Those fields are not valid for surface data.
doug
Corey Keller wrote:
> Hi Freesurfers,
>
> I have now successfully registered the functional volume and
> transformed the volume to a surface via mri_vol2surf. I then loaded
> the nifti surface into matlab with MRIread (nii =
> MRIread('example.nii'). nii.vol is a 1x149x797 matrix. Additionally,
> there are variables of vox2ras and vox2ras1 transformation matrices in
> the nii struct. Do you know how I get nii.vol into RAS coordinates and
> eventually plotted? Thanks!
>
> Best,
> Corey
>
> On Fri, Jul 2, 2010 at 10:06 AM, ythomas <ytho...@csail.mit.edu> wrote:
>
>> Is this a preprocessed (whole brain regression, bandpass filter, etc)
>> rest-state volume? If so, I would suggest using the volume before the
>> preprocessing (which works well for me).
>>
>> Thanks,
>> Thomas
>>
>> On Jul 2, 2010, at 9:58 AM, Corey Keller wrote:
>>
>>
>>> Hi Bruce,
>>>
>>> Thanks for the info. I am trying to register a resting state
>>> functional nifti file. I ran bbregister but it was not well aligned
>>> (pictures are attached). Our thought is that the contrast was not
>>> strong enough for freesurfer to detect enough common points with the
>>> anatomical volume. If we feed another example
>>> functional file with better contrast, could we then use that register
>>> file to apply to our data? Any thoughts on how we can do this
>>> betterwithout manually aligning? Thanks again.
>>>
>>> Best,
>>> Corey
>>>
>>> On Fri, Jul 2, 2010 at 9:30 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>
>>>> Hi Corey,
>>>>
>>>> yes, or you can try bbregister to do it automatically.
>>>>
>>>> cheers
>>>> Bruce
>>>> On Fri, 2 Jul 2010, Corey Keller wrote:
>>>>
>>>>
>>>>> Hi Freesurfers,
>>>>>
>>>>> I know this is probably an easy question, but I am having some trouble
>>>>> with it. I am trying to plot functional data (in nifti format) onto a
>>>>> pial or inflated surface in matlab. I am uring mri_vol2surf but am
>>>>> missing the register file. Do I find this from registering the
>>>>> functional data to the anatomical surface via tkregister? Thanks.
>>>>>
>>>>> -Corey
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>>
>>>>>
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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
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