yes, but the surface overlay is in mgz (or nii.gz) format
On 04/19/2016 03:05 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> below is the email I had written last Friday. I thought it got lost in
> the mix. I was told by Bruce to use identity.nofile as the
> transformation since my labels and T1s are already in the same space
> and I just want to resample my labels to the surfaces.
>
> *I will try, as you suggest, --regheader *
>
> When I do "mri_cor2label --help" it says it uses surface overlays or
> volumes. *I am not sure why I want to generate a volume with
> mri_vol2surf* - shouldn't I generate a surface overlay that I can then
> create as a label using mri_cor2label?
>
> many thanks
>
> Trisanna
>
>
>
> thanks Bruce
>
> I could not find identity.nofile anywhere, when I ran mri_vol2surf I
> got the following error
>
> trisanna@kaplan:~$ mri_vol2surf --mov
> /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz --o
> /data-01/trisanna/freesurfer/icbm-112 --reg identity.nofile --hemi lh
> srcvol = /data-01/trisanna/freesurfer/icbm-112/mri/labels5.mgz
> srcreg = identity.nofile
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> regio_read_register(): No such file or directory
> Could not open identity.nofile
>
>
>
> On Fri, Apr 15, 2016 at 8:40 AM, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
> Hi Trisanna
>
> you can give the transformation "file" named identity.nofile and it
> will assume that the transform is the identity. You can then use
> mri_vol2label to sample the label onto the surface and visualize it with:
>
> freeview -f lh.inflated:label=lh.labels.label
>
> or some such
>
> cheers
> Bruce
>
> On Thu, 14 Apr 2016, Trisanna Sprung-Much wrote:
>
> Hi there
>
> Just to reiterate my point above, when I open a surface created in
> Freesurfer with my labels.mgz (converted from minc) in Freeview (i.e. no
> transformations have been performed) I get the following snapshot
> #1. Clearly, my original labels are aligned with the surface, as they
> should
> be since Freesurfer did not alter the space. So, how can I use mrivol2surf
> to resample the surface such that the vertices carry the label info? What
> output format should I use in mrivol2surf? How can I open this output in
> Freeview?
>
> For instance, when I try a .dat that creates no transformation and
> save the
> output as .mgz and use Overlay in Freeview, I get snapshot #2. So,
> something
> is going wrong in my mrivol2surf command.
>
> My apologies for the questions
> Trisanna
>
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Tue, Apr 19, 2016 at 1:23 PM, Douglas N Greve
> <mailto:Freesurfer@nmr.mgh.harvard.edu>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> I'm not sure what identity.nofile is or what you are trying to do (no
> previous info in the email). If whatever you are trying to map to the
> surface is already in anatomical space (so no registration necessary),
> then you can use --regheader with mri_vol2surf. mri_cor2label will
> take
> a volume format as input (ie, mgz, nii.gz ,etc)
>
> On 04/19/2016 01:17 PM, Trisanna Sprung-Much wrote:
> >
> > Hi All!
> >
> > Could someone please tell me how to run mri_vol2surf using
> > identity.nofile as the transformation? I cannot find any
> documentation
> > on identity.nofile
> >
> > Additionally, if my next step is to use the output of
> mri_vol2surf in
> > mri_cor2label, which takes surface overlays OR volumes, what format
> > should my output be for mri_vol2surf?
> >
> > many thanks!
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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