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? 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?
Hi Bronwyn
it depends on the type of stats, but you would either map the Yeo annotations to your subjects, or map the stats from your subjects to fsaverage.
cheers Bruce
On Thu, 5 May 2016, 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:
- 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? 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?
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:
- 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
- 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
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
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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:
- 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
- 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 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe 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:
- 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/
- 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/
- 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 mailto: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 option2. 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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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.gzChoi2012_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:
- 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/
- 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/
- 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:
- 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
- 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
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.overs@neura.edu.au mailto: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 <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> 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 <mailto: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 option2. 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> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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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If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail._______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Hi Bronwyn,
You can first create a striatum mask in the native subject's space:
mri_binarize --i subject/mri/aparc+aseg.mgz --match 11 --match 12
--match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz
Then use the resulting mask to mask the striatum parcellation:
fslmaths Choi_atlas_AD_subject.nii.gz -mas striatum_mask.nii.gz
Choi_atlas_AD_subject_mask.nii.gz
Regards, Thomas
On Mon, May 9, 2016 at 11:40 AM, Bronwyn Overs b.overs@neura.edu.au wrote:
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 [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 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.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.gzChoi2012_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 <%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 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:
- 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/
- 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/
- 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.edugreve@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:
- 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
- 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 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Hi Doug,
I tried to run the mri_surf2surf command as follows and got this error:
[b.overs~]$ mri_surf2surf --srcsubject fsaverage --srcsurfval lh.Yeo2011_7Networks_N1000.annot --trgsubject testsubj --trgsurfval lh.Yeo2011_7Networks_N1000.annot --hemi lh --save-annot ERROR: Option --save-annot unknown [b.overs~]$
I could not see any --save annot option in the help file. I am running this correctly? Should I be suing the .mgz file as the input or is the annotation file ok as this is what I want to resample?
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
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
On 6/05/2016 12:24 am, Douglas Greve 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:
- 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
- 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
neura.edu.au http://neura.edu.au
Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Bronwyn,
Perhaps you can try something like this:
mri_surf2surf --srcsubject fsaverage --trgsubject testsubj --hemi lh --sval- annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000. annot --tval $SUBJECTS_DIR/testsubj/label/lh.Yeo2011_7Networks_N1000.annot
Regards, Thomas
On Fri, May 6, 2016 at 11:29 AM, Bronwyn Overs b.overs@neura.edu.au wrote:
Hi Doug,
I tried to run the mri_surf2surf command as follows and got this error:
[b.overs~]$ mri_surf2surf --srcsubject fsaverage --srcsurfval lh.Yeo2011_7Networks_N1000.annot --trgsubject testsubj --trgsurfval lh.Yeo2011_7Networks_N1000.annot --hemi lh --save-annot ERROR: Option --save-annot unknown [b.overs~]$
I could not see any --save annot option in the help file. I am running this correctly? Should I be suing the .mgz file as the input or is the annotation file ok as this is what I want to resample?
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 12:24 am, Douglas Greve 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:
- 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
- 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 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bronwyn Overs -
Bruce Fischl -
Douglas Greve -
Thomas Yeo