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> 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 > [image: 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 > neura.edu.au > > [image: Follow @neuraustralia on twitter] > <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook] > <https://www.facebook.com/NeuroscienceResearchAustralia>[image: Subscribe > to the NeuRA Magazine] <http://www.neura.edu.au/help-research/subscribe> > 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> > 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 >> [image: 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 <%2B61%202%209399%201883> >> neura.edu.au >> >> [image: Follow @neuraustralia on twitter] >> <https://twitter.com/neuraustralia>[image: Follow NeuRA on facebook] >> <https://www.facebook.com/NeuroscienceResearchAustralia>[image: >> Subscribe to the NeuRA Magazine] >> <http://www.neura.edu.au/help-research/subscribe> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. 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