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- fsaverage/mri.2mm
- These are volumes sampled into a 2mm space. The primary purpose of
- these is to support volume-based fMRI analysis as performed in
- FS-FAST. This 2mm space is the space that is used by default in
- FS-FAST to perform "talairach" group analysis (ie, in the mni305
- space). The raw functional data are sampled into this space when
- preproc-sess is run with the -mni305 flag. When a group analysis is
- done, the output space will be this 2mm space. It is possible to use a
- 1mm space, but this can create huge files.
- These files can be used to render the statistical results on a volume
- (though this is not really necessary as they can be rendered directly
- on the 1mm volumes). Also, the aseg.mgz created can be used to
- generate labels/masks of subcortical structures directly in the group
- average space. These can be used with mri_volcluster.
- These files were created with the following commands:
- # Resample each of these volumes using trilin
- foreach vol (orig brain brainmask mni305.cor T1)
- mri_vol2vol --mov ../mri/$vol.mgz --s fsaverage --tal \
- --o $vol.mgz --no-save-reg
- end
- # Resample the aseg
- mri_label2vol --seg ../mri/aseg.mgz --temp orig.mgz \
- --regheader ../mri/orig.mgz --o aseg.mgz
- Note: we don't want to do aparc+aseg because the surface-based
- labels should really be used in a surface-based analysis.
- # checks
- tkmedit -f T1.mgz -aux brain.mgz -seg ./aseg.mgz
- tkregister2 --mov ./orig.mgz --s fsaverage --regheader --reg junk
- #-----------------------------------------------------------
- Creation of subcortical mask. A challenge for doing analyses in three
- ROIs (left hemi, righ hemi, subcortical) is making the ROIs mutally
- exclusive while not excluding any voxels. This is particularly hard in
- this analysis because a cortical voxel in one subject can map to a
- subcortical voxel in another when using the transform to MNI305
- space.
- A map of the subcortical structures for each of the buckner 40 where
- mapped into the mni305 2mm space. A probability map was then
- created. This was repeated for the cortical ribbon and for cerebellum
- by itself.
- 1. An initial mask was created taking voxels with any
- subcortical origins in the native space as long as they had fewer than
- 80% cortex.
- 2. Cerebellum is a special case because it is so close to fusiform
- that it is easy to get bleed over. For this case, a mask was made of
- any cerebellum voxels that had at least 20% cortex. Any voxels in this
- mask were then excluded from the mask from step 1 to create a new
- mask.
- 3. Little islands were excluded by running connected components and
- taking the largest cluster.
- 4. This mask was then dialted by one voxel then eroded by one voxel to
- remove holes and make the final mask less jagged.
- # ----- Below For Version 5 --------------------#
- Everything above is for 5.1 and higher.
- The mask is created based on mri/subcort.prob.mgz which was created
- with make_average_subcort. subcort.prob.mgz is the raw probability of
- a voxel being in a subcortical gray matter structure based on the
- Buckner40. Inevitably, this mask will include more than just
- subcortial gray matter structures, but we would rather have the mask
- be too big than too small.
- # Resample into 2mm space
- mri_vol2vol --mov ../mri/subcort.prob.mgz \
- --s fsaverage --tal --o subcort.prob.mgz \
- --no-save-reg
- Threshold at .05 (meaning that at least 5% of the subjects at
- a voxel must have a subcortical label). Also dilate by 2 to
- expand the mask.
- mri_binarize --i subcort.prob.mgz --min .05 \
- --dilate 2 --o subcort.mask2.mgz
- Erode by 1. The net result of dilating by 2 then eroding
- by 1 is that holes are filled in and the edges are
- a little smoother.
- mri_binarize --i subcort.mask2.mgz --min .5 \
- --erode 1 --o subcort.mask.mgz
- rm subcort.mask2.mgz
- #-----------------------------------------------------------
- Creation of registration matrix between the 2mm fsaverage/mni305 space
- and the 2mm mni152 space. This can be used to convert data in the 2mm
- fsaverage/mni305 space into the mni152 2mm space.
- set d = $SUBJECTS_DIR/fsaverage
- # Create registration matrix between the full 256^3, 1mm3
- # volume and the 2mm space (simple regheader)
- tkregister2 --mov $d/mri.2mm/brain.mgz --targ $d/mri/brain.mgz \
- --regheader --reg $d/mri.2mm/reg.2mm.dat --noedit
- # Registration between the fsaverage/mni305 subject (full 256^3, 1mm3)
- # and the 2mm mni152 space. This was created by hand.
- # $FREESURFER_HOME/average/mni152.register.dat
- # Compute the registration between the 2mm fsaverage space and the
- # mni152 2mm space by concatenating the two matrices above.
- mri_matrix_multiply -im $d/mri.2mm/reg.2mm.dat \
- -iim $FREESURFER_HOME/average/mni152.register.dat \
- -om $d/mri.2mm/reg.2mm.mni152.dat
- # Check the registration
- tkregister2 --mov $d/mri.2mm/brain.mgz \
- --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
- --reg $d/mri.2mm/reg.2mm.mni152.dat
- # To view without reslicing
- tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
- -overlay sig.nii -reg reg.2mm.mni152.dat
- # To do the conversion/reslicing, run something like
- mri_vol2vol --mov sig.nii --reg reg.2mm.mni152.dat \
- --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
- --o sig.mni152.nii
- # To view with reslicing
- tkmedit -f $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \
- -overlay sig.mni152.nii
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