Duke-UNC Brain Imaging and Analysis Center
BIAC Forums | Profile | Register | Active Topics | Members | Search | FAQ
Username:
 Password:
Save Password   Forgot your Password?
 All Forums
 Support Forums
 Analysis Software Support
 Talairach brain		  New Topic  Reply to Topic
 Printer Friendly
Author Previous Topic Topic Next Topic  

ch186
New Member

20 Posts
Posted - Sep 29 2011 :  3:02:51 PM  Show Profile  Reply with Quote
Is there a Talairach brain somewhere in the User Scripts on Munin?

dvsmith
Advanced Member

USA
218 Posts
Posted - Oct 03 2011 :  11:36:11 AM  Show Profile  Visit dvsmith's Homepage  Reply with Quote
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
Go to Top of Page

ch186
New Member

20 Posts
Posted - Oct 03 2011 :  3:59:11 PM  Show Profile  Reply with Quote
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.
Go to Top of Page

dvsmith
Advanced Member

USA
218 Posts
Posted - Oct 03 2011 :  5:04:49 PM  Show Profile  Visit dvsmith's Homepage  Reply with Quote
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


Go to Top of Page
  Previous Topic Topic Next Topic  
 New Topic  Reply to Topic
 Printer Friendly
Jump To:
BIAC Forums © 2000-2010 Brain Imaging and Analysis Center Go To Top Of Page
This page was generated in 0.39 seconds. Snitz Forums 2000