[Freesurfer] Imaging Neuroscience

[Thomas Yeo]

External Email - Use Caution

Hi Everyone,

As you might have heard, all NeuroImage and NeuroImage:Reports editors have
resigned over Elsevier's very high publication fee, and have started a new
non-profit Open Access journal with MIT Press:
https://secure-web.cisco.com/1d8gc4yQK--K6_pnZ9cOod_o0laFRAu2-c0A6lgqNZKpRUlFjl_ZujGhc9Zc6Mqa7FJf-Aj2dWuAy18YyyO1hk0J-OesxpYpe73VrpLT5BM3hfLy3hfI-GTCToQVTFrRA5piuqOfNBS7HwSrzQL1mBFn6rmJhQhaKwFOz1xC838YnQBywAhZnfy2eneo62C7fA2kLZGZ3watecS8txYg528NRsYw-n_nxI7FpI0RwRaM8j3DTRgUsx1frpUB-2q7eckjlTGRlinJdWsSDZGHVE3mFmdX19WswI7PsD0kulJRYfWdXYQ83wwJaWm6PEMWoH-k8hENww8p2QSKKijqeCg/https%3A%2F%2Fimaging-neuroscience.org

Our resignation came with great regret, and a huge amount of thought and
discussion - please read our announcement (on the web page above) to get
more details.

We are now open for submission of new papers to Imaging Neuroscience. This
allows for the review process to proceed without delay. The production &
publication process for accepted papers will then wait until full journal
opening (aiming for mid-July).

Also, some authors with papers under review at NeuroImage have asked to
transfer over, into review at Imaging Neuroscience. We are ready for this;
please include all information about your review process to date in your
cover letter.

Thanks,
Thomas
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Re: [Freesurfer] Using Schaefer Atlas with freesurfer - looking for updates

[Thomas Yeo]

External Email - Use Caution

Hi Ricardo,

For various reasons, this was never incorporated into FreeSurfer.

But you can see the instructions here on how to generate the annot in the
individual subject native space:
https://secure-web.cisco.com/1-Lh57J3Z9FOx9JwTNS4-BU2K0FotqC5GmQozJGwZo6aDeS8eBN6MnXJJifWR_F6suqBp_1ciQl6J4H0VMgwWvrZminm4USHhxWVMRzpDQr6RsvRRXV7q04ZRaiSxRw0wzX0emq5xSw6XHY0uS7sdHAs9cH_KW0qlohsmsR0hKbSnPf526gW-9p_hDz__CbZ9wxptenRVnnweHXN3Ljzapl1uFU5LBnwXkrMNjMBJg4lVIu-l0qgyWCkG5pb0hSS0F0mmGfq-I798Oql-b8Y3hz1sudWoZe7M0VrYdsFuDB0s985ykydrUCJBRejbSslz/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FSchaefer2018_LocalGlobal%2FParcellations%2Fproject_to_individual%231-schaefer2018-parcellation-in-individual-surface-space

After you have the annot, you can run mris_anatomical_stats (
https://secure-web.cisco.com/1U2OrEatFFH5IdBqmpGFrYFMqQIN_C0VrhespawJ154Wdx3qzjR702E66wv-JkmwxdmIqdejYK-PtknL-4qibS224H5Ckfn-zwH95zulvCUdEp9sA_7-kWci0wiPRJRa88dj5QHD7fujNX8KtbTxhZWRxAmnegsvrXq1zEfkRk0B4nT5icisHrsMzBKLg_TV1NHSmdNOuWM76zKE7X0tl9kxQqmlTw5imdYTUrYNAR1WNux1XfypIxE_iS-P2NcFlPgU9Ty4LAJGiNoem8Inv0gRzEfsMBQFbqSQ7xjMDE-U7xVtklQOQR2uGbzvGMsEz/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_anatomical_stats).

Regards,
Thomas

On Thu, Sep 1, 2022 at 3:39 PM Riccardo Iandolo 
wrote:

> External Email - Use Caution
>
> Dear Freesurfer users,
>
> I'm looking for a follow-up to the following thread:
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1JnA1EMVhOJJyBHCoOygXBKQK-qi-iC1WstrhA8LK--WvM2WUMGGdHulv_ItK0fwWKnMgc-QX9oYZk6mOzK-zDbhEDxBRC8KhjL_R4O73dLL5z4c0VrGnrKtuf4CyFiCcZpfoUMyN2M6MPESG_TR7r_oVQUFmg0J4Cd299CRkemJqrJWh47cKcMblUDiS-5CUis48s893aJ2c4oyclUArP2IEtSo1f0D4Ym7raDuREEDypnux1xZ3RYNiguM0dlTVSoD-MhDIqpG3KDza59KRfO6hc2v7XUOh9_IQrflz3YS6r7wMfv37BCZ8a4hFHtPU/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2BUsing%2BSchaefer%2B2018%2Batlas%2Bwith%2BFreeSurfer%2522%26o%3Dnewest%26f%3D1
> 
>
> It seems that some developments were going one at that time in order to
> make this additional feature.
>
> If not, are there any suggestions on how I can proceed? My goal is to
> evaluate thickness in the areas of the Shaefer atlas (e.g. 200 Parcels, 17
> networks). I would like to use freesurer instead of other methods, because
> I've already run recon-all on my subjects
>
> I also found these two threads and I followed them:
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
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> 
>
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> 

Re: [Freesurfer] Parcellation issue

[Thomas Yeo]

External Email - Use Caution

Hi Rueben,

I am afraid I don't understand your question. The Yeo networks are
available in fsaverage and FSL MNI152 space.

If your data is already in fsaverage or FSL MNI152 space, you can simply
use the networks directly without running recon-all.

Can you elaborate more on what you are trying to do?

Regards,
Thomas

On Mon, Aug 15, 2022 at 7:20 AM Addison, Reuben  wrote:

> The Yeo et al, 2011 template
>
> Reuben A.
>
> Get Outlook for iOS 
> <https://secure-web.cisco.com/15lbsHnRV10gWZWym8hAq7jnJ3r-m7bvLeyJenniJmGOpMIsZEHKqBDJ2eF3NGSXqUdErU2WDGT2YW_lu4PS3Vof6Y948sJa49P63oeRql5Dma74Aum1LPqGWiqw9svLE3I-vbYDObRpvWjqMNibRyQRE_AxMxWkqa4Q0FtTE4R-x-ITxj5eg61OpzU--92q-aYXm3PZkrs9uUctKbwftQOE4PxNQ98bmm21Fm8nkOyNYJ9MO38zazIm4tNy-J2GigE0M_SzRmvBMmPQoTMz86mEnqv2TqH8UGPMG_MYSS6eyUvqOhocj7cb9agzXFqxGlXS25y0e2fUg2jCdk5LTdQ/https%3A%2F%2Faka.ms%2Fo0ukef>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Thomas Yeo <
> ytho...@csail.mit.edu>
> *Sent:* Sunday, August 14, 2022 6:59:51 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Parcellation issue
>
>
> External Email - Use Caution
>
> Hi Reuben,
>
> What template are you trying to use?
>
> Regards,
> Thomas
>
> On Tue, Aug 9, 2022 at 8:39 PM Addison, Reuben 
> wrote:
>
>
>
> I want to use a different template apart from the MNI for my parcellation
> (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in
> the readme. My question is – do I need to run this code before Recon-all or
> after
>
>
>
> In terminal (ASSUMING shell is bash),
>
>a) "cd" to unzipped folder containing this README file, fsaverage,
> fsaverage6, fsaverage5
>
>b) export SUBJECTS_DIR=`pwd`
>
>c) tksurfer fsaverage5 lh inflated -annotation
> fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot
>
>
>
>
>
>
>
> Reuben A.
> ___
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Re: [Freesurfer] Parcellation issue

[Thomas Yeo]

External Email - Use Caution

Hi Reuben,

What template are you trying to use?

Regards,
Thomas

On Tue, Aug 9, 2022 at 8:39 PM Addison, Reuben  wrote:

>
>
> I want to use a different template apart from the MNI for my parcellation
> (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in
> the readme. My question is – do I need to run this code before Recon-all or
> after
>
>
>
> In terminal (ASSUMING shell is bash),
>
>a) "cd" to unzipped folder containing this README file, fsaverage,
> fsaverage6, fsaverage5
>
>b) export SUBJECTS_DIR=`pwd`
>
>c) tksurfer fsaverage5 lh inflated -annotation
> fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot
>
>
>
>
>
>
>
> Reuben A.
> ___
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Re: [Freesurfer] postdoc

[Thomas Yeo]

External Email - Use Caution

Hi Everyone,

Apologies for sending this email twice, but interested candidates should
email me at yeoye...@gmail.com (rather than my MIT email).

Regards,
Thomas

On Thu, Aug 4, 2022 at 11:25 AM Thomas Yeo  wrote:

> Hi Everyone,
>
> I am looking for a postdoc to start this year or 2023. Candidates should
> have a PhD in neuroscience, machine learning or related fields.
>
> Research topics are quite flexible and can include can include developing
> machine learning algorithms for predicting disease progression from
> large-scale brain imaging data, individual-specific brain network
> organization, multi-modal fusion/prediction (e.g., relating brain imaging
> with wearable & smartphone data), neural mass modeling, deep phenotyping,
> brain network dynamics and naturalistic paradigms. I am particularly
> interested in applications to aging, Alzheimer’s disease dementia and
> neurodevelopment.
>
> Lab website can be found here 
> (https://secure-web.cisco.com/1b9gsm4fyGptbthNcW5MCGEzln1ZTqhkpinc48hpfFC50MfdDumIF5X_gknE4uWf52c9v5K55Xj-MgIBbUl6WSN1qFM4Lkf0jRMtqo8QYnlJ7SIYWByy4IWwHJmp7tM7_PJa6D6lgJ046spPMU7O7KDeByt7nGBWUojvMWqJLf-MZGh7clsxhT_UNbdc9l-tI03oYcvGtp_kQUFP_z5TVhcmp-M8L3O-b0LthBa2Wc21Qe5tqV2HO4MnZ9UlDJINiG-0MrHc6uf8Dl4OGwfJW7-ULB4fO92hCu-DtoFX1xIaq6apRxGPkUZLpgbl6dMdjtFHi-WtUO47kcCsuiebvuw/https%3A%2F%2Fsites.google.com%2Fview%2Fyeolab%2Fhome).
> Interested candidates can email their CV to me.
>
> Thanks,
> Thomas
>
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[Freesurfer] postdoc

[Thomas Yeo]

External Email - Use Caution

Hi Everyone,

I am looking for a postdoc to start this year or 2023. Candidates should
have a PhD in neuroscience, machine learning or related fields.

Research topics are quite flexible and can include can include developing
machine learning algorithms for predicting disease progression from
large-scale brain imaging data, individual-specific brain network
organization, multi-modal fusion/prediction (e.g., relating brain imaging
with wearable & smartphone data), neural mass modeling, deep phenotyping,
brain network dynamics and naturalistic paradigms. I am particularly
interested in applications to aging, Alzheimer’s disease dementia and
neurodevelopment.

Lab website can be found here 
(https://secure-web.cisco.com/163_oJDbnYF8kJLTi8C6K0GEnoNtFGd19DY-CEBe1pYtwKc5u_lOCaszWX1ur1DNvrMAXvVuSTBu0hNERfcbfbY4IaurnedCTIKybzAqNKHd38znjhFcer6rqxyC0O4Lf7g5ti4RHZsp6r3Gqo6gSVd_qR-F-psaG_3T8Szj_HZOjPoPHDHmA51T2ercEiqPBy_c9uoCKKlcaxGEs8-LyhRlxDyOxhuYIik8VNKmeF9uNWMFG63p0Sy99gVYQmZime2gXDvul8deJDMwUSBNurbs9Fjb31-L4_nOG2-ym-D7FMaMNRVK2jUrVfsXLIIA8onWaWh2AiGIJlCRJcKMcLg/https%3A%2F%2Fsites.google.com%2Fview%2Fyeolab%2Fhome).
Interested candidates can email their CV to me.

Thanks,
Thomas
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Re: [Freesurfer] Fwd: Yeo atlas for children!

[Thomas Yeo]

External Email - Use Caution

Hi Martin,

With regards to adolescents versus adults, there's obviously differences
between the two age groups. In our experience, when we re-estimate
parcellations from this study 
(https://secure-web.cisco.com/1TF7OmC5fKijUUx5uZkr1n5IUfkGr1RFX7MO-EmdsI3fo1_9zP0Jp-ETRw5NAjxS8BJDa6kKcSMMpJ2sdiX-ot-j-5QFedPJw2Pv_w_Lx09S2qip068nmS_qYJ7jPemY60cjnwP8Sv5YsnioL9TmWNC25owkxNqJp4Z23siRPlxWMF6odSKRD90PbJNM9pQK60dgMUgk07qeKbxs2PfIzD7evz-QcmOcS6NgyV6QttV9sTK7p2YtU6VOPRTXrkqV29tPjdaVkUQg-0QMGTS-45w/https%3A%2F%2Fdoi.org%2F10.1093%2Fcercor%2Fbhab101)
 in
kids (ABCD), the parcellations are not better based on various metrics we
computed, so I suspect it won't matter much. But the kids results are not
in our paper, so I am not sure the reviewer will buy this argument. For
this issue, you could reapply the Yeo2011 algorithm (
https://secure-web.cisco.com/1Z2srwkLUjJ_Dnco-Ccq_78ppkQhV3eTVmdR3bkvuvg64MLymHCpblVH7s3BbaYqCgmBhjfn2fLmvOxE52eTv_pNlqqJU66mrQ_kyS9r5xo7vnpF49mnl1CurnSQ-g0lBHQrOu-r1VaMu4bdeod4wOunBUn8z0Ilju3bxxxEVIBwddrah-4RY6d0MV-0qlYnFyxyw5vpq66r2twE7Xzv--mIsL85psoPahHst1Vto9_q39hxhT94w3fNtgOpITnrC9jSZStJGUBEPMuLDb7fWgQ/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FYeo2011_fcMRI_clustering)
to your sample and estimate cohort-specific networks and repeat your
analysis. We have also developed individual-specific versions of the
Yeo2011 networks (
https://secure-web.cisco.com/1ja6ZcGwaTlynHGpv68CpBe5wYiryA6Cd9PoPXavhiQcOfiz9Dqk182Jm1NOGknuS5V4LN5APd8rzUErhPpJ6N8fmbPbU1ofhucuPYirEkxbiN-f7KwiyDUiW26HQYY_APS_F3PptKP35VM14zsTm7TwwBSzRZcp1x2GUabhSkC2Uwedw4JQXh_Wned1PegQitYecAZLY0yG_RxpEISUp9zo-MvBV5DdGwVNYsVx8cRr1imnAjiZgQ241c3ZHSKJsuA3WlEi0QZmaYA9NYNL2Ng/https%3A%2F%2Fgithub.com%2FThomasYeoLab%2FCBIG%2Ftree%2Fmaster%2Fstable_projects%2Fbrain_parcellation%2FKong2019_MSHBM),
which you might find helpful, although it's probably not necessary based on
the reviewer's comments.

The other issue is whether a functional atlas might be appropriate for
structural data. I think that really depends on your question. For example,
if your question is whether default network cortical thickness might be
different between adolescents and adults, I think it's reasonable to use a
functional atlas where the default network is well defined. If you use a
structural atlas like the Desikan-Kiliany atlas, then you will still need
to use a functional atlas to roughly assign the Desikan-Kiliany parcels to
the default network, which does not seem that great either.

