Hi krishna,
First, I want to be the first to say I don't have this all figured out.
I've been struggling with it myself -- namely trying to get surfaces
back in true "orig" orientation, origin, etc., so that functional
volumes need not be messed with to ensure proper mapping. But that is a
taller order.
Second, it might be that mapping in Freesurfer might be easier. But
when you need to map in Caret, there is hope.
I'm not sure, without looking at your data (which I'm not dying to do,
but will if asked), but it might be that you just need a translated
version of your surface, like so:
#################################################
# Shift surface from Freesurfer space to orig
#################################################
X_OFFSET=`$FREESURFER_DIR/bin/mri_info --cras ../mri/orig.LPI.nii |
cut -f1 -d' '`
Y_OFFSET=`$FREESURFER_DIR/bin/mri_info --cras ../mri/orig.LPI.nii |
cut -f2 -d' '`
Z_OFFSET=`$FREESURFER_DIR/bin/mri_info --cras ../mri/orig.LPI.nii |
cut -f3 -d' '`
MATRIX="1.0 0.0 0.0 $X_OFFSET 0.0 1.0 0.0 $Y_OFFSET 0.0 0.0 1.0
$Z_OFFSET 0.0 0.0 0.0 1.0"
caret_command -surface-apply-transformation-matrix
Human.$CASE.$HEM_FLAG.Midthickness.coord Human.$CASE.$HEM_FLAG.topo
Human.$CASE.$HEM_FLAG.Midthickness_orig.coord -matrix $MATRIX
... where ../mri/orig.LPI.nii is simply a rotated/flipped version of
your orig volume in what I still call LPI orientation (left-to-right,
posterior-to-anterior, inferior-to-superior). I generated mine like so:
$FREESURFER_DIR/bin/mri_convert $VOLUME.mgz --reslice_like
$ATLAS_DIR/TEMPLATE.LPI.nii -rt nearest $VOLUME.LPI.nii
... where $ATLAS_DIR/TEMPLATE.LPI.nii is a null volume with these
characteristics:
it.wustl.edu 4% 3dinfo ./PUBS/OHBM/2010/PALS_B12.LR/TEMPLATE.LPI.nii
Dataset File: ./PUBS/OHBM/2010/PALS_B12.LR/TEMPLATE.LPI.nii
Geometry String:
"MATRIX(-1,-3.55271e-15,0,134.5764,0,-1,1.111172e-08,116.8553,-2.03682e-16,9.498479e-10,1,-131.896):256,256,256"
third (z) = Inferior-to-Superior [-orient LPI]
R-to-L extent: -120.424 [R] -to- 134.576 [L] -step- 1.000 mm [256
voxels]
A-to-P extent: -138.145 [A] -to- 116.855 [P] -step- 1.000 mm [256
voxels]
I-to-S extent: -131.896 [I] -to- 123.104 [S] -step- 1.000 mm [256
voxels]
(Off the top of my head, I'm not certain getting the cras offset from
the LPI version is strictly required here, but I think I had a good
reason for doing it that way in my code.)
After translating the surface by the cras offset (which I think of as
translating from Freesurfer coordinate space to orig space), then try
mapping to this translated surface.
I don't think it will be an issue for you, comparing your FS to Caret
mappings, but for some people, rotating/flipping the functional volumes
to LPI sometimes helps.
Donna
On 12/10/2010 11:36 AM, Krishna Srihasam wrote:
> Hi,
>
> So, I finally got my Freesurfer surfaces into caret. But when I try to
> put my functional activations on the imported surfaces in caret. They
> are out of place. I used "Map Volume to Surface" to overlay the
> activations on top of the imported surface. I tried both "Map to
> caret" and "Map to Spec File" and I am getting the same difference in
> locations of activations. What am I doing wrong?
>
> I have attached two files "ActivationsonCaret.jpg" and
> "ActivationonFreeSurfer.jpg" to highlight my problem.
>
> regards,
> krishna
>
> On 12/08/2010 12:07 PM, Donna Dierker wrote:
>> Hi Krishna,
>>
>> We haven't spent any time streamlining this process, but this script
>> worked for me a few months back:
>>
>> http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/import.sh
>> login pub
>> password download
>>
>> Edit the case name and hemisphere. You'd have to adapt it to run both
>> hems in one go.
>>
>> Note that this just imports; it doesn't register to F99 or F6.
>>
>> Donna
>>
>> On 12/08/2010 10:40 AM, Krishna Srihasam wrote:
>>
>>> Hi,
>>>
>>> Is there any way to convert my monkey freesurfer surfaces to caret?
>>>
>>> rgds,
>>> Krishna
>>> _______________________________________________
>>> caret-users mailing list
>>> [email protected]
>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>>>
>>>
>> _______________________________________________
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>>
>
>
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