Ok. Can't see any options in mris_smooth info reducing the number of
vertices. How would I do that?
Ta,
john
On 9 December 2011 17:22, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
> Yes, give it both --sval-xyz and --tval-xyz to indicate that the output is
> a surface. We usually use mris_smooth to smooth surfaces; I'm not sure
> whether this use of mri_surf2surf will work properly.
> doug
>
>
> Bruce Fischl wrote:
>
>> Hi John
>>
>> Doug can say for sure, but I think you want to give it the switch
>> --sval-xyz so it knows to expect a surface not a scalar field over the
>> surface.
>>
>> cheers
>> Bruce
>> On Wed, 7 Dec 2011, John Griffiths wrote:
>>
>> [ Douglas and Dan - sending this again as I didn't sent it to the list
>>> address before. Sorry. ]
>>>
>>> Thanks guys.
>>> When I run mri_info on the .mgz file I was using before it seems crash
>>> (nothing happens, and have to press ctrl+c to get the console back). So I
>>> suppose that partially explains mri_surf2surf not working. Not sure
>>> what's
>>> going wrong there - the command I used was
>>> mris_convert /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial
>>> /home/jdg45/lh.pial_converted.**mgz
>>>
>>> For the original question - I was using a converted .mgz file because
>>> when I
>>> just give it the path to the 'lh.pial' file in the same directory it
>>> says it
>>> cant determine the file type -
>>> mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval
>>> /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial --tval
>>> /home/jdg45/CBU070282_**smoother_surf.mgz --s CBU070282
>>> Standard output:
>>> ERROR: could not determine type of
>>> /work/imaging5/Freesurfer/**CBU070282/surf/lh.pial
>>> Standard error:
>>>
>>> Is there a .xxx suffix for those files I should be using?
>>> Incidentally, the reason I'm doing this is that I want to downsample a
>>> surface file; someone suggested to me to use mri_surf2surf with the
>>> 'trgicoorder' flag. Is this a good way to downsample a surface?
>>> Thanks,
>>> john
>>>
>>>
>>> On 6 December 2011 19:02, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
>>> wrote:
>>>
>>> surf2surf actually takes surface overlays (not surfaces
>>> themselves) as input, and they can be in any format that FS
>>> reads. The wiki is probably not up-to-date as those options are
>>> ok.
>>> doug
>>>
>>> Daniel Wakeman wrote:
>>> Hi John,
>>>
>>> It seems weird that you are using .mgz files (this
>>> suffix is for
>>> volume files) with mri_surf2surf (whose inputs
>>> should be surfaces).
>>> Also, it seems that several of the options you are
>>> trying I don't
>>> believe exist at least according to the wiki (e.g.
>>> -cortex -fwhm). Are
>>> you sure you are using the right command?
>>>
>>> D
>>>
>>> On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths
>>> <j.davidgriffi...@gmail.com> wrote:
>>> Dear list,
>>>
>>> I am having the following memory
>>> allocation problem when running
>>> mri_surf2surf. Can't find any mention of
>>> this error on the list or the
>>> internet - sorry if I've missed
>>> anything.
>>>
>>> mri_surf2surf --cortex --fwhm 5.0000
>>> --hemi lh --sval
>>> /home/jdg45/lh.pial_converted.**mgz --tval
>>> /home/jdg45/CBU070282_**smoother_surf.mgz
>>> --s CBU070282
>>> Standard output:
>>> srcsubject = CBU070282
>>> srcval =
>>> /home/jdg45/lh.pial_converted.**mgz
>>> srctype =
>>> trgsubject = CBU070282
>>> trgval =
>>> /home/jdg45/CBU070282_**smoother_surf.mgz
>>> trgtype =
>>> srcsurfreg = sphere.reg
>>> trgsurfreg = sphere.reg
>>> srchemi = lh
>>> trghemi = lh
>>> frame = 0
>>> fwhm-in = 0
>>> fwhm-out = 5
>>> label-src = (null)
>>> label-trg = lh.cortex.label
>>> OKToRevFaceOrder = 1
>>> Reading source surface reg
>>> /work/imaging5/Freesurfer/**
>>> CBU070282/surf/lh.sphere.reg
>>> Loading source data
>>> Standard error:
>>> MRIalloc: could not allocate 2032167524
>>> slices
>>>
>>> Cannot allocate memory
>>> Return code: 254
>>>
>>>
>>> Any suggestions?
>>>
>>>
>>> Thanks,
>>> john
>>>
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>>>
>>> The information in this e-mail is
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>>> addressed. If you believe this e-mail
>>> was sent to you in error and the
>>> e-mail
>>> contains patient information, please
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>>>
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>>
>>> Bugs:
>>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>>> FileDrop:
>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>>>
>>>
>>>
>>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs:
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop:
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
>
>
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