Regards,
Thomas

On Fri, Jun 25, 2021 at 12:52 AM Martin Juneja  wrote:

> External Email - Use Caution
>
>
> Hi all,
>
> I am reposting my concerns below. I would really appreciate any help.
>
> -- Forwarded message -
> From: Martin Juneja 
> Date: Fri, Jun 18, 2021 at 6:16 PM
> Subject: Yeo atlas for children!
> To: Freesurfer support list 
>
>
> Dear experts,
>
> I used Yeo's 17-network parcellation to study the association between
> network-wise cortical volume and a clinical variable in adolescents. I
> received the following two questions from the reviewers regarding the use
> of Yeo's atlas. I would really appreciate if someone could help us in
> addressing these questions:
>
>
>
> *1) Could the author justify their choice to use a functional parcellation
> on structural data? How is using this parcellation helpful in understanding
> the brain? All in all, the authors need to justify the superiority of using
> Yeo's 17-area parcellations on structural data over other methods of
> parcellation/analysis. *
> *2) One issue with Yeo's parcellation also stems from the fact that this
> parcellation was derived from adult connectomes. Could the authors also
> address this issue and provide examples that justify their approach.*
>
> Thanks.
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Re: [Freesurfer] striatal parcellation

[Thomas Yeo]

External Email - Use Caution

Hi Ana,

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
/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 /MNI152_FS/

3) Then do the following:

a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> 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 
>> 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 Tue, Feb 16, 2021 at 12:02 AM Marques Ana-raquel <
ar_marq...@chu-clermontferrand.fr> wrote:

> External Email - Use Caution
>
> 
>  Dear Freesurfer Team,
>
>
> we would like to perform a volumetric analysis in Parkinson's disease
> using freesurfer, and we have previously used recon all to perform tha
> surface based analysis and automate segmentation.
>
> We would also like to extract the different volumes of striatal
> parcellation using the
> Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.
>
>
> However, we can't find how to perform this parcellation, and how to add it
> to  the recon all steps?
>
>
>
> Thank you very much for your help!
>
> 
>
>
> Ana Marques
> MD, PhD
> Service de Neurologie
> Hopital Gabriel-Montpied
> CHRU Clermont-Ferrand
> ar_marq...@chu-clermontferrand.fr
> TEL: 04 73 751 600
> FAX: 04 73 751 596
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Re: [Freesurfer] cerebellar parcellation using the Buckner2011_17Networks atlas

[Thomas Yeo]

External Email - Use Caution

Hi Anna,

Just to clarify, you are saying the approach discussed in the email thread (
https://secure-web.cisco.com/11YmIxUdyE6MP2qZsI_1Q5e2j-7ZwBZsBSwwjucLd02V-n0kkFOu05sw1h_m1IQYUlCinucxr87MoZ03O3vT3Iu9krKnzliYaHWYB_mVe0eEi6sEYINc0S2Ya1Mb8sr46AH1I2JQ8Jv0U1Fct44csQVywA4rhse8c5O61ZCAc4oTAaBoB89HvIHy05VdX-6aRL1e-j0WQVa-x7qZsJF2QFFE3wIW4iqzZY2aM6sDYd05ff-3Epy1b4Y7lAXvDwHyKg6HJwpacBHGD4nivkR958Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg65121.html),
but it does not work well?

Which step is not working well? I also don't see an attachment.

Regards,
Thomas

On Wed, Jan 27, 2021 at 12:59 PM Hyo Kyoung An  wrote:

> External Email - Use Caution
>
> Dear expert,
> I am Anna, a medical school student at Pusan national University, Korea.
> I am writing this email because I'd like to ask you questions.
>
> I would like to measure the  cerebellar gray matter volume parcellated
> using the Buckner2011_17Networks atlas.
> 1. Is it possible to gain gray matter volume by this method? Or is there
> any other method to measure the cerebellar gray matter volume?
> 2. I've already tried to coregister the Buckner cerebellar parcellation in
> my samples with reference to *MailScanner has detected a possible fraud
> attempt from "secure-web.cisco.com" claiming to be*
>  
> https://secure-web.cisco.com/11YmIxUdyE6MP2qZsI_1Q5e2j-7ZwBZsBSwwjucLd02V-n0kkFOu05sw1h_m1IQYUlCinucxr87MoZ03O3vT3Iu9krKnzliYaHWYB_mVe0eEi6sEYINc0S2Ya1Mb8sr46AH1I2JQ8Jv0U1Fct44csQVywA4rhse8c5O61ZCAc4oTAaBoB89HvIHy05VdX-6aRL1e-j0WQVa-x7qZsJF2QFFE3wIW4iqzZY2aM6sDYd05ff-3Epy1b4Y7lAXvDwHyKg6HJwpacBHGD4nivkR958Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg65121.html
> .
> But the Bucker atlas didn't match with my subject image perfectly. :(
> Please check the attached file. I would like to ask you for advice.
> I look forward to hearing from you.
> Thank you very much.
>
> Best regards,
> Anna.
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Re: [Freesurfer] Striatum Mask for Choi et al 2012 {Disarmed}

[Thomas Yeo]

External Email - Use Caution

Hi Renxi,

Because there is typically a bit of error when you do the MNI152-native
projection, you should use the Choi parcellation with the "loose mask" (see
snapshots here:
https://secure-web.cisco.com/1T5bJ3eWFAY4iTktVauuA7egh6T999ndbgGMUBtHxahqEZXNLw8GIN83oTyKPzaNSqGnCYXwUBRiti3k4KWBDM2yjjREJmM5upv_2JKSG9MoKW6D8fSPmmhWK1jcdPYjk7phjBySaiL2Mkmqy9KQKD8zWY1v5J3A8dS3soDuIacpuCj7ZOw3WfliM6uBBcD0D1Xi0k-Px-VWTZ2WGhoB9d8FZgqsx-NvHR2-RYtlry__PgpyVkB9A5FtjllHSxTmevoEAI0_vBEtQ-q0vT-lacw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FStriatumParcellation_Choi2012)
and project it from MNI152 to the individual subject's native subject
space.

After that you can use the freesurfer anatomical segmentation of putamen +
caudate + nucleus accumbens (I hope my memory is correct!) in subject's
native space to mask the projected Choi's parcellation.

Regards,
Thomas

On Sun, Nov 15, 2020 at 4:16 PM RENXI LI  wrote:

> External Email - Use Caution
>
> Hi Freesurfer Experts:
>
> In $FREESURFER_HOME/average/Choi_JNeurophysiol12_MNI152 directory, there
> are a striatum parcellation masks based on functional connectivities to the
> cortical networks by Yeo et al 2011. I would like to register this striatum
> parcellation mask to each subject’s striatum mask. But to create the
> striatum mask in the native subject space using mri_binarize, which
> segmentation file do you recommend to use and which segmentations should I
> be including in the mask to cover all regions in Choi’s striatum mask?
>
> Best,
> Renxi
>
> ___
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Re: [Freesurfer] convert MNI152 coordinates into vertex index

[Thomas Yeo]

External Email - Use Caution

Hi Marina,

If you are already downloaded our lab's repo, then this function
MARS_findNV_kdTree.m (
https://github.com/ThomasYeoLab/CBIG/blob/master/external_packages/SD/SDv1.5.1-svn593/BasicTools/MARS_findNV_kdTree.m)
would help.

Alternatively, if you are comfortable with coding stuff yourself, you can
just read the fsaverage5 and fsaverage ?h.sphere meshes in matlab using
read_surf.m (freesurfer function). You can then find the closest vertex
yourself by computing Euclidean distances between the vertices.

Regards,
Thomas

On Thu, Apr 30, 2020 at 1:02 AM Marina Fernández <
marina.fdez.alva...@gmail.com> wrote:

> External Email - Use Caution
>
> Thank you for the information, Bruce and Thomas!
>
> Thomas, I think this utility is perfect! I tried it with fsaverage subject
> without problems.
>  Do you think I can use this function to calculate the vertex of the
> fsaverage5 (instead of the fsaverage)?
>
> Really, thank you very much, this help is very useful for us!
> Best regards,
> Marina
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Re: [Freesurfer] convert MNI152 coordinates into vertex index

[Thomas Yeo]

External Email - Use Caution

Hi Marina,

We do have a utility to convert from MNI152 to fsaverage space:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

Not sure if this is what you need.

Regards,
Thomas


On Wed, Apr 29, 2020 at 7:07 PM Marina Fernández <
marina.fdez.alva...@gmail.com> wrote:

> External Email - Use Caution
>
> Hi Bruce,
>
> Thank you very much for the information. It is very useful. I'm taking a
> look at both possibilities.
>
> Regarding the second option you gave me:
>
> you can just run through the list of vertices and find the one that is
>> closest to your MNI coord
>
>
>
> What file should I use to find the coordinates correspondence? Should I
> use [l/r].pial? Or maybe  [l/r].orig?
>
> Do you think it is a good idea to load that file in matlab and look for
> the closest coordinates there, and see what vertex index those coordinates
> correspond to?
>
> Thank you in advance.
>
> Best wishes,
> Marina
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Re: [Freesurfer] how to calculate the ROI volumes of grey matter using Desikan atlas

[Thomas Yeo]

External Email - Use Caution

Hi Kate,

The Desikan ROI volumes should be in the ?h.aparc.stats file after you run
recon-all. See Section 4.2 here (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#IndividualStatsfiles).


Regards,
Thomas

On Sun, Mar 15, 2020 at 7:22 PM Kate Marvel  wrote:

> External Email - Use Caution
>
>
> Hi Freesurfer community,
>
> I would like to know how to compute the
> ROI volumes of grey matter using Desikan atlas? Is there a threshold value
> set for this? is it 0.2?
>
> Thanks
>
> kate
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Re: [Freesurfer] Using Buckner Cerebellar Parcellation

[Thomas Yeo]

External Email - Use Caution

Hi Davide,

Here's a previous email I sent to the list about warping Choi's
striatum atlas to individual subject's striatum (which I have modified
for the cerebellum). Let us know if this works.

1) Assuming you are quite happy with the freesurfer cerebellum
parcellation in your 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
/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 /MNI152_FS/

3) Then do the following:

a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is
2mm resolution to the 1mm MNI152 template:

>> mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz
--regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest

Notice that I use norm.mgz of the MNI template rather than the
original MNI template. norm.mgz is the 256 x 256 x 256 conformed
version of the MNI template that recon-all puts through.

b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric
space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest

c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS
--targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z
--o Buckner_atlas_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 Buckner_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 Buckner_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 Sun, Feb 9, 2020 at 9:39 PM Davide Momi  wrote:

> External Email - Use Caution
>
> Dear Thomas,
>
> yes I am trying to warp the Buckner Parcellation to anatomical of all my
> subjects
> Please find below the command that I used:
>
> mri_vol2vol --mov
> ../Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \
>
>--s 114823 \
>
>  --targ 114823/mri/brainmask.mgz \
>
>  --o
> Buckner2011_atlas_freesurfer_internal_space.nii.gz \
>
>   --interp nearest
>
>
> Unfortunately the output is much bigger than the anatomical as I showed
> you in my previous email
>
>
> Would you have any suggestions?
>
>
> Thanks
>
>
>
>
>
> Il giorno sab 8 feb 2020 alle ore 21:43 Thomas Yeo 
> ha scritto:
>
>> External Email - Use Caution
>>
>> Hi Davide,
>>
>> Can you elaborate more? You are trying to warp the Buckner parcellation
>> from MNI parcellation to where?
>>
>> What's the exact command that you used?
>>
>> --Thomas
>>
>> On Sun, Feb 9, 2020 at 2:03 AM Davide Momi 
>> wrote:
>>
>>> External Email - Use Caution
>>>
>>> Dear expert,
>>>
>>> I am trying to coregister the Buckner cerebellar parcellation (
>>> http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011) in
>>> all my sample. However the results that I got using mri_vol2vol are not so
>>> good (see attached). Indeed in most cases the parcellation is bigger than
>>> the anatomical cerebellum of my subjects. Do you have any tips?
>>>
>>> Thanks
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] Using Buckner Cerebellar Parcellation

[Thomas Yeo]

External Email - Use Caution

Hi Davide,

Can you elaborate more? You are trying to warp the Buckner parcellation
from MNI parcellation to where?

What's the exact command that you used?

--Thomas

On Sun, Feb 9, 2020 at 2:03 AM Davide Momi  wrote:

> External Email - Use Caution
>
> Dear expert,
>
> I am trying to coregister the Buckner cerebellar parcellation (
> http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011) in
> all my sample. However the results that I got using mri_vol2vol are not so
> good (see attached). Indeed in most cases the parcellation is bigger than
> the anatomical cerebellum of my subjects. Do you have any tips?
>
> Thanks
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

[Thomas Yeo]

External Email - Use Caution

Hi Doug,

In which version of FreeSurfer does this bug appear? And under what
situation does this bug appear?

I swear I have used the command with similar flags, but did not experience
this bug.

Thanks,
Thomas

On Fri, Sep 13, 2019 at 10:58 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> This is a bug. I've fixed it in our development version. You can download
> an update from here
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surf2surf
>
>
> On 9/13/19 8:00 AM, Matthieu VANHOUTTE wrote:
>
>External Email - Use Caution
> Dear FS's experts,
>
> I am trying to downsample some surface data from fsaverage to fsaverage6
> with the following command:
>
>  mri_surf2surf --hemi lh --srcsubject fsaverage --sval
> ./lh.fsaverage.s8mm.mgh  --trgsubject fsaverage6 --tval
> ./lh.fsaverage6.s8mm.mgh --cortex
>
> However, the output surface data is a binary file contrary to the source
> one (please see attached).
>
> Would anyone have an idea of the problem?
>
> Best,
>
> Matthieu
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] MNI target to surface

[Thomas Yeo]

External Email - Use Caution

Hi Lauri,

You can also try this:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

Regards,
Thomas

On Tue, Jul 30, 2019 at 5:20 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Hi Lauri, try example 8b in
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> I just created it, so please let me know if something seems not right:)
> doug
>
>
> On 7/29/19 1:41 PM, Lauri Tuominen wrote:
> >  External Email - Use Caution
> >
> > Dear Freesurfers,
> > I am targeting the MNI152 coordinate -38,44,26 with TMS. I would like to
> use this target as an ROI/seed in surface based analyses.
> >
> > How would I:
> > 1. Transfer the coordinate onto fsaverage surface?
> > 2. Expand the coordinate into a 5mm radius sphere.
> >
> > Thank you so much!
> > Lauri Tuominen
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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>
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Re: [Freesurfer] mais_ca_label

[Thomas Yeo]

External Email - Use Caution

Hi Valentina,

We will send you the files. They will also be incorporated into FreeSurfer
at some point.

Thanks,
Thomas

On Fri, Jul 19, 2019 at 10:11 PM Bruce Fischl 
wrote:

> Hi Valentina
>
> you need to create it with mris_ca_train. I think Thomas usually just
> uses mri_surf2surf to map across subjects, but perhaps he can comment.
>
> cheers
> Bruce
>
> On Fri, 19 Jul 2019, Valentina
> Mancini wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear Freesurfer experts,
> >
> >
> > we are trying to use your function "mris_ca_label" in order to get
> > an annotation file in the subject's space using the Schaefer-Yeo atlas.
> >
> >
> > However, we noticed that a "special classifier array" is required among
> > the inputs.
> >
> > Could you pleas give us more information about the type of file required
> and
> > where we can find it?
> >
> >
> >
> > Thank you and best regards,
> >
> >
> >
> > Valentina Mancini
> >
> >
> >
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Re: [Freesurfer] Parcellation to FS surface annotation

[Thomas Yeo]

External Email - Use Caution

Hi Brady,

You can use:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion
You
will have to use nearest neighbor interpolation since the parcels should
have integer values.

Or you can try out the Schaefer parcellations (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal)
that
were estimated in the fsaverage surface space, so it won't suffer from
interpolation issues :)

Regards,
Thomas

On Wed, Jun 19, 2019 at 11:31 AM Williamson, Brady <
brady.william...@cchmc.org> wrote:

> External Email - Use Caution
>
> Hello,
>
> I am trying to convert parcellations in MNI space (BrainNetome and
> Craddock 200) to a surface annotation file in fsaverage space. I have seen
> several posts that seem to talk about steps that may be applicable but none
> of them are very efficient. Is there an easy/direct way to do this
> conversion? It seems like I am missing something really obvious, like a one
> line command, that would do the trick.
>
> Thank you for any assistance,
> Brady
>
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>
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Re: [Freesurfer] Yeo Atlas Download

[Thomas Yeo]

External Email - Use Caution

Hi Hans,

Which link are you downloading from? The following link (
ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip)
from https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011
works
fine for me.

--Thomas

On Tue, Jun 11, 2019 at 3:13 PM Aster, Hans-Christoph 
wrote:

> External Email - Use Caution
>
> Dear Freesurfer Team,
>
>
>
> I cannot download the „Resting State Cortical Parcellation in nonlin
> MNI152 space” with several machines. Is there something  wrong with the
> server? The error message is: Server Connection was reset.
>
>
>
> Thank you in advance, kind regards
>
> Hans
>
>
>
> ---
>
>
>
> Dr. med. univ. Hans-Christoph Aster
>
> Neurologische Klinik
>
> Universitätsklinikum Würzburg
>
> Josef-Schneider-Str. 11
>
> D-97080 Würzburg
>
> Tel. +49 931 201 23668
>
> aste...@ukw.de
>
> http://www.neurologie.ukw.de/
>
>
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Re: [Freesurfer] Convert Yeo's 17-network confidence map into MNI152 volumetric space

[Thomas Yeo]

External Email - Use Caution

Hi Yang Hu,

To map the confidence maps from fsaverage to MNI space, you can use the
following tool we developed:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

This is essentially the same approach we used to map the Yeo parcellation
from fsaverage to MNI space.

