Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> 于2019年11月18日周一下午2:33写道：

What was your original recon-all command?

On 11/18/19 1:48 PM, An wrote:
>
>         External Email - Use Caution
>
> 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 ran recon-all for the anatomical volume and saved all
> outputs(mri,labels,surf and etc.) in the bert folder. I use it because
> I need to specify the required flag -s in bbregister in order to
> register the functional volume to its anatomical volume.
>
> Many thanks.
>
> Best,
> An
>
> Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu
> <mailto:DGREVE@mgh.harvard.edu>> 于2019年11月18日周一下午1:31写道：
>
> 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>
> > <mailto: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>>
> > >>> <mailto: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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