Hi Thomas,
I am not sure which file you are referring to when you say
"Choi_atlas1mm.nii.gz". The files I have from the freesurfer wiki are:
Choi_JNeurophysiol12_MNI152_README
Choi2012_7Networks_ColorLUT.txt
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_ColorLUT.txt
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
FSL_MNI152_FreeSurferConformed_1mm.nii.gz
Which if any of these should I designate as the source in step 3a?
Also for step 2 I used "FSL_MNI152_FreeSurferConformed_1mm.nii", is this
correct?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
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Barker Street Randwick Sydney NSW 2031 Australia
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On 6/05/2016 12:50 am, Thomas Yeo wrote:
Hi Doug, the Choi file is a striatal functional connectivity atlas
which we distribute. It's under the average directory.
Hi Bronwyn,
To transform the Choi's striatal atlas to your individual subject,
Here's a (non-ideal) suggestion I previously suggested to another user:
1) Assuming you are quite happy with the freesurfer striatal
parcellation in your individual subjects, then I am assuming
freesurfer nonlinear registration (talairach.m3z) is working quite
well. Talairach.m3z warps your subject to an internal freesurfer space
(kinda like MNI305, but not quite). Let's say the freesurfer recon-all
output is at <something>/SUBJECT_FS/
2) Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the
MNI152 1mm template to the internal freesurfer space. Let's say the
freesurfer recon-all output is at <something>/MNI152_FS/
3) Then do the following:
a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
>> setenv SUBJECTS_DIR <something>
>> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
>> setenv SUBJECTS_DIR <something>
>> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s
AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z
talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest
--inv-morph
This is not optimal because of the double interpolation. You might
want to use the MNI template instead of the Choi_atlas to test the
above, so you can check the goodness of the warp. The final warped MNI
template should hopefully look identical to your subject. If that
works, then use the Choi_atlas. Note that mri_vol2vol does not work
properly for talairach.m3z below version 5, so you should use version
5x mri_vol2vol.
Regards,
Thomas
On Thu, May 5, 2016 at 10:24 PM, Douglas Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
On 5/4/16 11:40 PM, Bronwyn Overs wrote:
Hi Freesurfer Mailing List,
I wish to extract stats for my sample for the Yeo 2011 cortical
parcellations and the Choi 2012 striatal parcellations (7
networks) that are provided for download on the freesurfer wiki.
My questions are as follows:
1. I noticed that the Yeo 2011 annot files are already available
in fsaverage/label. How do I map these annot file to each of my
subjects so that I can extract stats?
Use mri_surf2surf with the --save-annot option
2. For the Choi 2012 files I wish to use
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
. How do I map this file to each of my subjects so that I can
extract stats for the 7Network parcellation?
I don't know about this file. Where is it? Is it something we
distribute?
doug
--
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 <tel:%2B61%202%209399%201883>
neura.edu.au <http://neura.edu.au>
Follow @neuraustralia on twitter
<https://twitter.com/neuraustralia>Follow NeuRA on facebook
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe
to the NeuRA Magazine
<http://www.neura.edu.au/help-research/subscribe>
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