Regards,
Thomas

On Mon, Apr 1, 2019 at 7:06 PM huyang  wrote:

> External Email - Use Caution
>
> Dear FreeSurfer experts and users,
>
> I would like to convert Yeo's 17-network confidence map into MNI152
> volumetric space and I tried the following commands (but failed):
> (1)
> mri_surf2vol --so $SUBJECTS_DIR/fsaverage/surf/lh.white
> $SUBJECTS_DIR/fsaverage/label/lh.Yeo2011_17NetworksConfidence_N1000.mgz \
> --so $SUBJECTS_DIR/fsaverage/surf/rh.white
> $SUBJECTS_DIR/fsaverage/label/rh.Yeo2011_17NetworksConfidence_N1000.mgz \
> --lta $FREESURFER_HOME/average/mni152.register.dat --o
> Yeo2011_17NetworksConfidence.nii.gz
> (2)
> mri_surf2vol --surfval
> $SUBJECTS_DIR/fsaverage/label/lh.Yeo2011_17NetworksConfidence_N1000.mgz
> --hemi lh --fillribbon \
>--reg $FREESURFER_HOME/average/mni152.register.dat
> --template ${FSLDIR}/data/standard/MNI152_T1_1mm_brain.nii.gz \
>--o lh_Yeo2011_17NetworksConfidence.nii.gz
>
> Best,
>
> Yang Hu
>
>
>
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Can you send us snapshots of what you are seeing? I am not sure what you
mean by "labels of different colors that disagree with anatomical location
and boundaries of the networks".

On Thu, Mar 28, 2019 at 12:08 AM  wrote:

> My apologies, the right hemisphere does not contain the color of each
> region but only an unique color. The left hemisphere contains labels of
> different colors that disagree with anatomical location and boundaries of
> the networks.
> If I use the original ColorLUT cointained in freeview (at opening) the
> anatomy of the networks of the file that is computed by mri_aprac2seg is ok
> but the labels is wrong.
>
> Il 27 marzo 2019 alle 16.17 Thomas Yeo  ha
> scritto:
>
> External Email - Use Caution
>
>
> Hi Stefano,
>
> How are you using the colortable? Are you just passing it as a flag to
> mri_aparc2aseg?
>
> As far as I know (and I am NOT very knowledgeable, so I could be wrong),
> the volumetric file (Yeo_17Net.mgz) does not contain the color information.
> So when I said you should use the colortable, I meant you should use it
> with the viewer. I am not sure about tkmedit, but for freeview, you can
> load your volume and then also load your own colortable.
>
> Regards,
> Thomas
>
> On Wed, Mar 27, 2019 at 11:13 PM < std...@virgilio.it> wrote:
>
> The problem persists.
>
> We are sure that the command lines which I'm using are corrected?
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval subj/label/rh.Yeo2011_17Networks_N1000
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> --tval subj/label/lh.Yeo2011_17Networks_N1000
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt
>
>
> Il 27 marzo 2019 alle 15.40 Aihuiping Xue < xueaihuip...@gmail.com> ha
> scritto:
>
> Hi Stefano,
>
> I created a lookup table for your case. You can load your .mgz file and
> try this lookup table in freeview.
>
> This is a temporary solution. We will modify the annot files and provide
> another version of lookup table. But that will take some time. I hope this
> lookup table can solve your problem for now.
>
> Best Regards,
> XUE Aihuiping
>
> < std...@virgilio.it> 于2019年3月27日周三 下午10:26写道：
>
> Yes the left hemisphere is fine.
>
> The error occurs again. The labels for posterior DMN and anterior DMN
> are the same and numbered like 1016 and 2016, despite I have modified the
> txt.
>
> Thanks
>
> Stefano
>
> Il 27 marzo 2019 alle 13.09 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> External Email - Use Caution
>
>
> Hi Stefano,
>
> Sorry. Can you confirm left hemisphere is ok?
>
> I think in this version of the annot file, the right hemisphere regions
> will start off as 2058, rather than 2001. So instead of numbering from 2001
> to 2057, it should be from 2058 to 2114.
>
> Sorry about that. There are some intricacies between the annot format and
> mri_aparc2aseg that we were not aware of. We are trying to fix the issue
> now, but not so soon.
>
> Regards,
> Thomas
>
> On Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it> wrote:
>
> I have renumbered and run:
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt
> When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN
> "2016 is visualized but labeled as rh_parahippocampal.
>
> What's happened?
>
> Thanks
>
> Best regards,
>
> Stefano
>
> Il 26 marzo 2019 alle 13.05 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
>     External Email - Use Caution
>
>
> Renumber for visualization purpose.
>
> Do you mean how to re-number in the colortable? Just open the colortable
> in a text editing software and edit.
>
> Thanks,
> Thomas
>
> On Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it> wrote:
>
> Thanks.
>
> Should I renumber for visualization purpose or for fs-fast?
>
> How can I do it?
>
>
> Il 26 marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> Hi Stefa

Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Hi Stefano,

How are you using the colortable? Are you just passing it as a flag to
mri_aparc2aseg?

As far as I know (and I am NOT very knowledgeable, so I could be wrong),
the volumetric file (Yeo_17Net.mgz) does not contain the color information.
So when I said you should use the colortable, I meant you should use it
with the viewer. I am not sure about tkmedit, but for freeview, you can
load your volume and then also load your own colortable.

Regards,
Thomas

On Wed, Mar 27, 2019 at 11:13 PM  wrote:

> The problem persists.
>
> We are sure that the command lines which I'm using are corrected?
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval subj/label/rh.Yeo2011_17Networks_N1000
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> --tval subj/label/lh.Yeo2011_17Networks_N1000
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt
>
>
> Il 27 marzo 2019 alle 15.40 Aihuiping Xue  ha
> scritto:
>
> Hi Stefano,
>
> I created a lookup table for your case. You can load your .mgz file and
> try this lookup table in freeview.
>
> This is a temporary solution. We will modify the annot files and provide
> another version of lookup table. But that will take some time. I hope this
> lookup table can solve your problem for now.
>
> Best Regards,
> XUE Aihuiping
>
> < std...@virgilio.it> 于2019年3月27日周三 下午10:26写道：
>
> Yes the left hemisphere is fine.
>
> The error occurs again. The labels for posterior DMN and anterior DMN
> are the same and numbered like 1016 and 2016, despite I have modified the
> txt.
>
> Thanks
>
> Stefano
>
> Il 27 marzo 2019 alle 13.09 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> External Email - Use Caution
>
>
> Hi Stefano,
>
> Sorry. Can you confirm left hemisphere is ok?
>
> I think in this version of the annot file, the right hemisphere regions
> will start off as 2058, rather than 2001. So instead of numbering from 2001
> to 2057, it should be from 2058 to 2114.
>
> Sorry about that. There are some intricacies between the annot format and
> mri_aparc2aseg that we were not aware of. We are trying to fix the issue
> now, but not so soon.
>
> Regards,
> Thomas
>
> On Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it> wrote:
>
> I have renumbered and run:
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt
> When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN
> "2016 is visualized but labeled as rh_parahippocampal.
>
> What's happened?
>
> Thanks
>
> Best regards,
>
> Stefano
>
> Il 26 marzo 2019 alle 13.05 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> External Email - Use Caution
>
>
> Renumber for visualization purpose.
>
> Do you mean how to re-number in the colortable? Just open the colortable
> in a text editing software and edit.
>
> Thanks,
> Thomas
>
> On Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it> wrote:
>
> Thanks.
>
> Should I renumber for visualization purpose or for fs-fast?
>
> How can I do it?
>
>
> Il 26 marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> Hi Stefano,
>
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001,
> 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
>
> If so, you will just need the right colortable to view the Yeo_17Net.mgz.
> We are currently generating a new colortable that should work for you. This
> might take a while.
>
> If you are in a hurry, you can download the colortable here (
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
> but as you can see the range of values are not in the 1000-2000 range. So
> what you need to do is for the left hemisphere structures, you need to
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere
> structures, you need to renumber them from 58 to 114

Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Hi Stefano,

Did you see the colortable that Aihuiping attached? Does it work for you?

Thanks,
Thomas

On Wed, Mar 27, 2019 at 11:08 PM  wrote:

> Please see the attached file.
>
>
> Il 27 marzo 2019 alle 15.39 Thomas Yeo  ha
> scritto:
>
> External Email - Use Caution
>
>
> Hi Stefano,
>
> Can you attach your updated colortable, so we can take a look?
>
> Thanks,
> Thomas
>
> On Wed, Mar 27, 2019 at 10:27 PM < std...@virgilio.it> wrote:
>
> Yes the left hemisphere is fine.
>
> The error occurs again. The labels for posterior DMN and anterior DMN
> are the same and numbered like 1016 and 2016, despite I have modified the
> txt.
>
> Thanks
>
> Stefano
>
> Il 27 marzo 2019 alle 13.09 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> External Email - Use Caution
>
>
> Hi Stefano,
>
> Sorry. Can you confirm left hemisphere is ok?
>
> I think in this version of the annot file, the right hemisphere regions
> will start off as 2058, rather than 2001. So instead of numbering from 2001
> to 2057, it should be from 2058 to 2114.
>
> Sorry about that. There are some intricacies between the annot format and
> mri_aparc2aseg that we were not aware of. We are trying to fix the issue
> now, but not so soon.
>
> Regards,
> Thomas
>
> On Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it> wrote:
>
> I have renumbered and run:
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt
> When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN
> "2016 is visualized but labeled as rh_parahippocampal.
>
> What's happened?
>
> Thanks
>
> Best regards,
>
> Stefano
>
> Il 26 marzo 2019 alle 13.05 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> External Email - Use Caution
>
>
> Renumber for visualization purpose.
>
> Do you mean how to re-number in the colortable? Just open the colortable
> in a text editing software and edit.
>
> Thanks,
> Thomas
>
> On Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it> wrote:
>
> Thanks.
>
> Should I renumber for visualization purpose or for fs-fast?
>
> How can I do it?
>
>
> Il 26 marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> Hi Stefano,
>
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001,
> 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
>
> If so, you will just need the right colortable to view the Yeo_17Net.mgz.
> We are currently generating a new colortable that should work for you. This
> might take a while.
>
> If you are in a hurry, you can download the colortable here (
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
> but as you can see the range of values are not in the 1000-2000 range. So
> what you need to do is for the left hemisphere structures, you need to
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere
> structures, you need to renumber them from 58 to 114 to 2001 to 2057.
>
> Regards,
> Thomas
>
> On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it> wrote:
>
> Hi, my concern is the mri_aparc2aseg command line.
>
> In summary, I have done:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
>
>
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
>
> The output is correct by the color label is those of aparc.
>
> Probably the error is the match between the annotations and annot-table.
>
> Could you check the command lines, please?
>
> Thanks
>
> Stefano
>
>
>
> Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D.&q

Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Hi Stefano,

Can you attach your updated colortable, so we can take a look?

Thanks,
Thomas

On Wed, Mar 27, 2019 at 10:27 PM  wrote:

> Yes the left hemisphere is fine.
>
> The error occurs again. The labels for posterior DMN and anterior DMN
> are the same and numbered like 1016 and 2016, despite I have modified the
> txt.
>
> Thanks
>
> Stefano
>
> Il 27 marzo 2019 alle 13.09 Thomas Yeo  ha
> scritto:
>
> External Email - Use Caution
>
>
> Hi Stefano,
>
> Sorry. Can you confirm left hemisphere is ok?
>
> I think in this version of the annot file, the right hemisphere regions
> will start off as 2058, rather than 2001. So instead of numbering from 2001
> to 2057, it should be from 2058 to 2114.
>
> Sorry about that. There are some intricacies between the annot format and
> mri_aparc2aseg that we were not aware of. We are trying to fix the issue
> now, but not so soon.
>
> Regards,
> Thomas
>
> On Wed, Mar 27, 2019 at 6:14 PM < std...@virgilio.it> wrote:
>
> I have renumbered and run:
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt
> When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN
> "2016 is visualized but labeled as rh_parahippocampal.
>
> What's happened?
>
> Thanks
>
> Best regards,
>
> Stefano
>
> Il 26 marzo 2019 alle 13.05 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> External Email - Use Caution
>
>
> Renumber for visualization purpose.
>
> Do you mean how to re-number in the colortable? Just open the colortable
> in a text editing software and edit.
>
> Thanks,
> Thomas
>
> On Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it> wrote:
>
> Thanks.
>
> Should I renumber for visualization purpose or for fs-fast?
>
> How can I do it?
>
>
> Il 26 marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> Hi Stefano,
>
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001,
> 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
>
> If so, you will just need the right colortable to view the Yeo_17Net.mgz.
> We are currently generating a new colortable that should work for you. This
> might take a while.
>
> If you are in a hurry, you can download the colortable here (
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
> but as you can see the range of values are not in the 1000-2000 range. So
> what you need to do is for the left hemisphere structures, you need to
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere
> structures, you need to renumber them from 58 to 114 to 2001 to 2057.
>
> Regards,
> Thomas
>
> On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it> wrote:
>
> Hi, my concern is the mri_aparc2aseg command line.
>
> In summary, I have done:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
>
>
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
>
> The output is correct by the color label is those of aparc.
>
> Probably the error is the match between the annotations and annot-table.
>
> Could you check the command lines, please?
>
> Thanks
>
> Stefano
>
>
>
> Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." <
> dgr...@mgh.harvard.edu> ha scritto:
>
> Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know
> what is in that txt file. You can verify the segids by just bringing up the
> segmentation in freeview and clicking on a voxel. If you load the
> segmentation with that color table and everything looks ok, then the color
> table  is ok.
>
> On 3/10/1

Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Hi Stefano,

Sorry. Can you confirm left hemisphere is ok?

I think in this version of the annot file, the right hemisphere regions
will start off as 2058, rather than 2001. So instead of numbering from 2001
to 2057, it should be from 2058 to 2114.

Sorry about that. There are some intricacies between the annot format and
mri_aparc2aseg that we were not aware of. We are trying to fix the issue
now, but not so soon.

Regards,
Thomas

On Wed, Mar 27, 2019 at 6:14 PM  wrote:

> I have renumbered and run:
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt
> When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN
> "2016 is visualized but labeled as rh_parahippocampal.
>
> What's happened?
>
> Thanks
>
> Best regards,
>
> Stefano
>
> Il 26 marzo 2019 alle 13.05 Thomas Yeo  ha
> scritto:
>
> External Email - Use Caution
>
>
> Renumber for visualization purpose.
>
> Do you mean how to re-number in the colortable? Just open the colortable
> in a text editing software and edit.
>
> Thanks,
> Thomas
>
> On Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it> wrote:
>
> Thanks.
>
> Should I renumber for visualization purpose or for fs-fast?
>
> How can I do it?
>
>
> Il 26 marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu> ha
> scritto:
>
> Hi Stefano,
>
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001,
> 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
>
> If so, you will just need the right colortable to view the Yeo_17Net.mgz.
> We are currently generating a new colortable that should work for you. This
> might take a while.
>
> If you are in a hurry, you can download the colortable here (
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
> but as you can see the range of values are not in the 1000-2000 range. So
> what you need to do is for the left hemisphere structures, you need to
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere
> structures, you need to renumber them from 58 to 114 to 2001 to 2057.
>
> Regards,
> Thomas
>
> On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it> wrote:
>
> Hi, my concern is the mri_aparc2aseg command line.
>
> In summary, I have done:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
>
>
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
>
> The output is correct by the color label is those of aparc.
>
> Probably the error is the match between the annotations and annot-table.
>
> Could you check the command lines, please?
>
> Thanks
>
> Stefano
>
>
>
> Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." <
> dgr...@mgh.harvard.edu> ha scritto:
>
> Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know
> what is in that txt file. You can verify the segids by just bringing up the
> segmentation in freeview and clicking on a voxel. If you load the
> segmentation with that color table and everything looks ok, then the color
> table  is ok.
>
> On 3/10/19 4:05 PM, std...@virgilio.it wrote:
>
> External Email - Use Caution
>
> I will use freeview.
>
> Have you any suggestion on the use of fcseed-config option?
>
> Are you agree with the command line listed below?
>
> fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd
> rest -mean -cfg lh.SEED.config -overwrite
>
> My concerns are on -segids. Are the ids included in the file
> 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
>
> How can I select a specific seed (id) to be used in -segids?
>
> Thanks
>

Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Renumber for visualization purpose.

Do you mean how to re-number in the colortable? Just open the colortable in
a text editing software and edit.

