On 07/17/2012 05:17 PM, Garikoitz Lerma Usabiaga wrote:

Thanks Doug,

I've done it with the one in SPM:

tkmedit -f $SPM8_DIR/canonical/avg152T1.nii -overlay ROI45.nii -fthresh 0.5

is this ok or should I test it with the one from FSL as well? My partner is working with SPM and MarsBar.

That is ok. How does it look? Until it looks ok in the volume, it is not worth trying to map it onto the surface.
doug

Both in FS and in SPM the ROI is the same, troubles start when I register it (spmregister) and try to visualize in the MNI305 fsaverage with tkmedit. After the mri_vol2surf  the ROI is completely displaced (compared with the lh.aparc.annot or lh.aparc.2009a.annot, it is always bigger and displaced).

Do you think the problem is the registration between 152 and 305?

thanks!

Gari

On 2012-07-17, at 19:43, Douglas N Greve wrote:

Hi Gari,

Does it appear in the right place if you run

tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz -overlay ROI45.nii

doug

On 07/17/2012 01:20 PM, Garikoitz Lerma Usabiaga wrote:

Hi freesurfer experts,

I want to use a volume based MNI152 ROI in Freesurfer, when I check it

over fsaverage with the following command the ROI is not in the

correct position...:

/

/tkmedit fsaverage T1.mgz -overlay ROI45.nii//-overlay-reg $FREESURFER_HOME/average/mni152.register.dat

/

/

And I have the same problem when I convert it to surface:

cd $SUBJECTS_DIR/fsaverage/surf

mri_vol2surf \

 --mov ../../ROI2/ROI45.nii \

 --reg $FREESURFER_HOME/average/mni152.register.dat \

 --projdist-max 0 1 0.1 \

 --interp nearest \

 --hemi lh \

 --out lh.fsaverage.ROI45.mgh \

 --reshape

- Is this a correct way of using it? Should I get proper results or I

am missing anything? and,

- Does it make sense creating a new fsaverage using the

/spm8/canonical/avg152T1.nii, then applying the ROI which is already

in 152 space, and referring the cortical thickness of all the subjects

to this "new fsaverage"? (the functional analysis is being carried in

SPM as well).

Many thanks for your answers,

Gari

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