Why are you using --t1? If this is fmri, it should be --t2

On 11/21/19 3:27 PM, An wrote:
>
>         External Email - Use Caution
>
> The image in the previous email uses the command tkregisterfv to
> visualize the registration result after step2 bbregister, where I
> uncheck the boxes of the surface layers. The full command of my
> bbregister is: bbregister --mov fMRI.nii --s subjid --reg register.dat
> --t1.
> I attached both the registration result with checking the boxes of the
> surface layers and my final result mapped onto surface below.
> The log file is also attached to this email, please take a look at
> your convenience.
>
> Many thanks.
>
> Best,
> An
>
> image.png image.png
>
> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
> <mailto:DGREVE@mgh.harvard.edu>> 于2019年11月21日周四 下午2:49写道：
>
>     It is hard to say from that image, but it does not look registered
>     to me.
>     - your bbregister command is not valid as it is, please give the full
>     command
>     - please send the bbregister log file
>     - to look at the registration, use tkregisterfv. It will show the
>     surfaces over the fMRI
>
>     On 11/21/19 1:20 PM, An wrote:
>     >
>     >         External Email - Use Caution
>     >
>     > Hi Prof. Greve,
>     >
>     > Thanks for your reply. I do it in the following steps:
>     > 1. ran recon-all on the anatomical volume: recon-all -i MRI.nii -s
>     > subjid -all
>     > 2. register the fMRI series with the anatomical volume by using
>     > bbregister: bbregister --mov fMRI.nii --s subjid --reg register.dat
>     > 3. assign values from volumes to each surface vertex through the
>     > command mri_vol2surf: mri_vol2surf --src MRI.nii --out putput.mgz
>     > --srcreg register.dat --hemi lh
>     >
>     >  I also attached the registered image after step2. It looks like
>     they
>     > are not perfectly aligned. Is there anyway to improve that and also
>     > the final result?
>     >
>     > Many thanks.
>     >
>     > Best,
>     > An
>     > image.png
>     >
>     > Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
>     <mailto:DGREVE@mgh.harvard.edu>
>     > <mailto:DGREVE@mgh.harvard.edu <mailto:DGREVE@mgh.harvard.edu>>>
>     于2019年11月21日周四 下午12:42写道：
>     >
>     >     35% sounds high to me. Did you actually check the registration
>     >
>     >     You can always load the the fMRI as an overlay in freeview, try
>     >     tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz
>     >     Also, please include command lines you used
>     >
>     >     On 11/21/19 10:03 AM, An wrote:
>     >     >
>     >     >         External Email - Use Caution
>     >     >
>     >     > Hi there,
>     >     >
>     >     > I want to map the intensities of the fMRI 4D volumes onto its
>     >     surface
>     >     > in order to get the functional values on each vertex in
>     each frame.
>     >     >
>     >     > I have done the following steps for achieving this:
>     >     > 1. ran recon-all on its anatomical volume.
>     >     > 2. register the fMRI series with the anatomical volume by
>     using
>     >     > bbregister.
>     >     > 3. assign values from volumes to each surface vertex
>     through the
>     >     > command mri_vol2surf.
>     >     >
>     >     > I have got a result of mapping the 4D volumes intensities
>     onto its
>     >     > surfaces but there are 35.5% vertices assigned 0 value in
>     every
>     >     time
>     >     > frame.
>     >     >
>     >     > I am wondering is the ratio reasonable and how could I
>     improve the
>     >     > result? I guess resolution would be one of reasons causing the
>     >     high 0
>     >     > value ratio, my fMRI data is 2mm^3 and anatomical data is
>     1mm^3.
>     >     >
>     >     > Many thanks for your help.
>     >     >
>     >     > Best,
>     >     > An
>     >     >
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