Thanks,
Thomas

On Tue, Mar 26, 2019 at 6:44 PM  wrote:

> Thanks.
>
> Should I renumber for visualization purpose or for fs-fast?
>
> How can I do it?
>
>
> Il 26 marzo 2019 alle 4.01 Thomas Yeo  ha scritto:
>
> Hi Stefano,
>
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001,
> 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
>
> If so, you will just need the right colortable to view the Yeo_17Net.mgz.
> We are currently generating a new colortable that should work for you. This
> might take a while.
>
> If you are in a hurry, you can download the colortable here (
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
> but as you can see the range of values are not in the 1000-2000 range. So
> what you need to do is for the left hemisphere structures, you need to
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere
> structures, you need to renumber them from 58 to 114 to 2001 to 2057.
>
> Regards,
> Thomas
>
> On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it> wrote:
>
> Hi, my concern is the mri_aparc2aseg command line.
>
> In summary, I have done:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
>
>
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
>
> The output is correct by the color label is those of aparc.
>
> Probably the error is the match between the annotations and annot-table.
>
> Could you check the command lines, please?
>
> Thanks
>
> Stefano
>
>
>
> Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." <
> dgr...@mgh.harvard.edu> ha scritto:
>
> Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know
> what is in that txt file. You can verify the segids by just bringing up the
> segmentation in freeview and clicking on a voxel. If you load the
> segmentation with that color table and everything looks ok, then the color
> table  is ok.
>
> On 3/10/19 4:05 PM, std...@virgilio.it wrote:
>
> External Email - Use Caution
>
> I will use freeview.
>
> Have you any suggestion on the use of fcseed-config option?
>
> Are you agree with the command line listed below?
>
> fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd
> rest -mean -cfg lh.SEED.config -overwrite
>
> My concerns are on -segids. Are the ids included in the file
> 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
>
> How can I select a specific seed (id) to be used in -segids?
>
> Thanks
>
> Stefano
>
>
> Il 10 marzo 2019 alle 17.17 Bruce Fischl 
>  ha scritto:
>
> Hi Stefano
>
> is there a reason you are using tkmedit and not freeview? We deprecated
> tkmedit a long time ago now
>
> cheers
> Bruce
> On Sun, 10 Mar 2019, std...@virgilio.it wrote:
>
> External Email - Use Caution
>
> Thanks.
>
> My error is in tkmedit
>
> tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
>
> Il 9 marzo 2019 alle 11.09 Thomas Yeo 
>  ha scritto:
>
> External Email - Use Caution
>
> Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but
> Yeo_17Net.mgz is empty?
> Your tkmedit command seems to assume Yeo_17Net.mgz is in
> /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output
> be in the mri folder?
>
> On Sat, Mar 9, 2019 at 5:47 PM < std...@virgilio.it> wrote:
>
> External Email - Use Caution
>
> I have run:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh
> --sval-annot/Applications/freesurfer/1000subjects_referenc

Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Hi Stefano,

Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001,
1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?

If so, you will just need the right colortable to view the Yeo_17Net.mgz.
We are currently generating a new colortable that should work for you. This
might take a while.

If you are in a hurry, you can download the colortable here (
https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
but as you can see the range of values are not in the 1000-2000 range. So
what you need to do is for the left hemisphere structures, you need to
renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere
structures, you need to renumber them from 58 to 114 to 2001 to 2057.

Regards,
Thomas

On Sun, Mar 24, 2019 at 12:18 AM  wrote:

> Hi, my concern is the mri_aparc2aseg command line.
>
> In summary, I have done:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
>
> The output is correct by the color label is those of aparc.
>
> Probably the error is the match between the annotations and annot-table.
>
> Could you check the command lines, please?
>
> Thanks
>
> Stefano
>
>
>
> Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." <
> dgr...@mgh.harvard.edu> ha scritto:
>
> Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know
> what is in that txt file. You can verify the segids by just bringing up the
> segmentation in freeview and clicking on a voxel. If you load the
> segmentation with that color table and everything looks ok, then the color
> table  is ok.
>
> On 3/10/19 4:05 PM, std...@virgilio.it wrote:
>
> External Email - Use Caution
>
> I will use freeview.
>
> Have you any suggestion on the use of fcseed-config option?
>
> Are you agree with the command line listed below?
>
> fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd
> rest -mean -cfg lh.SEED.config -overwrite
>
> My concerns are on -segids. Are the ids included in the file
> 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
>
> How can I select a specific seed (id) to be used in -segids?
>
> Thanks
>
> Stefano
>
>
> Il 10 marzo 2019 alle 17.17 Bruce Fischl 
>  ha scritto:
>
> Hi Stefano
>
> is there a reason you are using tkmedit and not freeview? We deprecated
> tkmedit a long time ago now
>
> cheers
> Bruce
> On Sun, 10 Mar 2019, std...@virgilio.it wrote:
>
> External Email - Use Caution
>
> Thanks.
>
> My error is in tkmedit
>
> tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
>
> Il 9 marzo 2019 alle 11.09 Thomas Yeo 
>  ha scritto:
>
> External Email - Use Caution
>
> Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but
> Yeo_17Net.mgz is empty?
> Your tkmedit command seems to assume Yeo_17Net.mgz is in
> /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output
> be in the mri folder?
>
> On Sat, Mar 9, 2019 at 5:47 PM < std...@virgilio.it> wrote:
>
> External Email - Use Caution
>
> I have run:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh
> --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20
> 11_17Networks_N1000.annot --tval
> $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
>
> to check the output
>
> tksurfer subj rh inflated -annot
> $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
>
> My concern is here:
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000
>
> --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabel

Re: [Freesurfer] Using Schaefer 2018 atlas with FreeSurfer

[Thomas Yeo]

External Email - Use Caution

Hi Fatih,

Instead of mri_label2vol and mri_concat, you can simply call

mri_aparc2aseg --s yoursubject --annot
Schaefer2018_400Parcels_7Networks_order_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz. Here is our suggestion.

We are working on an addition to recon-all, but it won't be so quick :)

Thanks,
Thomas

On Fri, Mar 15, 2019 at 4:26 AM Fatih SOĞUKPINAR <
fatihsogukpina...@gmail.com> wrote:

> External Email - Use Caution
>
>   Dear FreeSurfer developers
>  *For my MRI data, I have cortical parcellations and segmentations for
> the Destrieux and Desikan-Killiany atlases. Now, **I am attempting to use
> Schaefer 2018 atlas
> (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal
> )
> for cortical parcellation together with FreeSurfer. Currently what I have
> tried is:*
>
>  *1)* mri_surf2surf --srcsubject fsaverage --trgsubject $SubjectID --hemi
> lh --sval-annot
> /ourSchaferAtlasDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order.annot
> --tval
> ourSubjectDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order_native.annot
>  *2) *the same of 1) for the right hemisphere
>  *3) *mri_label2vol --annot
> ourSubjectDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order_native.annot
> --temp  ourSubjectDirectory/mri/our T1.nii --o
> ourSubjectDirectory/mri/sch_lh.mgz --subject $SubjectID --identity --hemi lh
> * 4) * the same of 3) for the right hemisphere
> * 5)* mri_concat ourSubjectDirectory/mri/sch_lh.mgz
> ourSubjectDirectory/mri/sch_rh.mgz --sum --o
> ourSubjectDirectory/mri/sch_lh+rh.mgz
>
> However, at this point, the resulting .mgz file (sch_lh+rh.mgz) is a bit
> strange : When I open the file in matlab, I see that it's volume field is
> 218*182*182 , while the same data results in 256*256*256 for Destrieux
> Atlas. Furthermore, values of the volume field of sch_lh+rh.mgz change
> between 0-200 , while this is 0-12175 for the Destrieux Atlas. These
> effects are also apparent in the ultimate results (parcellation.nii images,
> which I generate by using .mgz files). They are not aligned properly and
> their intensity is also erroneous. I suspect that we have a mistake in the
> above pipeline.
>
> *My questions are: *
> * 1) Is there simpler way to do this task? (For example, a simple addition
> to the recon-all function, etc.)*
> * 2) If not, what else should I do to be able to get the correct
> parcellations ? *
> *PS: I am a bit new to the FreeSurfer and MRI processing, so please accept
> my apologizes if this is a simple question... *
>   Thank you in advance and best regards.
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but
Yeo_17Net.mgz is empty?

Your tkmedit command seems to assume Yeo_17Net.mgz is in
/Applications/freesurfer/subjects/subject_prova/. But shouldn't the output
be in the mri folder?


On Sat, Mar 9, 2019 at 5:47 PM  wrote:

> External Email - Use Caution
>
> I have run:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
>
> to check the output
>
> tksurfer subj rh inflated -annot
> $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
>
>
> My concern is here:
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt
>  --sval-annot
> yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
>
>
> tkmeditfv fsaverage orig.mgz -ov
> /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
>
> Yeo_17Net.mgz is empty.
>
>
>
> Stefano
>
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <
> dgr...@mgh.harvard.edu> ha scritto:
>
> You have to convert the annotation to a volume using mri_aparc2aseg
> (look at recon-all.log for an example, but note that you'll need to
> specify the output so that it does not overwrite). You'll then need to
> look in the output segmentation and see what the segmentation ids are
>
> On 3/7/19 4:13 PM, std...@virgilio.it wrote:
> >
>
> External Email - Use Caution
>
> Hi list,
>
> I'd like to use the regions included in Yeo 17 networks
> (
> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering
> ).
>
> in FS-FAST.
>
> Which is the command line to be used to create a segmentation in
> $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like
> to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
>
> Thanks
>
> Stefano
>
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Hi Stefano,

You can try the following

1) *Transform from fsaverage to subject's surface*
mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot
(repeat for rh)

2) *Transform from subject's surface into your subject's volume*
mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz.

Thanks,
Thomas

On Fri, Mar 8, 2019 at 7:29 PM  wrote:

> External Email - Use Caution
>
> Hi Doug,
>
> my apologies, I have tried to do it with some errors. Could you suggest
> the command line, please?
>
> Stefano
>
> Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <
> dgr...@mgh.harvard.edu> ha scritto:
>
> You have to convert the annotation to a volume using mri_aparc2aseg
> (look at recon-all.log for an example, but note that you'll need to
> specify the output so that it does not overwrite). You'll then need to
> look in the output segmentation and see what the segmentation ids are
>
> On 3/7/19 4:13 PM, std...@virgilio.it wrote:
> >
>
> External Email - Use Caution
>
> Hi list,
>
> I'd like to use the regions included in Yeo 17 networks
> (
> https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering
> ).
>
> in FS-FAST.
>
> Which is the command line to be used to create a segmentation in
> $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like
> to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
>
> Thanks
>
> Stefano
>
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Re: [Freesurfer] Converting MNI152 coorindates to fsaverage space

[Thomas Yeo]

External Email - Use Caution

Hi Tim,

Case #8 is transforming between MNI152 and MNI305 spaces. MNI305 is
different from fsaverage: one is a volumetric space and one is a surface
space.

If you are indeed looking for a transformation between MNI152 volumetric
space and fsaverage surface space, you can consider the following:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

Regards,
Thomas

On Sat, Feb 9, 2019 at 11:11 PM Tim Schäfer  wrote:

> External Email - Use Caution
>
> > Dear list,
> >
> > I have some points of interest (volume coordinates, e.g. '5.9, -27.7,
> 49.7') in MNI152 space. I would like to transform them to fsaverage space.
> >
> > How should I do that?
> >
>
> To answer my own question, this seems to be explained as use case #8 on
> the following website (at the bottom):
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
> To be precise, the website explains the transformation in the opposite
> direction, so one should use the inverse of the matrix given on the website.
>
> --
> Tim
>
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Re: [Freesurfer] Yeo labels

[Thomas Yeo]

External Email - Use Caution

Hi Duygu,

I don't think that's the case at this moment. We usually use the following
command:

mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot

Thanks,
Thomas

On Wed, Jan 9, 2019 at 9:25 AM Tosun, Duygu  wrote:

> External Email - Use Caution
>
> Is there a recon-all flag similar to -label_v1 or -ba-labels to
> automatically create label and stat files for Yeo network parcellations?
>
>
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Re: [Freesurfer] Map image in MNI onto fsaverage

[Thomas Yeo]

External Email - Use Caution

Hi John,

Not sure if you still need this, but you can use our approach instead:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

Regards,
Thomas

On Tue, Nov 20, 2018 at 2:15 AM john Anderson 
wrote:

> External Email - Use Caution
>
> Dear Freesurfer experts,
> I have the mean PET images for a number of subjects in MNI152 space. For
> visualization purposes, I would like to map this mean image onto brain
> surface. How can I do it. I appreciate any suggestion you may provide.
> Thanks!
> John
>
>
>
>
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Re: [Freesurfer] Cerelellar parcellation labels Request

[Thomas Yeo]

External Email - Use Caution

Hi Fan,

Yes. It seems that the link to the SUIT atlas is outdated. However, we are
not the SUIT developers. You should consult the SUIT package (
http://www.diedrichsenlab.org/imaging/suit.htm) :)

Regard,
Thomas

On Thu, Nov 8, 2018 at 1:48 PM dongnandi1  wrote:

> External Email - Use Caution
>
> Hi Freesurfer experts,
>
> The cerebellar 7 and 17 networks parcellation cannot be downloaded.
>
> The link to cerebellar parcellation in SUIT is out of date too.
>
>
>
> so, if you can kindly share the cerebellar 17-network parcellation and
> their anatomy labels, I would be particularly grateful!
>
>  Best wishes
>
>
> Fan
>
> 2018/11/08
>
>
>
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Re: [Freesurfer] Cortical Parcellations in individual space using Yeo et al 2011

[Thomas Yeo]

External Email - Use Caution

Hi Emma,

I know it's been a long time, but my RA recently explored this and we think
that mri_aparc2aseg might be a better option that mri_label2vol. Anyway,
here's the updated process for mapping the Yeo2011 networks from fsaverage5
to individual volumetric space:

1) Transform from fsaverage to subject's surface
mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot
(repeat for rh)

2) Transform from subject's surface into your subject's volume
Instead of using "mri_label2vol", we now recommend using "mri_aparc2aseg".
This will give you ROIs that fully cover subject's grey matter.

mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz. Here is our suggestion:
a) Find the indices of left/right cerebral cortex by extracting the voxels
with a value of 3 or 42 in the subject's aseg.
b) Use those indices to mask out the voxels that are not cerebral cortex in
your outputfile.mgz file (i.e. set non cerebral cortical voxels to be 0).
c) For the cortical voxels, you may subtract 1000 for those between 1000
and 2000; and subtract 2000 for those greater than 2000.

Thanks,
Thomas

On Wed, Feb 15, 2017 at 11:52 AM Thomas Yeo  wrote:

> Hi Emma,
>
> I recommend that you follow the mri_surf2surf and mri_label2vol route.
> As recommended in the other emails, you should probably load the
> resulting parcellations and make sure they look ok.
>
> As far as I know, "mris_ca_train" and "mris_ca_label" are not quite so
> applicable here because they require multiple subjects with
> resting-state parcellations in order to train the classifier. We are
> working on an individual subject 7-network and 17-network parcellation
> algorithm, but it's not ready yet.
>
> What kind of edits have you already done? If your edits involve
> correcting the gray/white matter segmentation and the cortical
> surfaces, then your edits should be reflected (since mri_surf2surf and
> mri_label2vol should utilized the updated cortical surfaces). However,
> if your edits involving editing the Desikan's parcellation itself,
> then probably not.
>
> Regards,
> Thomas
>
> On Wed, Feb 15, 2017 at 6:11 AM, Bailin, Emma
>  wrote:
> > Hello,
> >
> >
> >
> > I’m preparing to do resting state analyses and I’d like to use the Yeo
> 2011
> > network atlas for the cortical parcellations. Looking through the
> archive, I
> > know that mri_surf2surf with the –sval-annot flag can be used to convert
> the
> > fsaverage from the Yeo et al 2011 study to an individual subject space,
> but
> > I noticed a caveat to this when I called mri_surf2surf –help. The caveat
> is
> > on example 5: “this is not a substitute for running the cortical
> > parcellation! The parcellations that it maps to the new subject may not
> be
> > appropriate for that subject.”
> >
> >
> >
> > Given this information, I’ve got a few questions:
> >
> >
> >
> > 1)  How accurate is the mapping using mri_surf2surf? That is, is it
> good
> > for preliminary data, but not for the final analysis?
> >
> > 2)  How do you run the cortical parcellation using the Yeo 2011
> atlas?
> > [I know that mris_ca_train and mris_ca_label exist, but I’m unsure if
> they
> > are the right commands to run when I’m not building my own atlas]
> >
> > 3)  If I do the cortical parcellations using the Yeo 2011 atlas, will
> > the edits/labels I’ve done using the Desikan atlas remain accurate? This
> > goes back to the second question, as I’m not sure where in the general
> > processing stage I need to go.
> >
> >
> >
> > Thank you!
> >
> >
> >
> > Sincerely,
> >
> >
> >
> > Emma Bailin
> >
> >
> >
> > Emma Bailin
> >
> > Research Coordinator
> >
> > Laboratory for Visual Neuroplasticity
> >
> > Schepens Eye Research Institute
> >
> > Mass. Eye and Ear Infirmary
> >
> > Harvard Medical School
> >
> >
> >
> > Mass. Eye and Ear Confidentiality Notice: This e-mail and any files
> > transmitted with it are confidential and are intended solely for the use
> of
> > the individual(s) addressed in the message above. Thi

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

External Email - Use Caution

Hi Bronwyn,

I know it's been a long time, but my RA recently explored this and we think
that mri_aparc2aseg might be a better option that mri_label2vol. Anyway,
here's the updated process for mapping the Yeo2011 networks from fsaverage5
to individual volumetric space:

1) *Transform from fsaverage to subject's surface*
mri_surf2surf --srcsubject fsaverage5 --trgsubject yoursubject --hemi lh
--sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval
$SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot
(repeat for rh)

2) *Transform from subject's surface into your subject's volume*
Instead of using "mri_label2vol", we now recommend using "mri_aparc2aseg".
This will give you ROIs that fully cover subject's grey matter.

mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz

One thing to note: "mri_aparc2aseg" will automatically add 1000 for left
cerebral cortex voxels and add 2000 for right cerebral cortex voxels.
Therefore, for example, a left hemisphere voxel in network 5 will have a
value of 1005 in your outputfile.mgz. Here is our suggestion:
a) Find the indices of left/right cerebral cortex by extracting the voxels
with a value of 3 or 42 in the subject's aseg.
b) Use those indices to mask out the voxels that are not cerebral cortex in
your outputfile.mgz file (i.e. set non cerebral cortical voxels to be 0).
c) For the cortical voxels, you may subtract 1000 for those between 1000
and 2000; and subtract 2000 for those greater than 2000.

