| T O P I C R E V I E W |
| ch186 |
Posted - Sep 29 2011 : 3:02:51 PM
Is there a Talairach brain somewhere in the User Scripts on Munin? |
| 3 L A T E S T R E P L I E S (Newest First) |
| dvsmith |
Posted - Oct 03 2011 : 5:04:49 PM
Are you sure your ROIs are actually in "Talairach space" and not MNI/ICBM? These are frequently mislabeled, as you can see from Matthew Brett's webpage (http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach) and a series of discussions in NeuroImage (http://www.ncbi.nlm.nih.gov/pubmed/17870621).
How did you get your ROIs? Assuming they are true NIFTI files with a that header looks like what I have printed below, then they're already in MNI space (the key fields are the sform, pixdims, and dims).
wl-10-180-148-31:~ dvsmith$ fslhd MNI152_T1_2mm_brain.nii.gz
filename MNI152_T1_2mm_brain.nii.gz
sizeof_hdr 348
data_type INT16
dim0 3
dim1 91
dim2 109
dim3 91
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 2.0000000000
pixdim2 2.0000000000
pixdim3 2.0000000000
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 352
cal_max 8000.0000
cal_min 3000.0000
scl_slope 1.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name MNI_152
qform_code 4
qto_xyz:1 -2.000000 0.000000 -0.000000 90.000000
qto_xyz:2 0.000000 2.000000 -0.000000 -126.000000
qto_xyz:3 0.000000 0.000000 2.000000 -72.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Right-to-Left
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name MNI_152
sform_code 4
sto_xyz:1 -2.000000 0.000000 0.000000 90.000000
sto_xyz:2 0.000000 2.000000 0.000000 -126.000000
sto_xyz:3 0.000000 0.000000 2.000000 -72.000000
sto_xyz:4 0.000000 0.000000 0.000000 1.000000
sform_xorient Right-to-Left
sform_yorient Posterior-to-Anterior
sform_zorient Inferior-to-Superior
file_type NIFTI-1+
file_code 1
descrip FSL3.3
aux_file
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| ch186 |
Posted - Oct 03 2011 : 3:59:11 PM
I have some ROIs that are in Talairach space that I converted to MNI space but I wanted to view the original ROIs overlayed on the Talairach brain to compare to my transformations to MNI. I was having trouble finding the Talairach brain to overlay my ROIs on. |
| dvsmith |
Posted - Oct 03 2011 : 11:36:11 AM
There are ton of atlases in $FSLDIR/data/standard. I would avoid using a "Talairach brain" since that is based on one hemisphere of an elderly woman... A good alternative would be any of the probabilistic atlases based on the histology of several individuals (http://www.fmrib.ox.ac.uk/fsl/data/atlas-descriptions.html).
Cheers,
David
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