You mean you want to display your group volume-based results on the
average surface? That's unusual, but it can be done. You need to create
a registration file between your group average and the standard space
templage, eg, something like:
fslregister --mov $FSLDIR/etc/standard/avg152T1.nii.gz --s
youraveragesubject --reg register.dat
Check it visually:
tkregister2 --mov $FSLDIR/etc/standard/avg152T1.nii.gz --s
youraveragesubject --reg register.dat --surf
Then render your FLAME results on the surface
tksurfer youraveragesubject lh inflated -overlay flamestat.nii.gz
--overlay-reg register.dat
You can map the surface-based ROIs into the standard space with
something like:
mri_label2vol --annot $SUBJECTS_DIR/youraveragesubject/label/lh.aparc.annot
--temp FSLDIR/etc/standard/avg152T1.nii.gz --reg register.dat
--subject ouraveragesubject --hemi lh
--o lh.aparc.mni152.nii.gz
This will create a segmentation volume. The mapping between segmentation
index and brain area can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt
doug
Martin Kavec wrote:
Hi,
I can not find my way to map the results of the FSL fMRI group analysis
(FLAME1+2) from different subjects on their average surface. Here is in more
details what I have done:
1. fMRI analysis of each subject in FSL
2. group analysis (FLAME1+2) in FSL
3. cortical reconstruction of each subject in FS
4. average subject, surface, volume in FS
and I would like to
a) project results of 2 on results of 4
b) project an ROI from histological atlas on a)
Is this doable? Thanks a lot in advance.
Martin
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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