use mri_surf2surf to transform it to fsaverage, then go from there.
cheers
Bruce
On Fri,
23 Jul 2010, Corey Keller wrote:
> Hi Freesurfers,
>
> Thanks for all of the help so far. I just have one more quick
> follow-up question. Just to remind you I was attempting to plot a
> functional map on a pial surface in matlab. The solution was to index
> the functional map so that I just color-coat the pial surface
> accordingly instead of the usual gray. We are now trying to transform
> this functional data so that it will plot on the pial surface of the
> average subject, fsaverage. Any help will be much appreciated. Thanks
> again.
>
> -Corey
>
>
> On Fri, Jul 2, 2010 at 2:27 PM, Corey Keller <corey.j.kel...@gmail.com> wrote:
> Hi,
>
> I figured out how to plot it on my pial surface. Here's my code if
> anyone is wondering. Thanks again for your help.
>
> In freesurfer
>
> bbregister --s CL --mov ./CL/lfo_example.nii.gz --init-fsl --reg
> register.dat --bold
> tkregister2 --mov ./CL/lfo_example.nii.gz --reg register.dat --surf
> mri_vol2surf --src --reg register.dat --out *.nii.gz --hemi lh
>
> In matlab
>
> mgh = MRIread('*.mgh');
> surf_data = mgh.vol;
> iter = round((surf_data+2)*16)';
> % indexing colormap
> map = cmap(round((surf_data+2)*16),:);
> tripatch(cortex.lh,h,map);
> shading interp; lighting gouraud; material dull;
> switch 'l'
> case 'r'
> l=light('Position',[1 0 0]);
> view(90,0)
> case 'ri'
> l=light('Position',[1 0 0]);
> view(90,-90)
> case 'l'
> l=light('Position',[-1 0 0]);
> view(270,0)
> case 'li'
> l=light('Position',[-1 0 0]);
> view(270,-45)
> end
> axis off, hold on
>
> On Fri, Jul 2, 2010 at 11:19 AM, Corey Keller <corey.j.kel...@gmail.com>
> 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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>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
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>>>>
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