Hi Thomas,
Thanks, I have taken your advise and used the LooseMask for the 7
network parcellation in steps 3a and b. How do I now mask it again with
FreeSurfer's segmentation of striatal regions as you have suggested?
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
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On 9/05/2016 12:29 pm, Thomas Yeo wrote:
Hi Bronwyn,
I was using that as a placeholder. You can use any of these:
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
Depending on whether you want the 7 or 17 networks and/or whether you
want to use the loose or tight mask. My suggestion is to use the
LooseMask and then after the parcellation has been project to the
subject's native space, you can mask it again with FreeSurfer's
segmentation of striatal regions (e.g., caudate, putamen and nucleus
accumbens) in your subject's native MRI.
For Step 2, you can use FSL_MNI152_FreeSurferConformed_1mm.nii or you
can use the MNI152 1mm template distributed by FSL.
Regards,
Thomas
On Mon, May 9, 2016 at 9:37 AM, Bronwyn Overs <b.ov...@neura.edu.au
<mailto:b.ov...@neura.edu.au>> wrote:
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
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>
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<https://twitter.com/neuraustralia>Follow NeuRA on facebook
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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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