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I don't understand what you are trying to do. I'm very confused by your
mentioning of bert. What does bert have to do with any of your data?
On 11/14/19 10:47 AM, An wrote:
>
> External Email - Use Caution
>
> Oops sorry for the mistakenly reply. I will pay more attention in the
> future.
>
> Bert is the folder with the anatomical data. I tried the following
> steps with the 4D volume but failed. Then I checked the registration
> result after bbregister and found that the volume was not registered.
> After that I tried another 4D volume to do the steps and successfully
> got the sampled intensity onto the surface.
>
> The difference between the new 4D volume I used and the previous one
> is that there are two transformation matrices between them. The 4D
> dataset that I previously used but failed is the volume already
> registered to its anatomical volume(by using others tools). The new 4D
> volume that I tried and succeed is the volume not registered.
>
> I have no idea why the 4D volume after the transformation would cause
> a failed result. Could you please let me know that?
>
> Many thanks.
>
> Best,
> An
>
> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
> <mailto:DGREVE@mgh.harvard.edu>> 于2019年11月13日周三 下午12:20写道：
>
> If you have an anatomical MR that you have run through recon-all,
> then
> just use that one instead of bert in your steps below
> ps. Please remember to post to the FS list and not to us personally
>
> On 11/12/19 8:41 PM, an wrote:
> >
> > External Email - Use Caution
> >
> > Many thanks.
> >
> > I got the 4D fMRI dataset from others and it is not raw data. In
> order
> > to run mri_vol2surf, I need to calculate the register.dat for the
> > required flag --srcreg so I tried in this way.
> >
> > FYI, the 4D fMRI dataset should have been registered with its
> > anatomical MR volume by using other tools.
> >
> > For now I only ran the recon-all on its anatomical MR volume
> without
> > running the functional stream as I don't have the raw data.
> >
> > Should I also run the raw fMRI data from scratch by using
> functional
> > stream? Or if I can run mri_vol2surf independently, which command
> > should I use to get a register.dat file?
> > In addition, the intensity of the 4D fMRI dataset I have is between
> > [-1, 1] and not integers, would this cause any problem?
> >
> > Best,
> > An
> >
> >
> > On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote:
> >> Don't do the 1st step.
> >> Why are you registering it to bert? I'm pretty sure bert did not
> >> participate in your fmri study
> >> When you run mri_vol2surf, it will probably work better with
> >> --projfrac 0.5
> >>
> >> On 11/11/2019 1:32 PM, An wrote:
> >>>
> >>> External Email - Use Caution
> >>>
> >>> Hi Prof. Greve,
> >>>
> >>> Thanks for your reply and sorry for the confusion.
> >>>
> >>> I have a 4D fMRI dataset with 10 time frames, where the
> intensity of
> >>> each voxel is between [-1,1] and not integers. I want to map the
> >>> intensities of the volumes on its corresponding surface in
> order to
> >>> get the functional values on each vertex in each frame. I have
> >>> already run its corresponding anatomical image in freesurfer.
> >>>
> >>> To achieve it, I tried the following steps:
> >>> 1. conform the fmri series by using mri_convert
> >>> 2. register the fmri series with the anatomy image by using
> >>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg
> register.dat
> >>> 3. assign values from volumes to each vertex by using
> mri_vol2surf:
> >>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg
> >>> register.dat --hemi lh
> >>> I also tried the -regheader in mri_vol2surf: mri_vol2surf
> --src
> >>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh
> >>>
> >>>
> >>> The /4Dvol.nii /aligns very well with the orig.mgz in
> freeview. But
> >>> after step2, the registered volume looks wrong. I am wondering
> could
> >>> I use bbregister to register multi-frame fMRI series to a single
> >>> volume?
> >>> I also tried to use --regheader to replace the --srcreg file in
> >>> mri_vol2surf as the output register.dat in step2 is wrong. But
> the
> >>> output is still wrong.
> >>>
> >>> Many thanks.
> >>>
> >>> Best,
> >>> An
> >>>
> >>> 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11日周一 下午12:16写道：
> >>>
> >>> When you say it is 4D, what do you mean? That each label
> has its
> >>> own frame?
> >>>
> >>> On 11/6/19 5:59 PM, 曲岸 wrote:
> >>> >
> >>> > External Email - Use Caution
> >>> >
> >>> > Hi there,
> >>> >
> >>> > I am working with creating a surface parcellation from a
> >>> volumetric
> >>> > parcellation and have some questions as follows:
> >>> >
> >>> > 1. If the volumetric parcellation is a labeled 4D
> multi-frame
> >>> dataset,
> >>> > could I still use the mris_sample_parc? Or could
> mri_vol2surf
> >>> get the
> >>> > sampled labels for every vertex?
> >>> >
> >>> > 2. For the 4D multi-frame dataset and mri_vol2surf output
> >>> results,
> >>> > which GUI should I use to visualize it? I tried freeview
> for 4D
> >>> > multi-frame dataset but it looks weird.
> >>> >
> >>> > 3. Is there any command to separate multi-frame volume to
> >>> single frame
> >>> > volumes?
> >>> >
> >>> > Many thanks!
> >>> >
> >>> >
> >>> > Best,
> >>> > An
> >>> >
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