in this paper (Cohen-Adad, 2013) http://www.sciencedirect.com/science/article/pii/S1053811913000700 [1]
I have already performed recon-all on MPRAGE data. I have also carried out the following steps:
- Reconstruct cortical surface
- Register T1 to the surface
- Sample T1 at a given cortical depth
- Register surface to fsaverage
I have now been told to use the T2* information from the fourth echo of separately acquired T2* weighted data and to 'overlay' (I'm not sure if this is the correct usage of this technical term) it on the surfaces produced (as above) of the MPRAGE data. I realize that I can't perform recon-all on this T2* weighted data. I am assuming that I need to carry out steps similar to 1)-4) on this new data, but I'm not sure. Would you have any guidance on how to go about this?
Any help would be appreciated!
Thank you!
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