Thanks,
Thomas

On Thu, Jun 23, 2016 at 2:26 PM Bronwyn Overs  wrote:

> Thanks very much Thomas.
>
> 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]
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> to the NeuRA Magazine] <http://www.neura.edu.au/help-research/subscribe>
> On 23/06/2016 4:20 pm, Thomas Yeo wrote:
>
> You should be able to use the 5.3 version.
>
> Regards,
> Thomas
>
> On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs 
> wrote:
>
>> Hi Thomas,
>>
>> Thanks for your reply.
>>
>> The fsaverage directory I have for fs v 5.1 does not include the lh and
>> rh Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version
>> of fsaverage. Can I still use the 5.3 version annot files or would I need a
>> seperate set processed with version 5.1?
>>
>> 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 23/06/2016 3:17 pm, Thomas Yeo wrote:
>>
>> Hi Bronwyn,
>>
>> You raise a good point. You can consider creating a cortical mask using
>> aparc+aseg.mgz and use that to mask the networks.
>>
>> However, another approach (which might be more accurate) is to take
>> cortical networks in fsaverage space and transform to your subject's
>> surface and then transform into your subject's volume:
>>
>> # Transform from fsaverage to subject's surface
>> >> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi
>> lh --sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
>> $SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*
>>
>> # Transform from subject's surface into your subject's volume (I am not
>> super sure about this. You probably want to double check the output is
>> correct)
>> >> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
>> outfile.nii.gz --hemi lh --subject HS_001 **--regheader*
>>
>> --Thomas
>>
>> On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs 
>> wrote:
>>
>>> Hi Mailing List,
>>>
>>> I am attempting to apply the Yeo 2011 7-network fucntional parcellations
>>> to a 

Re: [Freesurfer] Morphing Buckner2011 MNI152 to subject's space {Disarmed}

[Thomas Yeo]

External Email - Use Caution

Hi Katherine,

Yes. This is still the best way if you have already run recon-all.

Regards,
Thomas

On Sat, Oct 6, 2018 at 8:21 AM Katherine Damme 
wrote:

> Hello,
>
> I have a tone of FS people who have been run through Recon-all and I am
> happy with the output but I would like to expand the existing labels to
> include the Buckner 7 tight labels. Is this still the best way to update my
> subject labels to include these labels?
>
> On Sat, Nov 26, 2016 at 8:07 PM Thomas Yeo  wrote:
>
>> Hi Noam,
>>
>> This should be a two step procedure, rather than a one-step procedure.
>> Here's a previous email I sent to the list about warping Choi's
>> striatum atlas to individual subject's striatum (which I have modified
>> for the cerebellum for you). Let us know if this works.
>>
>> 1) Assuming you are quite happy with the freesurfer cerebellum
>> parcellation in your 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
>> /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 /MNI152_FS/
>>
>> 3) Then do the following:
>>
>> a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is
>> 2mm resolution to the 1mm MNI152 template:
>>
>> >> mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz
>> --regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest
>>
>> Notice that I use norm.mgz of the MNI template rather than the
>> original MNI template. norm.mgz is the 256 x 256 x 256 conformed
>> version of the MNI template that recon-all puts through.
>>
>> b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric
>> space:
>>
>> >> setenv SUBJECTS_DIR 
>> >> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ
>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
>> Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest
>>
>> c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your
>> subject:
>>
>> >> setenv SUBJECTS_DIR 
>> >> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS
>> --targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z
>> --o Buckner_atlas_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 Buckner_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 Buckner_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, Nov 24, 2016 at 6:31 AM, Peled, Noam 
>> wrote:
>> > Dear group,
>> > I'm trying to morph the Buckner2011 cerebellum segmentation map from
>> MNI152
>> > to subject's space:
>> > mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ
>> > Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>> --m3z
>> > talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest
>> > --inv-morph
>> > It worked with the 17 networks, but didn't work with the 7 networks
>> version.
>> > Any ideas? This is really strange.
>> >
>> > Thanks,
>> > Noam
>> > (function(){(function n(e) { "use strict"; function t(e) { if
>> (e.parentNode)
>> > if (e.childNodes.length > 1) { for (var t =
>> > document.createDocumentFragment(); e.childNodes.length > 0; ) { var n =
>> > e.childNodes[0]; t.appendChild(n); } e.parentNode.replaceChild(t, e); }
>> else
>> > e.firstChild ? e.parentNode.replaceChild(e.firstChild, e) :
>> > e.parentNode.removeChild(e); } function n(e) { if (e) try { for (var n =
>> > e.querySelectorAll(".gr_"), r = n.length, o = 0; r > o; o++) t(n[o]); }
>> > catch (i) {} } function r(e) { try { Object.defineProperty(e,
>> "innerHTML", {
>> > 

Re: [Freesurfer] Yeo-2011 individual ROIs

[Thomas Yeo]

External Email - Use Caution

Hi Ehsan,

Not sure if any is exactly what you need:

1) We have divided the 7 and 17 networks into 51/114 ROIs (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering).
Note that these are group-level parcellations in fsaverage space, so you
have to use mri_surf2surf to project to individual subjects' surface.

2) We have also released code for 17-network parcellation of individual
subjects' resting-fMRI data (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Kong2019_MSHBM
).

3) Finally, we have released a 400-region parcellation, as well as other
resolutions (100 to 1000 parcels), which map to the original 7 and 17
networks (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal
).

Regards,
Thomas

On Thu, Jul 19, 2018 at 12:51 AM Ehsan Tadayon 
wrote:

> External Email - Use Caution
>
> Hi,
>
> Is there an easy way to sub-parcellate each network in Yeo-2011 (for
> instance network 7) into several clusters (ROIs) for an individual subject?
>
> thanks
> Ehsan.
>
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Re: [Freesurfer] Projecting meta-analytic map on the surface

[Thomas Yeo]

External Email - Use Caution

Hi Srishti,

We recently wrote a paper on projecting data from Colin27/MNI152 to
fsaverage surface (https://www.biorxiv.org/content/early/2018/04/27/302794).
The paper is in press at HBM.

The code is available here:
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion

Regards,
Thomas

On Thu, May 10, 2018 at 9:03 AM, srishti goel <23srishtig...@gmail.com>
wrote:

> External Email - Use Caution
>
> Hello Freesurfers,
>
> I have a network based map that has been produced from a meta analysis
> using NeuroElf on the standard colins template. I want to project this map
> on the surface of an MNI template.
> Does anyone have thoughts about how that could be achieved?
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
>
>
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>
>
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> 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
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Re: [Freesurfer] Fw: Yeo Atlas Network 3 segmentation FEF

[Thomas Yeo]

External Email - Use Caution

Hi Catherine,

We have extracted the 7 and 17 networks into 51 and 114 regions
respectively. See figures in
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering

Unfortunately, we have only provided the parcellation in fsaverage5 (
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels),
so you should add one more mri_surf2surf step to upsample the parcellation
from fsaverage5 to fsaverage. Check that it is good and then proceed with
your previous steps.

I am emailing the freesurfer list, so that my reply might hopefully be
useful for other folks.

Regards,
Thomas

On Thu, May 3, 2018 at 8:46 AM, Catherine Joe <catherine@uq.net.au>
wrote:

> Hello Dr Yeo,
>
>
> Yes, I want to be able to split network 3 into different component regions
> so that I can have a nii file for FEF. This will then allow me to get the
> signal intensity and hopefully, the volume of the FEF region for each
> participant in my Honour's project.
>
>
> Thank you.
>
>
> Kind regards,
>
> Catherine
> --
> *From:* Thomas Yeo <ytho...@csail.mit.edu>
> *Sent:* Thursday, 3 May 2018 9:36:52 AM
>
> *To:* Catherine Joe
> *Cc:* 李婧玮
> *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF
>
> Hi Catherine,
>
> Can I verify what you need is network 3 split into different component
> regions like FEF, etc?
>
> Regards,
> Thomas
>
> On Wed, May 2, 2018 at 11:08 AM Catherine Joe <catherine@uq.net.au>
> wrote:
>
> Hi Dr Yeo and Jingwei,
>
>
> Yes, I did use that link to subscribe to the mailing list about 2.5 weeks
> ago and they still haven't gotten back to me. I simply thought I didn't get
> a confirmation email and tried again, which was the message I forwarded to
> you today. Just now, I tried subscribing again.
>
>
> So the commands I've used so far is as follows:
>
> mri_surf2surf --srcsubject fsaverage --trgsubject subject11GS --hemi lh
> --sval-annot $subjectdir/Yeo_Neurophysiol11_Freesurfer/
> fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval lh.7Networks.annot
>
> (same was done for the rh before doing mri_aparc2aseg)
>
>
> mri_aparc2aseg --s subject11GS --o $subjectdir/subject11GS/test/test.mgz
> --annot 7Networks --annot-table path_to/Yeo2011_7Networks_colorlux.txt
>
>
> mri_annotation2label --subject subject11GS --outdir
> $subjectdir/subject11GS/test --hemi lh --annotation
> $subjectdir/subject11GS/label/lh.7Networks.annot
>
>
> mri_label2vol --label $subjectdir/subjet11GS/test/lh.7Networks_3.label
> --temp $subjectdir/subject11GS/mri/rawavg.mgz --subject subject11GS
> --hemi lh 00o $subjectdir/subject11GS/test/lh7Networks.nii.gz --proj frac
> 0 1 0.01 --reg $subjectdir/subject11GS/corticalroi/subject11GS_
> register.dat
>
>
> And after doing that, all I got was the volume for network 3 but not
> actually having any separation with the FEF and the other areas.
>
>
> Thank you for your help.
>
>
> Kind regards,
>
> Catherine
>
> --
> *From:* yeoye...@gmail.com <yeoye...@gmail.com> on behalf of Thomas Yeo <
> ytho...@csail.mit.edu>
> *Sent:* Wednesday, 2 May 2018 10:33:18 AM
> *To:* Catherine Joe
> *Cc:* 李婧玮
> *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF
>
> Hi Catherine,
>
> Have you tried subscribing to the mailing here (
> http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)?
>
> Can you please let me know the exact commands you have tried so far?
>
> I am cc-ing my grad student (Jingwei), who might be able to answer more
> rapidly. Please reply all to keep her in the loop.
>
> Thanks,
> Thomas
>
> On Wed, May 2, 2018 at 8:14 AM, Catherine Joe <catherine@uq.net.au>
> wrote:
>
> Hi Dr Yeo,
>
>
> Thank you for your help before with actually aligning and extracting your
> atlas. I know that you mentioned before that I should try and email into
> the FreeSurfer mailing list for any further queries.
>
> However, as you can see, I am apparently not subscribed to the list even
> though I sent in a request before. I've been trying to send in a question
> for the past week.
>
> I was wondering if you'd be able to help me with this problem I've had
> after extracting the Network 3 ROI. The message I tried sending to the
> FreeSurfer Mailing list is as below:
>
>
> Hello,
>
>
> I'm having trouble getting the segmentation for the FEF using the Yeo
> Atlas 2011 Network 3. Although I've been able to get Network 3 as a volume
> file, it doesn

Re: [Freesurfer] Region in Yeo_17Network_16 as seed in FS-FAST

[Thomas Yeo]

Hi Stefano,

The Yeo 17 networks have been extracted into 114 regions in fsaverage space
(
https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering
).

You can map them to individual subjects' space using mri_surf2surf.

Regards,
Thomas

On Sat, Mar 3, 2018 at 7:48 PM,  wrote:

> Hi list,
>
> I should use the the region describing the mPFC in Yeo_17Network_16 (DMN)
> as a seed in FS-FAST (FC analysis)
>
> How can I do to isolated this regions?
>
> Thanks
>
>
> Stefano
>
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Re: [Freesurfer] Yeo atlas FreeSurfer

[Thomas Yeo]

Hi Martin,

Those postfix are based on anatomical location. If you load the parcels on
freeview with the associated colortable, you should be able to infer what
the postfix are referring to.

Off the top of my head (but you should double check by loading on freeview):

1) FrOper = frontal operculum

2) PFCl = Prefrontal Cortex Lateral

3) FEF = frontal eye fields

4) ParOper = parietal operculum

5) TempOcc = temporal occipital

6) PHC = parahippocampal complex

7) PFCmp = I think mp stands for medial posterior, but I am not super sure,
you probably want to visualize this and double check.

Thanks,
Thomas

On Thu, Oct 19, 2017 at 1:16 AM, Martin Juneja <mj70...@gmail.com> wrote:

> Dear Dr. Yeo,
>
> Thanks a lot for your reply.
> Actually, I have already analyzed the effect of treatment on these 7
> functional networks. I just want to report what are the areas which
> constitute each of these network.
>
> Somehow in the reference you sent, I could not find name of each regions
> of interest which are part of these networks. In the zip folder you sent, I
> found following information. Is there a way I can still get full name of
> ROIs e.g. here I do not know FrOper, PFCI etc.
>
> I would really appreciate any help.
>
> Thanks !
>
> *Network 1:*
> 1 7Networks_LH_Vis 120  18 134   0
>
> *Network 2:*
>   2  7Networks_LH_SomMot  70 130 180   0
>
> *Network 3:*
>   3   7Networks_LH_DorsAttn_Post   0 118  14   0
>   47Networks_LH_DorsAttn_FEF   0 118  15   0
>   5   7Networks_LH_DorsAttn_PrCv   0 119  14   0
>
> *Network 4:*
>   6 7Networks_LH_SalVentAttn_ParOper 196  58 250   0
>   7 7Networks_LH_SalVentAttn_TempOcc 196  58 251   0
>   8  7Networks_LH_SalVentAttn_FrOper 196  59 250   0
>   97Networks_LH_SalVentAttn_PFCl 196  59 251   0
>  10 7Networks_LH_SalVentAttn_Med 197  58 250   0
>
> *Network 5:*
>  11  7Networks_LH_Limbic_OFC 220 248 164   0
>  12 7Networks_LH_Limbic_TempPole 220 248 165   0
>
> *Network 6:*
>  137Networks_LH_Cont_Par 230 148  34   0
>  14   7Networks_LH_Cont_Temp 230 148  35   0
>  15   7Networks_LH_Cont_PFCd 230 149  34   0
>  16   7Networks_LH_Cont_PFCl 230 149  35   0
>  177Networks_LH_Cont_OFC 231 148  34   0
>  18   7Networks_LH_Cont_PFCv 231 148  35   0
>  19   7Networks_LH_Cont_pCun 231 149  34   0
>  20   7Networks_LH_Cont_Cing 231 149  35   0
>  21  7Networks_LH_Cont_PFCmp 230 148  33   0
>
> *Network 7:*
>  22 7Networks_LH_Default_Par 205  62  78   0
>  237Networks_LH_Default_Temp 205  62  79   0
>  24 7Networks_LH_Default_PFC 205  63  78   0
>  25     7Networks_LH_Default_PCC 205  63  79   0
>  26 7Networks_LH_Default_PHC 206  62  78   0
>
>
> On Wed, Oct 18, 2017 at 6:44 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
>
>> Hi Martin,
>>
>> We have previously split the networks into 114 regions:
>> https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_JNeur
>> ophysiol11_SplitLabels.zip?dl=0 . See Figure 1 in the first reference
>> below. If you decide to use these regions, please kindly cite the
>> following papers:
>>
>> 1) Yeo BTT, Tandi J, Chee MWL. Functional connectivity during rested
>> wakefulness predicts vulnerability to sleep deprivation. Neuroimage
>> 111:147-158, 2015
>>
>> 2) Krienen FM, Yeo BTT, Buckner RL. Reconfigurable state-dependent
>> functional coupling modes cluster around a core functional architecture.
>> Philosophical Transactions of the Royal Society B, 369:20130526, 2014
>>
>> Thanks,
>> Thomas
>>
>> On Wed, Oct 18, 2017 at 3:48 AM, Martin Juneja <mj70...@gmail.com> wrote:
>>
>>> Hi experts,
>>>
>>> I am using Yeo atlas (7 networks) in my analysis. Where can I find name
>>> of all the regions involved in each of these 7 networks in Yeo atlas?
>>>
>>> Thanks.
>>>
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>>> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Yeo atlas FreeSurfer

