it's not delicate - it's just confusing for us when you use it as it
refers to a specific dataset
cheers
Bruce
On Mon, 18 Nov 2019, An wrote:
External Email - Use Caution
Sorry for the confusion, I don't know it has a delicated meaning. I just
followed the steps on the
freesurfer download and install webpage to install the software and then ran
the recon-all command.
I will try to avoid this kind of issues in the future.
Many thanks.
Best,
An
Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> 于2019年11月18日周一 下午4:47写道：
why did you call it bert? It just makes things confusing
On 11/18/19 2:53 PM, An wrote:
>
> External Email - Use Caution
>
> Here is my recon-all command line:
> recon-all -i ana_Vol.nii -s bert -all
> Many thanks.
>
> Best,
> An
>
>
> Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu
> <mailto:dgr...@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. <dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>
> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@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. <dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>
> > <mailto:dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>
> > > <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@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. <dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>
> > <mailto:dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>
> > > <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>>>
> > > >>> <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>
> > <mailto:dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>
> > > <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@mgh.harvard.edu>
> > <mailto:dgr...@mgh.harvard.edu
> <mailto:dgr...@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
> > > >>> >
> > > >>> >
_______________________________________________
> > > >>> > Freesurfer mailing list
> > > >>> > Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
> > > >>> >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >>>
> > > >>>
> > > >>> _______________________________________________
> > > >>> Freesurfer mailing list
> > > >>> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>>
> > > >>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >>>
> > > >>>
> > > >>> _______________________________________________
> > > >>> Freesurfer mailing list
> > > >>> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > >>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >>
> > > >>
> > > >> _______________________________________________
> > > >> Freesurfer mailing list
> > > >> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> > > >>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > > >
> > >
> > >
> > >
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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