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.overs@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

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 <greve@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



 
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