[Thomas Yeo]

Hi Martin,

We have previously split the networks into 114 regions:
https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_JNeurophysiol11_SplitLabels.
zip?dl=0 . See Figure 1 in the first reference below. If you decide to use
these regions, please kindly cite the following papers:

1) Yeo BTT, Tandi J, Chee MWL. Functional connectivity during rested
wakefulness predicts vulnerability to sleep deprivation. Neuroimage
111:147-158, 2015

2) Krienen FM, Yeo BTT, Buckner RL. Reconfigurable state-dependent
functional coupling modes cluster around a core functional architecture.
Philosophical Transactions of the Royal Society B, 369:20130526, 2014

Thanks,
Thomas

On Wed, Oct 18, 2017 at 3:48 AM, Martin Juneja  wrote:

> Hi experts,
>
> I am using Yeo atlas (7 networks) in my analysis. Where can I find name of
> all the regions involved in each of these 7 networks in Yeo atlas?
>
> Thanks.
>
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[Freesurfer] New Openings for Postdoctoral Fellows

[Thomas Yeo]

Dear Everyone,

My lab has new openings for postdoctoral fellows. Please see job
descriptions here: https://yeolab.weebly.com/jobs.html

Thanks,
Thomas
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Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

[Thomas Yeo]

Hi Adam,

Language activations definitely hit Default B, but Default B is also
activated by tasks such as theory of mind (see Figure 4 here:
https://www.biorxiv.org/content/biorxiv/early/2017/06/19/149567.full.pdf),
so I am not sure we can consider it to be a pure language network.

Although there has been papers trying to delineate language networks using
resting-state fMRI, my experience is that it's not something that easily
pops out of resting-state data, compared with task or meta-analytic data
(e.g., see component 5 here:
http://people.csail.mit.edu/ythomas/publications/2015BrainmapInteractive/index.html
)

Regards,
Thomas

On Thu, Oct 5, 2017 at 3:30 PM, Adam Martersteck <acmar...@gmail.com> wrote:

> Hi Dr. Yeo,
>
> Just a related question -- do you have an opinion on if one of the network
> solutions corresponds to the language network? I realize they are all
> bilateral, with no significantly left lateralized one. But do you think one
> of the DMN solutions (such as Default B in the paper you linked, much more
> representative on the LH surface view) might represent the language network?
>
> -Adam
>
> On Thu, Oct 5, 2017 at 2:07 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
>
>> Hi Chintan,
>>
>> Sorry. At that time, we wanted to not bias the interpretation of the
>> networks by naming them. But that may be a bit idealistic. We have
>> subsequently named the networks.
>>
>> To map networks 1 to 17 to the names, the easiest way is to load the
>> annot in freeview and hover your mouse over it and then visually match it
>> to Figure 1 of this paper (http://people.csail.mit.edu/y
>> thomas/publications/2015SleepDeprivation-NeuroImage.pdf). When I do so,
>> I get the following, but you probably want to double check!
>>
>> 1) Network 1: Visual A
>>
>> 2) Network 2: Visual B
>>
>> 3) Network 3: SomMot A
>>
>> 4) Network 4: SomMot B
>>
>> 5) Network 5: DorsAttn A
>>
>> 6) Network 6: DorsAttn B
>>
>> 7) Network 7: Sal/VentAttn A
>>
>> 8) Network 8: Sal/VentAttn B
>>
>> 9) Network 9: Limbic B
>>
>> 10) Network 10: Limbic A
>>
>> 11) Network 11: Control C
>>
>> 12) Network 12: Control A
>>
>> 13) Network 13: Control B
>>
>> 14) Network 14: TempPar
>>
>> 15) Network 15: Default C
>>
>> 16) Network 16: Default A
>>
>> 17) Network 17: Default B
>>
>> Regards,
>> Thomas
>>
>>
>> On Thu, Oct 5, 2017 at 2:54 AM, Mehta, Chintan <chintan.me...@yale.edu>
>> wrote:
>>
>>> Dear Freesurfer users,
>>>
>>> I am examining the Yeo 2011 17 Network atlases in Freesurfer 6.0. The
>>> regions are labeled 1 through 17. Is there a reference table mapping these
>>> numbers with the names of cognitive networks described by Yeo, et al.
>>> (2011) ( <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3174820/>
>>> https://www.ncbi.nlm.nih.gov/pubmed/21653723)? For example, would
>>> network 1 correspond to visual networks? I cannot find descriptions in the
>>> readme files except the color look-up table.
>>>
>>>
>>> Thank you.
>>>
>>> Best,
>>>
>>> Chintan
>>>
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>>
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Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

[Thomas Yeo]

Hi Chintan,

Sorry. At that time, we wanted to not bias the interpretation of the
networks by naming them. But that may be a bit idealistic. We have
subsequently named the networks.

To map networks 1 to 17 to the names, the easiest way is to load the annot
in freeview and hover your mouse over it and then visually match it to
Figure 1 of this paper (http://people.csail.mit.edu/ythomas/publications/
2015SleepDeprivation-NeuroImage.pdf). When I do so, I get the following,
but you probably want to double check!

1) Network 1: Visual A

2) Network 2: Visual B

3) Network 3: SomMot A

4) Network 4: SomMot B

5) Network 5: DorsAttn A

6) Network 6: DorsAttn B

7) Network 7: Sal/VentAttn A

8) Network 8: Sal/VentAttn B

9) Network 9: Limbic B

10) Network 10: Limbic A

11) Network 11: Control C

12) Network 12: Control A

13) Network 13: Control B

14) Network 14: TempPar

15) Network 15: Default C

16) Network 16: Default A

17) Network 17: Default B

Regards,
Thomas


On Thu, Oct 5, 2017 at 2:54 AM, Mehta, Chintan 
wrote:

> Dear Freesurfer users,
>
> I am examining the Yeo 2011 17 Network atlases in Freesurfer 6.0. The
> regions are labeled 1 through 17. Is there a reference table mapping these
> numbers with the names of cognitive networks described by Yeo, et al.
> (2011) ( 
> https://www.ncbi.nlm.nih.gov/pubmed/21653723)? For example, would network
> 1 correspond to visual networks? I cannot find descriptions in the readme
> files except the color look-up table.
>
>
> Thank you.
>
> Best,
>
> Chintan
>
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[Freesurfer] Open Letter to NIH Director Francis Collins

[Thomas Yeo]

Dear Everyone,

Please note the following NIH petition regarding the impending
classification of basic science research as clinical trials:
https://ipetitions.com/petition/open-letter-nih-collins

Regards,
Thomas
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Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Corinna,

You can download here:
https://www.dropbox.com/s/yj1gbpmpgho7wtm/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0

Regards,
Thomas


On Thu, Jun 29, 2017 at 5:45 AM, Corinna Bauer <corinna...@gmail.com> wrote:

> Dear Dr. Yeo,
>
> Our research group is currently trying to segment the Yeo atlas into
> separate labels, but just came across this thread which indicates that you
> have already done this. Would you be willing to re-share the link to your
> previously extracted individual labels from your 7 and 17 networks?
>
> Thank you!
>
> Corinna
>
> On Thu, May 14, 2015 at 4:54 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
>
>> Hi Annie,
>>
>> I have previously extracted individual regions from the 7 and 17
>> networks. You can download them here
>> (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol
>> 11_SplitLabels.zip?dl=0).
>> Please see the README in the folder for more explanations. There
>> should be a precuneus DMN region.
>>
>> The 17 networks consist of 114 regions that have been previously
>> published:
>>
>> 1) Krienen et al., Reconfigurable state-dependent functional coupling
>> modes cluster around a core functional architecture. Philosophical
>> Transactions of the Royal Society B, 369:20130526, 2014
>>
>> 2) Yeo et al., Functional connectivity during rested wakefulness
>> predicts vulnerability to sleep deprivation. Neuroimage 111:147-158,
>> 2015
>>
>> Hope this helps.
>>
>> Cheers,
>> Thomas
>>
>> On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 <poohann1...@gmail.com> wrote:
>> > Hello Dr. Yeo,
>> >
>> > Thank you for your previous help and reply. We've worked out the way to
>> > switch the resolution of parcellation and successfully extracted the
>> > anatomical information using your mask derived from iFC work.
>> >
>> > However, we came across a new problem to apply the cortical mask and
>> need
>> > your kind help again. We aim to conduct a seed-based analysis to
>> investigate
>> > structural covariance based on the network defined by iFC, and find your
>> > work of cortical parcellation conceptually perfectly suit our research
>> > question. Based on the current approach, however, it seemed that we
>> could
>> > only extract the anatomical information from the whole well-defined
>> network,
>> > but not the specific hub within the network (e.g., the anatomical
>> > information of the precuneus from the DMN). We wonder if you have any
>> > suggestion to resolve our problem, ie, to be specific, is there any way
>> to
>> > only extract the discrete hub information rather than the whole network?
>> >
>> > We really appreciate your generous help. Thank you very much.
>> >
>> > p.s. This email would also forward to my senior colleague, Dr.
>> Hsiang-Yuan
>> > Lin, who is a child and adolescent psychiatrist doing imaging research
>> in
>> > Taiwan.
>> >
>> >
>> > 2015-05-13 19:15 GMT+08:00 陳昱潔 <poohann1...@gmail.com>:
>> >>
>> >> Hi Professor Yeo :
>> >>
>> >> Thank you for helping us so much!
>> >> After mris_anatomical_stat I tried aparcstats2table to extract the
>> table.
>> >> But I failed with generating the table.
>> >>
>> >>
>> >> Best wishes,
>> >> Annie
>> >>
>> >> 2015-05-12 8:29 GMT-04:00 Thomas Yeo <ytho...@csail.mit.edu>:
>> >>
>> >>> Hi Annie,
>> >>>
>> >>> I assume this means 5202 is your subject ID? Maybe you should check if
>> >>> /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Network
>> s_N1000.annot
>> >>> exist?
>> >>>
>> >>> If so, you can run mris_anatomical_stats to generate statistics for
>> >>> the parcellation.
>> >>>
>> >>> Cheers,
>> >>> Thomas
>> >>>
>> >>> On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 <poohann1...@gmail.com> wrote:
>> >>> > Hi Professor Yeo :
>> >>> > After I rechecked the directory and run again mri_surf2surf
>> >>> > I got the result:
>> >>> > "Saving target data
>> >>> > Converting to target annot
>> >>> > Saving to target annot
>> >>> >
>> >>> > /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Network
>> s_N1000.annot"
>> >&g

Re: [Freesurfer] Cortical Parcellations in individual space using Yeo et al 2011

[Thomas Yeo]

Hi Emma,

I recommend that you follow the mri_surf2surf and mri_label2vol route.
As recommended in the other emails, you should probably load the
resulting parcellations and make sure they look ok.

As far as I know, "mris_ca_train" and "mris_ca_label" are not quite so
applicable here because they require multiple subjects with
resting-state parcellations in order to train the classifier. We are
working on an individual subject 7-network and 17-network parcellation
algorithm, but it's not ready yet.

What kind of edits have you already done? If your edits involve
correcting the gray/white matter segmentation and the cortical
surfaces, then your edits should be reflected (since mri_surf2surf and
mri_label2vol should utilized the updated cortical surfaces). However,
if your edits involving editing the Desikan's parcellation itself,
then probably not.

Regards,
Thomas

On Wed, Feb 15, 2017 at 6:11 AM, Bailin, Emma
 wrote:
> Hello,
>
>
>
> I’m preparing to do resting state analyses and I’d like to use the Yeo 2011
> network atlas for the cortical parcellations. Looking through the archive, I
> know that mri_surf2surf with the –sval-annot flag can be used to convert the
> fsaverage from the Yeo et al 2011 study to an individual subject space, but
> I noticed a caveat to this when I called mri_surf2surf –help. The caveat is
> on example 5: “this is not a substitute for running the cortical
> parcellation! The parcellations that it maps to the new subject may not be
> appropriate for that subject.”
>
>
>
> Given this information, I’ve got a few questions:
>
>
>
> 1)  How accurate is the mapping using mri_surf2surf? That is, is it good
> for preliminary data, but not for the final analysis?
>
> 2)  How do you run the cortical parcellation using the Yeo 2011 atlas?
> [I know that mris_ca_train and mris_ca_label exist, but I’m unsure if they
> are the right commands to run when I’m not building my own atlas]
>
> 3)  If I do the cortical parcellations using the Yeo 2011 atlas, will
> the edits/labels I’ve done using the Desikan atlas remain accurate? This
> goes back to the second question, as I’m not sure where in the general
> processing stage I need to go.
>
>
>
> Thank you!
>
>
>
> Sincerely,
>
>
>
> Emma Bailin
>
>
>
> Emma Bailin
>
> Research Coordinator
>
> Laboratory for Visual Neuroplasticity
>
> Schepens Eye Research Institute
>
> Mass. Eye and Ear Infirmary
>
> Harvard Medical School
>
>
>
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Re: [Freesurfer] Fwd: LGI using Yeo Atlas

[Thomas Yeo]

Hi Martin,

Sorry for the slow reply. Antonin is right about the mri_segstats.

To map the surface parcellation from fsaverage to your individual
subject's anatomical space, you can do the following:

# Transform from fsaverage to subject's surface
>> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh 
>> --sval-annot lh.Yeo2011_17Networks_N1000.annot  --tval 
>> $SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot

# Transform from subject's surface into your subject's volume (I am
not super sure about this. You probably want to double check the
output is correct)
>> mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot --o 
>> outfile.nii.gz --hemi lh --subject HS_001 --regheader

Regards,
Thomas

On Sat, Feb 11, 2017 at 5:01 AM, Antonin Skoch  wrote:
> Dear Martin,
>
> I think that this thread is relevant for you:
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34508.html
>
> You would have to map Yeo atlas to individual brain and then extract the LGI
> values using command:
>
> mri_segstats --annot my_subject_id lh aparc --i
> $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
>
> where aparc replace by name of your generated Yeo atlas annot file.
>
> Regards,
>
> Antonin Skoch
>
>
> Hi everyone,
>
> I was wondering if someone could please address the following question
> regarding FreeSurfer usage.
>
> I would really appreciate any help.
>
> Thanks.
>
> Hi,
>
> I used following command to extract LGI values from a set of subjects:
>
> recon-all -s  -localGI
>
> Output stats is saved in lh.aparc_lgi.stats file. By default, its
> calculating LGI values of 35 areas using *Desikan-Killiany Atlas *but I am
> interested in calculating LGI values using Yeo atlas of 7 networks. I was
> wondering how can I change the default atlas to Yeo atlas to get LGI value
> for each subject.
>
> Thanks a lot.
>
>
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[Freesurfer] Postdoctoral fellow in mental disorder subtypes

[Thomas Yeo]

Dear All,

I am looking for a neuroscience/psychology postdoc to apply machine
learning algorithms (possibly developed in our lab) to discover and
understand mental disorder subtypes from existing large-scale public
databases.

See recent example from our lab
(http://www.pnas.org/content/113/42/E6535). Experience with
psychiatric disorders (especially ASD and ADHD) is a plus, but not
required.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in neuroscience, psychology or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists. Programming experience is
required. He or she does NOT need to code a new algorithm, but must be
able to apply existing code (or modify existing code) for his or her
project.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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[Freesurfer] Postdoctoral Fellow in Machine Learning in Neuroimaging

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop machine learning algorithms
for large-scale publicly available MRI and behavioral data. Experience
with probabilistic machine learning (aka graphical models) or deep
learning is a plus.

