Sorry I'm not as familiar with that script, but I am familiar with scripts we
use for importing human freesurfer files into Caret. Hopefully these excerpts
might help:
#Find c_ras offset between FreeSurfer surface and volume and generate matrix to
transform surfaces
MatrixX=`$FreeSurferInstallationDirectory/bin/mri_info --cras
$InputFreesurferSubjectDirectory/mri/orig.mgz | cut -f1 -d' '`
MatrixY=`$FreeSurferInstallationDirectory/bin/mri_info --cras
$InputFreesurferSubjectDirectory/mri/orig.mgz | cut -f2 -d' '`
MatrixZ=`$FreeSurferInstallationDirectory/bin/mri_info --cras
$InputFreesurferSubjectDirectory/mri/orig.mgz | cut -f3 -d' '`
Matrix1=`echo "1 0 0 ""$MatrixX"`
Matrix2=`echo "0 1 0 ""$MatrixY"`
Matrix3=`echo "0 0 1 ""$MatrixZ"`
Matrix4=`echo "0 0 0 1"`
MatrixCRAS=`echo "$Matrix1"" ""$Matrix2"" ""$Matrix3"" ""$Matrix4"`
for Surface in white pial ; do
caret_command -surface-apply-transformation-matrix
$OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere."$Surface"_orig.initial_mesh.coord.gii
$OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere.initial_mesh.topo.gii
$OutputRootDir/$Subject/$InitialMeshDirectory/$Subject.$Hemisphere."$Surface"_orig.initial_mesh.coord.gii
-matrix $MatrixCRAS
done
Also, it might matter which volume you use (e.g., orig.mgz vs others).
On Jul 20, 2012, at 3:55 PM, Pablo Polosecki wrote:
> Hi Donna,
>
> I tried converting to RAS (this converst the heder information, which
> apparently Caret does use) and the data matrix. The problem is the
> same: the axes are correct (i.e., R points to the right side, D is
> dorsal, etc). However, the surface and the volume still don't match in
> Caret just like before. The issue seems to be some sort of offset in
> the center of coordinates (when I click on the surface, the
> highlighted points seem to be on a sensible medio-lateral and
> dorso-ventral position. The problem is that the highlighted voxel is
> too posterior in the volume view). Does this make sense or hint to a
> possible solution to you perhaps? Worst case scenario, I could eyeball
> how big this translation offset is, open the volume in matlab and have
> it translate the data matrix. That way, it would roughly look okay,
> but perhaps there is a more graceful way of handling this.
> Thank you again,
> Pablo
>
> On Fri, Jul 20, 2012 at 3:14 PM, Donna Dierker <[email protected]>
> wrote:
>> Be aware that what AFNI/Caret calls LPI, Freesurfer calls RAS. ;-)
>>
>> Can you try having mri_convert write the volume out as RAS, instead of
>> LPI? Freesurfer will read the header and do the right flipping/rotating
>> so that the surface aligns with it. Freesurfer did the right thing, as it
>> understands that label. But that understanding is not what other software
>> desires, in this case. (At least that's my read of your problem.)
>>
>> I think the axes don't need rotating anymore, but all three need flipping.
>>
>>> Dear List,
>>>
>>> I successfully completed the FS-to-F99 tutorial and now I am trying to
>>> reproduce the steps with my own FreeSurfer dataset. According to the
>>> FS-to-F99 tutorial, I need to have my mri volume "into LPI
>>> orientation" and "the surfaces and volume need to be in register". My
>>> original volume is in LIA orientation and is in register with my
>>> surface, in the sense that when I open both on FreeSurfer's tkmedit
>>> they are well-aligned to each other (I don't know how to check that
>>> they are in register otherwise). If I use this surface and volume on
>>> FS-to-F99's Stage-1 script and open the resulting spec file with
>>> Caret, the volume's axes are wrong and the points on the surface and
>>> in the volume don't match (I see this by clicking on the surface and
>>> looking what is then highlighted on the volume window). If I transform
>>> the volume into LPI orientation (using FreeSurfer's mri_convert
>>> command), the new volume has the desired orientation and,
>>> interestingly, it is still well-aligned to the surface in FreeSurfer's
>>> tkmedit. However, when I use this surface and volume on the FS-toF99's
>>> Stage-1 script, the volume and the surface are still not well-aligned,
>>> even though the axes labels are now correct. How could I fix things so
>>> that my volume and surface are in register when shown in Caret?
>>>
>>> Thank you very much,
>>> Pablo
>>> _______________________________________________
>>> caret-users mailing list
>>> [email protected]
>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>
>>
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