The ultimate goal is automatic scientific discovery (see recent paper
from our lab: http://www.pnas.org/content/113/42/E6535). Topics are
flexible, e.g., multi-modal fusion, individual-subject brain
parcellation, individual subject behavior prediction, dynamic
functional connectivity, meta-analysis, neural mass modeling,
multi-scale neuroscience, graph theory, mental disorder subtypes, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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Re: [Freesurfer] Morphing Buckner2011 MNI152 to subject's space {Disarmed}

[Thomas Yeo]

Hi Noam,

This should be a two step procedure, rather than a one-step procedure.
Here's a previous email I sent to the list about warping Choi's
striatum atlas to individual subject's striatum (which I have modified
for the cerebellum for you). Let us know if this works.

1) Assuming you are quite happy with the freesurfer cerebellum
parcellation in your 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
/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 /MNI152_FS/

3) Then do the following:

a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is
2mm resolution to the 1mm MNI152 template:

>> mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz 
>> --regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest

Notice that I use norm.mgz of the MNI template rather than the
original MNI template. norm.mgz is the 256 x 256 x 256 conformed
version of the MNI template that recon-all puts through.

b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ 
>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o 
>> Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest

c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS 
>> --targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z --o 
>> Buckner_atlas_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 Buckner_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 Buckner_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, Nov 24, 2016 at 6:31 AM, Peled, Noam  wrote:
> Dear group,
> I'm trying to morph the Buckner2011 cerebellum segmentation map from MNI152
> to subject's space:
> mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ
> Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --m3z
> talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest
> --inv-morph
> It worked with the 17 networks, but didn't work with the 7 networks version.
> Any ideas? This is really strange.
>
> Thanks,
> Noam
> (function(){(function n(e) { "use strict"; function t(e) { if (e.parentNode)
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Re: [Freesurfer] questions about split region from the 7 and 17 networks, from huasheng liu

[Thomas Yeo]

Hi Huasheng,

Here you go: 
https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip

I am also cc-ing the freesurfer list.

--Thomas

On Tue, Aug 30, 2016 at 11:05 AM, liuhas_20040125
 wrote:
> Dear professor Yeo :
>
>
>
>   My name is Huasheng Liu, I'm from central south university, china.
>
>   I read the emails you wrote to Yu-chieh Chen in freesurfer's mail-archive,
>
> (from:
> https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html)
>
> and you provided a link to files you extracted individual regions from the 7
> and 17 networks:
>
>
>
> " I have previously extracted individual regions from the 7 and 17
> networks. You can download them here
> (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0)."
>
>
>
>
>
>   It seems the link has broken, and i can't get zip file, can you kindly
> give me a copy?
>
>
>
>
>
>   Thank you very much for read this email and sorry for occupied your time.
>
>
>
>  Best wishes!
>  Huasheng Liu
>
>
>
> 2016-08-30
> 
> liuhas_20040125
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Re: [Freesurfer] Labels to MNI152, SPM compatible

[Thomas Yeo]

One possibility is the header information. I looked at the header
information and they are not exactly the same between the template and
atlas. Perhaps you can try the following:

>> mri_convert --targ Template_T1_IXI555_MNI152.nii --mov 
>> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz 
>> --regheader --interp nearest --o Yeo2011_headerfixed.nii.gz

Please note that this would involve a nearest interpolation. Hope this
would work.

--Thomas

On Thu, Aug 4, 2016 at 7:06 PM, Matyáš Kuhn <matyas.k...@gmail.com> wrote:
> Hi,
>
> I was using Mango and MriCron to view the results. But you are right that in
> freeview it looks just fine :) I saved the yeo atlas image as nifti and it
> is now looking well also on mango and MRIcroN. So I suppose that the problem
> was with analyze format.
>
> Thank you all for the help :)
>
> Matyas
>
>
> Dne 3.8.2016 v 4:43 Thomas Yeo napsal(a):
>
> Hi Matyas,
>
> In freeview, looks fine to me. See attached.
>
> Can you send us your screenshot?
>
> Regards,
> Thomas
>
> On Tue, Aug 2, 2016 at 9:39 PM, Matyáš Kuhn <matyas.k...@gmail.com> wrote:
>
> The Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
> comes from
> http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
> and the description says it is the FSL MNI152 1mm template interpolated
> and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume
> (obtained by putting the FSL MNI152 1mm template through recon-all ). So
> I supposed it is in MNI305 after it was processed with freesurfer. When
> I overlap the
> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz and
> Template_T1_IXI555_MNI152.nii it is really shifted so I think it is not
> in MNI152.
>
> When I add the --invertmtx then the result is still the same, empty image.
>
> I uploaded those images here:
> https://dl.dropboxusercontent.com/u/70539709/Freesurfer_question.zip ,
> if you want to try yourself.
>
>
> Thank you,
>
> Matyas
>
>
>
> Dne 2.8.2016 v 14:55 Douglas Greve napsal(a):
>
>   From the names, it looks like both the seg vol and the template vol are
> both in mni152. Where did
> Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz come
> from? One thing you can try is to invert the registration by adding
> --invertmtx to the command line.
>
>
> On 8/2/16 8:18 AM, Matyáš Kuhn wrote:
>
> Hi Freesurfer experts,
>
> I just started to use Freesurfer and I was wondering how can I convert
> images from MNI305 which uses Freesurfer to MNI152 which is used by SPM.
> We would like to get MNI152 template of Yeo parcelation
> ()
> so we can overlay with our results from SPM fMRI analysis.
>
> I tried this:
> mri_label2vol --seg
> /path_to_analysis/Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz
> \
> --temp
> /path_to_analysis/Template_T1_IXI555_MNI152.nii \
> --reg
> $FREESURFER_HOME/average/mni152.register.dat \
> --o /path_to_analysis/output_mni152.nii
>
> which resulted in image full of zeros (so maybe problem with
> registration?). The "Template_T1_IXI555_MNI152.nii" is the MNI152
> template which is used by Computational anatomical toolbox 12 for SPM
> from Christian Gaser and his group.
>
> Thanks in advance for any suggestions,
>
> Matyas
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> The information in this 

[Freesurfer] fMRI Postdoctoral Fellow

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc with either strong machine learning
background OR system neuroscience background. Prior experience with
fMRI is a plus.

Topics are flexible. Example topics include individual-subject brain
parcellations, relationships between behavior and brain networks,
dynamic functional connectivity, meta-analysis, neural mass modeling,
graph theoretic modeling of brain networks, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in neuroscience, computer science, electrical
engineering, statistics or related fields. The successful applicant
will work with an interdisciplinary team of computer scientists and
neuroscientists.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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Re: [Freesurfer] Failure to use yeo-7/17 networks maps as templates in MRIcron

[Thomas Yeo]

Hi Hsiang-Yuan,

I do not know how color file works for MRIcron, so I am unable to help.

Regards,
Thomas

On Tue, Jul 5, 2016 at 2:41 AM, Hsiang-Yuan Lin <louisli...@gmail.com> wrote:
> Hi Thomas,
>
> Thanks for swift instruction. It works well. However, I have further
> question: could I write the color lut into header? Because I used your
> suggested Colorlut information to create a new .lut file and put them into
> MRIcron templates folder with the correctely oriented Yeo2011_7network
> template. But it failed to present the designated color in MRIcron.
>
> Thank you!
>
> Best,
> Hsiang-Yuan
>
> On Mon, Jul 4, 2016 at 4:37 PM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
>>
>> Hi Hsiang-Yuan,
>>
>> That's because the header information is different. You can do the
>> following:
>>
>> >> mri_vol2vol --mov Yeo2011Parcellation.nii.gz --targ
>> >> FSL_MNI2mm_template.nii.gz --regheader --nearest --o Yeo2011_FSL2mm.nii.gz
>>
>> The output file "Yeo2011_FSL2mm.nii.gz" should have an orientation
>> compatible with mricron. Can you let me know if this works.
>>
>> Thanks,
>> Thomas
>>
>> On Mon, Jul 4, 2016 at 12:58 AM, Hsiang-Yuan Lin <louisli...@gmail.com>
>> wrote:
>> > Hi Prof. Yeo,
>> >
>> > I have problems utilizing yeo 7/17 cortical network parcellation maps as
>> > templates in MRIcron (I aim to use your cortical parcellation maps to
>> > underlay my findings in order to derive the implications based on iFC
>> > networks). To be specific, there is an orientation problem in the
>> > current
>> > version of parcellation maps in MNI space.
>> >
>> > Thank you for your help in advance.
>> >
>> > Best,
>> > Hsiang-Yuan
>> >
>> > --
>> > Hsiang-Yuan Lin, M.D.
>> > Attending Psychiatrist & Adjunct Lecturer
>> > Department of Psychiatry & Child Mental Health Center
>> > National Taiwan University Hospital and College of Medicine
>> > email: louisli...@gmail.com
>> > CV:
>> >
>> > https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
>> > https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
>> >
>> >
>> >
>> > --
>> > Hsiang-Yuan Lin, M.D.
>> > Attending Psychiatrist & Adjunct Lecturer
>> > Department of Psychiatry & Child Mental Health Center
>> > National Taiwan University Hospital and College of Medicine
>> > email: louisli...@gmail.com
>> > CV:
>> >
>> > https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
>> > https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
>
>
>
>
> --
> Hsiang-Yuan Lin, M.D.
> Attending Psychiatrist & Adjunct Lecturer
> Department of Psychiatry & Child Mental Health Center
> National Taiwan University Hospital and College of Medicine
> email: louisli...@gmail.com
> CV:
> https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
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Re: [Freesurfer] Failure to use yeo-7/17 networks maps as templates in MRIcron

[Thomas Yeo]

Hi Hsiang-Yuan,

That's because the header information is different. You can do the following:

>> mri_vol2vol --mov Yeo2011Parcellation.nii.gz --targ 
>> FSL_MNI2mm_template.nii.gz --regheader --nearest --o Yeo2011_FSL2mm.nii.gz

The output file "Yeo2011_FSL2mm.nii.gz" should have an orientation
compatible with mricron. Can you let me know if this works.

Thanks,
Thomas

On Mon, Jul 4, 2016 at 12:58 AM, Hsiang-Yuan Lin  wrote:
> Hi Prof. Yeo,
>
> I have problems utilizing yeo 7/17 cortical network parcellation maps as
> templates in MRIcron (I aim to use your cortical parcellation maps to
> underlay my findings in order to derive the implications based on iFC
> networks). To be specific, there is an orientation problem in the current
> version of parcellation maps in MNI space.
>
> Thank you for your help in advance.
>
> Best,
> Hsiang-Yuan
>
> --
> Hsiang-Yuan Lin, M.D.
> Attending Psychiatrist & Adjunct Lecturer
> Department of Psychiatry & Child Mental Health Center
> National Taiwan University Hospital and College of Medicine
> email: louisli...@gmail.com
> CV:
> https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
>
>
>
> --
> Hsiang-Yuan Lin, M.D.
> Attending Psychiatrist & Adjunct Lecturer
> Department of Psychiatry & Child Mental Health Center
> National Taiwan University Hospital and College of Medicine
> email: louisli...@gmail.com
> CV:
> https://drive.google.com/file/d/0B3jQGSXih2aeY2o1QnJwUVJjU1U/view?usp=sharing
> https://www.researchgate.net/profile/Hsiang_Yuan_Lin2
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Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

Hi Sabin,

I think fslmeants should work. But you might need to first run
mri_binarize to convert Buckner_atlas_FSSub.nii.gz into individual
ROIs.

Also can you tell us which step generated the error "ERROR: must
specify a segmentation volume"? Is this the final step? Have you tried
overlaying Buckner_atlas_FSSub.nii.gz onto your individual subject in
freeview to check that the previous steps have worked?

Thanks,
Thomas

On Mon, Jun 27, 2016 at 6:53 PM, Sabin Khadka <mr.sabinkha...@gmail.com> wrote:
> Hi Thomas- On second thought is it valid to simply do if I want average time
> series of the cerebellum regions?
>
> fslmeants -i fmcpr.anat.nii.gz -m Buckner_atlas_FSSub.nii.gz >>
> avgCerebellum.txt
>
> Is this correct?
>
>
> Cheers,
> Sabin Khadka
>
> On Mon, Jun 27, 2016 at 11:36 AM, Sabin Khadka <mr.sabinkha...@gmail.com>
> wrote:
>>
>> Hi Thomas and Doug-
>>
>> Thanks for you suggestions. Per your suggestions I performed following
>>
>> recon-all -i
>> $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/FSL_MNI152_FreeSurferConformed_1mm.nii.gz
>> -subjid Yeo2011_MNI152_FS
>>
>> recon-all -no-isrunning -autorecon-all -subjid Yeo2011_MNI152_FS
>>
>> mri_vol2vol --mov
>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
>> \
>> --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
>> talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest
>>
>> mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
>> BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
>> Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph
>>
>> mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8 --match 47 --o
>> cerebellum_mask_FSSub.nii.gz
>>
>> fslmaths Buckner2011_atlas_FSSub.nii.gz -mas cerebellum_mask_FSSub.nii.gz
>> Buckner_atlas_FSSub
>>
>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
>> fmcpr.anat.nii.gz
>>
>> mri_segstats --i Buckner_atlas_FSSub.nii.gz --i fmcpr.anat.nii.gz --avgwf
>> test.txt
>>
>> However, I got the following error
>> ERROR: must specify a segmentation volume
>>
>> Am I doing anything wrong here. Do you have any suggestions/fixes?
>>
>>
>> Cheers,
>> Sabin Khadka
>>
>> On Fri, Jun 24, 2016 at 6:30 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
>>>
>>> Hi Doug, thanks.
>>>
>>> Hi Sabin, you can use the following steps to transform the Buckner
>>> cerebellum atlas to your subject's native anatomical space and then
>>> follow Doug's instructions (taken and adapted from another user
>>> Bronwyn's email):
>>>
>>> 1. Run MNI152 1mm template through recon-all
>>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
>>> Yeo2011_MNI152_FS
>>>
>>> 2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
>>> nonlinear volumetric space
>>> mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ
>>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
>>> BucknerAtlas1mm_FSI.nii.gz --nearest
>>>
>>> 3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
>>> volumetric space to each subject:
>>> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
>>> BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o
>>> Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph
>>>
>>> 4. Create a cerebellum gray matter mask in the native subject's space
>>> by applying mri_binarize to aparc+aseg.mgz of the subject
>>> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o
>>> cerebellum_mask_subjID.nii.gz
>>>
>>> 5. Using this mask to mask the Buckner cerebellum parcellations
>>> fslmaths Buckner2011_atlas_subjID.nii.gz -mas
>>> cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz
>>>
>>> Regards,
>>> Thomas
>>>
>>> On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve
>>> <gr...@nmr.mgh.harvard.edu> wrote:
>>> > yes
>>> >
>>> >
>>> >
>>> > On 6/24/16 9:19 AM, Thomas Yeo wrote:
>>> >>
>>> >> Hi Doug,
>>> >>
>>> >> Would your mri_segstats command work if instead of aseg.mgz, Sabin
>>> >> passed in the cerbellum parcellation in the same anatomical space as
>>> >> aseg?
>>> >>
>&g

Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

Hi Doug, thanks.

Hi Sabin, you can use the following steps to transform the Buckner
cerebellum atlas to your subject's native anatomical space and then
follow Doug's instructions (taken and adapted from another user
Bronwyn's email):

1. Run MNI152 1mm template through recon-all
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS

2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to freesurfer
nonlinear volumetric space
mri_vol2vol --mov BucknerAtlas1mm.nii --s Yeo2011_MNI152_FS --targ
$FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
BucknerAtlas1mm_FSI.nii.gz --nearest

3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear
volumetric space to each subject:
mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
BucknerAtlas1mm_FSI.nii.gz --m3z talairach.m3z --o
Buckner2011_atlas_subjID.nii.gz --nearest --inv-morph

4. Create a cerebellum gray matter mask in the native subject's space
by applying mri_binarize to aparc+aseg.mgz of the subject
mri_binarize --i subjID/mri/aparc+aseg.mgz --match 8 --match 47 --o
cerebellum_mask_subjID.nii.gz

5. Using this mask to mask the Buckner cerebellum parcellations
fslmaths Buckner2011_atlas_subjID.nii.gz -mas
cerebellum_mask_subjID.nii.gz Buckner_atlas_subjID_mask.nii.gz

Regards,
Thomas

On Fri, Jun 24, 2016 at 4:47 PM, Douglas Greve
<gr...@nmr.mgh.harvard.edu> wrote:
> yes
>
>
>
> On 6/24/16 9:19 AM, Thomas Yeo wrote:
>>
>> Hi Doug,
>>
>> Would your mri_segstats command work if instead of aseg.mgz, Sabin
>> passed in the cerbellum parcellation in the same anatomical space as
>> aseg?
>>
>> --Thomas
>>
>> On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
>> <gr...@nmr.mgh.harvard.edu> wrote:
>>>
>>> After you run preproc-sess, there will be a file called
>>> register.dof6.dat.
>>> Map fmri into the anatomical space, something like
>>>
>>> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
>>> fmcpr.anat.nii.gz
>>>
>>> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
>>>
>>> However, I don't think that the aseg has those cerebellum parcellations.
>>>
>>> On 6/21/16 5:52 PM, Sabin Khadka wrote:
>>>
>>> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305
>>> space. I
>>> process my fmri data with
>>>
>>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
>>> -per-run -stc odd
>>> and then to extract ROI time series values I did
>>>
>>> mri_segstats --annot fsaverage rh aparc --i
>>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
>>> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>>>
>>> and for cortical time series
>>>
>>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
>>> --id
>>> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id
>>> 58
>>> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>>> subCorticalTimeSeries.txt
>>>
>>> Now I am not sure as how to extract cerebellum ROIs (time series as
>>> described in Buckner et.al 2011)? If there are any other additional steps
>>> I
>>> need to perform ? or if I have to use some other scripts commands (other
>>> than mri_segstats).
>>>
>>>
>>> Cheers,
>>> Sabin Khadka
>>>
>>> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo <ytho...@csail.mit.edu>
>>> wrote:
>>>>
>>>> Hi Sabin,
>>>>
>>>> The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical
>>>> substructures of the cerebellum (e.g., Crus I, etc). Is that what you
>>>> want? Or are you looking to use the functional parcels defined in
>>>> Buckner 2011?
>>>>
>>>> In addition, I do not know how mri_segstats works, so I cannot verify
>>>> how you call the command is correct. Maybe others can provide feedback
>>>> here.
>>>>
>>>> However, the Buckner cerebellar parcellations in
>>>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152
>>>> space. From your command, I assume your data is in MNI305 space. So
>>>> you might need to transform the parcellation from MNI152 to MNI305.
>>>>
>>>> Thanks,
>>>> Thomas
>>>>
>>>> On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka <mr.sabinkha...@gmail.com>
>>&g

Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

Hi Doug,

Would your mri_segstats command work if instead of aseg.mgz, Sabin
passed in the cerbellum parcellation in the same anatomical space as
aseg?

--Thomas

On Thu, Jun 23, 2016 at 11:28 PM, Douglas Greve
<gr...@nmr.mgh.harvard.edu> wrote:
> After you run preproc-sess, there will be a file called register.dof6.dat.
> Map fmri into the anatomical space, something like
>
> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
> fmcpr.anat.nii.gz
>
> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
>
> However, I don't think that the aseg has those cerebellum parcellations.
>
> On 6/21/16 5:52 PM, Sabin Khadka wrote:
>
> Hi Yeo- Thanks very much for your answer. Yes the data is in mni305 space. I
> process my fmri data with
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
> -per-run -stc odd
> and then to extract ROI time series values I did
>
> mri_segstats --annot fsaverage rh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>
> and for cortical time series
>
> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id
> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58
> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
> subCorticalTimeSeries.txt
>
> Now I am not sure as how to extract cerebellum ROIs (time series as
> described in Buckner et.al 2011)? If there are any other additional steps I
> need to perform ? or if I have to use some other scripts commands (other
> than mri_segstats).
>
>
> Cheers,
> Sabin Khadka
>
> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
>>
>> Hi Sabin,
>>
>> The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical
>> substructures of the cerebellum (e.g., Crus I, etc). Is that what you
>> want? Or are you looking to use the functional parcels defined in
>> Buckner 2011?
>>
>> In addition, I do not know how mri_segstats works, so I cannot verify
>> how you call the command is correct. Maybe others can provide feedback
>> here.
>>
>> However, the Buckner cerebellar parcellations in
>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152
>> space. From your command, I assume your data is in MNI305 space. So
>> you might need to transform the parcellation from MNI152 to MNI305.
>>
>> Thanks,
>> Thomas
>>
>> On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka <mr.sabinkha...@gmail.com>
>> wrote:
>> > Hi all,
>> >
>> > I am trying to extract mean time series BOLD data using FSFAST from
>> > Cortical
>> > ROIs + sub cortical ROIs and cerebellum.
>> >
>> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm
>> > 6
>> > -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000
>> > --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
>> > mri_segstats --annot fsaverage rh aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
>> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>> >
>> > and for cortical time series
>> >
>> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
>> > --id
>> > 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id
>> > 58
>> > --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>> > subCorticalTimeSeries.txt
>> >
>> > But I am not sure on how exactly to extract time series from cerebellar
>> > regions. So if I want to extract time series from regions as described
>> > in
>> > Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628
>> > in
>> > FreeSurferCololLUT.txt? If not could you please direct me to processes
>> > that
>> > I can use.
>> >
>> > Cheers,
>> > Sabin Khadka
>> >
>> > ___
>> > 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 erro

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

You should be able to use the 5.3 version.

Regards,
Thomas

On Thu, Jun 23, 2016 at 2:16 PM, Bronwyn Overs <b.ov...@neura.edu.au> wrote:

> Hi Thomas,
>
> Thanks for your reply.
>
> The fsaverage directory I have for fs v 5.1 does not include the lh and rh
> Yeo2011_7Networks_N1000.annot files. I only have this in the 5.3 version of
> fsaverage. Can I still use the 5.3 version annot files or would I need a
> seperate set processed with version 5.1?
>
> 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 23/06/2016 3:17 pm, Thomas Yeo wrote:
>
> Hi Bronwyn,
>
> You raise a good point. You can consider creating a cortical mask using
> aparc+aseg.mgz and use that to mask the networks.
>
> However, another approach (which might be more accurate) is to take
> cortical networks in fsaverage space and transform to your subject's
> surface and then transform into your subject's volume:
>
> # Transform from fsaverage to subject's surface
> >> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
> --sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
> $SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*
>
> # Transform from subject's surface into your subject's volume (I am not
> super sure about this. You probably want to double check the output is
> correct)
> >> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
> outfile.nii.gz --hemi lh --subject HS_001 **--regheader*
>
> --Thomas
>
> On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs <b.ov...@neura.edu.au>
> wrote:
>
>> Hi Mailing List,
>>
>> I am attempting to apply the Yeo 2011 7-network fucntional parcellations
>> to a set of fs MRIs processed with v5.1.0. Below are listed the first three
>> steps I plan to take and I am seeking advice as to:
>>
>> A) Whether this approach is valid.
>> B) Steps to take next.
>>
>>
>>
>> * Steps 1-3: *
>>
>> *1. Run MNI152 1mm template through recon-all*
>> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
>> Yeo2011_MNI152_FS
>> recon-all -all -subjid Yeo2011_MNI152_FS
>>
>> *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space*
>> mri_vol2vol --mov
>> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s
>> Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
>> talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest
>>
>> *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:*
>> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
>> Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz
>> --nearest --inv-morph
>>
>>
>> When previously mapping the Choi 2012 straital parcellations, steps 4 and
>> 5 were:
>>
>> 4. *Creating a striatal mask in the native subject's space from
>> freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens
>> (26 & 58)*:
>> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match
>> 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz
>>
>> *5. **Using this mask to mask the choi striatal parcellations*
>> fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz
>> Yeo_atlas_subjID_mask.nii.gz
>>
>>
>> Do I need to do a similar thing for the Yeo cortical parcellations and if
>> so what regions should I include in the cortical mask?
>> --
>>
>> 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

Re: [Freesurfer] Yeo 2011 Functional Cortical Parcellations

[Thomas Yeo]

Hi Bronwyn,

You raise a good point. You can consider creating a cortical mask using
aparc+aseg.mgz and use that to mask the networks.

However, another approach (which might be more accurate) is to take
cortical networks in fsaverage space and transform to your subject's
surface and then transform into your subject's volume:

# Transform from fsaverage to subject's surface
>> mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh
--sval-annot *lh.Yeo2011_17Networks_N1000.annot*  --tval
$SUBJECTS_DIR/yoursubject/label/*lh.Yeo_17Network_native.annot*

# Transform from subject's surface into your subject's volume (I am not
super sure about this. You probably want to double check the output is
correct)
>> *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot **--o
outfile.nii.gz --hemi lh --subject HS_001 **--regheader*

--Thomas

On Wed, Jun 22, 2016 at 8:25 AM, Bronwyn Overs  wrote:

> Hi Mailing List,
>
> I am attempting to apply the Yeo 2011 7-network fucntional parcellations
> to a set of fs MRIs processed with v5.1.0. Below are listed the first three
> steps I plan to take and I am seeking advice as to:
>
> A) Whether this approach is valid.
> B) Steps to take next.
>
>
>
> * Steps 1-3: *
>
> *1. Run MNI152 1mm template through recon-all*
> recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
> Yeo2011_MNI152_FS
> recon-all -all -subjid Yeo2011_MNI152_FS
>
> *2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space*
> mri_vol2vol --mov
> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s
> Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
> talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest
>
> *3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:*
> mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ
> Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz
> --nearest --inv-morph
>
>
> When previously mapping the Choi 2012 straital parcellations, steps 4 and
> 5 were:
>
> 4. *Creating a striatal mask in the native subject's space from
> freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens
> (26 & 58)*:
> mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match
> 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz
>
> *5. **Using this mask to mask the choi striatal parcellations*
> fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz
> Yeo_atlas_subjID_mask.nii.gz
>
>
> Do I need to do a similar thing for the Yeo cortical parcellations and if
> so what regions should I include in the cortical mask?
> --
>
> 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]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
>
> ___
> 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.
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Re: [Freesurfer] FSFAST- Cerebellum

[Thomas Yeo]

Hi Sabin,

The structures 601-628 FreeSurferCololLUT.txt correspond to anatomical
substructures of the cerebellum (e.g., Crus I, etc). Is that what you
want? Or are you looking to use the functional parcels defined in
Buckner 2011?

In addition, I do not know how mri_segstats works, so I cannot verify
how you call the command is correct. Maybe others can provide feedback
here.

However, the Buckner cerebellar parcellations in
$FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is in MNI152
space. From your command, I assume your data is in MNI305 space. So
you might need to transform the parcellation from MNI152 to MNI305.

Thanks,
Thomas

On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka  wrote:
> Hi all,
>
> I am trying to extract mean time series BOLD data using FSFAST from Cortical
> ROIs + sub cortical ROIs and cerebellum.
>
> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305 -fwhm 6
> -per-run -stc oddmri_segstats --annot fsaverage lh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid 1000
> --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> mri_segstats --annot fsaverage rh aparc --i
> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>
> and for cortical time series
>
> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13 --id
> 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id 54 --id 58
> --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
> subCorticalTimeSeries.txt
>
> But I am not sure on how exactly to extract time series from cerebellar
> regions. So if I want to extract time series from regions as described in
> Buckner et.al 2011. Could I just use mri_segstats for the labels 601-628 in
> FreeSurferCololLUT.txt? If not could you please direct me to processes that
> I can use.
>
> Cheers,
> Sabin Khadka
>
> ___
> Freesurfer mailing list
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> 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
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Re: [Freesurfer] Question on Yeo 2015 cognitive atlas

[Thomas Yeo]

Hi Josh,

Thanks for your interest. The networks are in MNI152 space. My
understanding is that you want to map the networks onto the structural
T1 data of your subjects. Here's my suggestion on how to do it:

1) Assuming you are quite happy with the freesurfer recon-all of your
individual subjects, then this means that freesurfer nonlinear
(volumetric) 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 /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 /MNI152_FS/

3) Then do the following:

a) First sample C1-C12 (Yeo_components2mm.nii.gz) to norm.mgz of
MNI152_FS (because C1-C12 are 2mm, but norm.mgz is 1mm isotropic):

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov Yeo_components2mm.nii.gz --s MNI152_FS --targ 
>> /MNI152_FS/mri/norm.mgz --regheader --o Yeo_components1mm.nii.gz

b) Warp the Yeo_components1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov Yeo_components1mm.nii.gz --s MNI152_FS --targ 
>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o 
>> Yeo_components_internal_space.nii.gz

c) Warp Yeo_components_internal_space.nii.gz to your subject:

>> setenv SUBJECTS_DIR 
>> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS 
>> --targ Yeo_components_internal_space.nii.gz --m3z talairach.m3z --o 
>> Yeo_components_subject_space.nii.gz --interp nearest --inv-morph

This is not optimal because of the multiple interpolation, but the
networks are quite smooth anyway, so it should be ok.

You might want to use the FSL MNI152 2mm template instead of
Yeo_components2mm.nii.gz to test the steps 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
Yeo_components2mm.nii.gz. 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 Wed, May 18, 2016 at 3:53 AM, Josh Gray  wrote:
> Hello,
>
> I am interested in applying the Yeo 2015 cognitive atlas to structural data.
> Basically, I want to quantify networks C1-12 in my structural data by
> exporting the voxel size of each network for each subject into an text file
> (so I would have left and right hemisphere voxel totals for networks C1-12
> for each subject). It is analogous to what is routinely done with the
> desikan and destrieux atlas. I know you can change the threshold of the
> networks, but I suspect 1e-5 is fine (i.e., what is depicted on the
> website). Is there a quick way to do this?
>
> Thank you,
> Josh Gray
>
> --
> Graduate Student
> Psychology Dept. - Clinical Program
> Experimental & Clinical Psychopharmacology Laboratory
> University of Georgia
>
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

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.ov...@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.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 <%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:
>>
>> 1) Assuming you are quite happy with the freesurfer striatal parcellation
>> in your individual

Re: [Freesurfer] cerebellar surface

[Thomas Yeo]

Hi Jim,

Yes. I believe so.

Regards,
Thomas

On Tue, May 10, 2016 at 9:32 PM, Alexopoulos, Dimitrios <
alexopoulo...@kids.wustl.edu> wrote:

> Thanks for the info.
>
>
>
> So the cerebellum surface needs to be generated independently from the
> default cerebral/supratentorial surface generated by recon-all?
>
>
>
> Jim
>
>
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Thomas Yeo
> *Sent:* Monday, May 09, 2016 6:20 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] cerebellar surface
>
>
>
> Hi Jim,
>
>
>
> You can use mri_tessellate.
>
>
>
> Regards,
>
> Thomas
>
>
>
> On Mon, May 9, 2016 at 11:11 PM, Alexopoulos, Dimitrios <
> alexopoulo...@kids.wustl.edu> wrote:
>
> Hi all,
>
>
>
> Freesurfer generates a volumetric parcellation of the cerebellum, but is
> there a method to generate the surface reconstruction, or perhaps just a
> hull surface from freesurfer output.
>
>
>
> Jim
>
>
>
>
>
> *The materials in this email are private and may contain Protected Health
> Information. If you are not the intended recipient, be advised that any
> unauthorized use, disclosure, copying, distribution or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited. If you have received this email in error, please immediately
> notify the sender via telephone or return email.*
>
>
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Re: [Freesurfer] cerebellar surface

[Thomas Yeo]

Hi Jim,

You can use mri_tessellate.

Regards,
Thomas

On Mon, May 9, 2016 at 11:11 PM, Alexopoulos, Dimitrios <
alexopoulo...@kids.wustl.edu> wrote:

> Hi all,
>
>
>
> Freesurfer generates a volumetric parcellation of the cerebellum, but is
> there a method to generate the surface reconstruction, or perhaps just a
> hull surface from freesurfer output.
>
>
>
> Jim
>
>
>
>
> The materials in this email are private and may contain Protected Health
> Information. If you are not the intended recipient, be advised that any
> unauthorized use, disclosure, copying, distribution or the taking of any
> action in reliance on the contents of this information is strictly
> prohibited. If you have received this email in error, please immediately
> notify the sender via telephone or return email.
>
> ___
> 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.
>
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

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
> /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 /MNI152_FS/
>
> 3) Then do the following:
>
> a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
>
> >> setenv SUBJECTS_DIR 
> >> 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 
> >> 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,
>

Re: [Freesurfer] Stats for Yeo and Choi Parcellations

[Thomas Yeo]

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
/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 /MNI152_FS/

3) Then do the following:

a) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:

>> setenv SUBJECTS_DIR 
>> 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 
>> 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 
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
> neura.edu.au
>
> [image: Follow @neuraustralia on twitter]
> [image: Follow NeuRA on facebook]
> [image: Subscribe
> to the NeuRA Magazine] 
>
>
> ___
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>
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> contains patient information, please contact the Partners Compliance
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[Freesurfer] Postdoctoral Fellow in Machine Learning in Neuroimaging

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop machine learning algorithms for fMRI.

Topics are flexible. Example topics include individual-subject brain
parcellations, dynamic functional connectivity, meta-analysis, neural
mass modeling, monkey-human homologies, mental disorder subtypes, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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Re: [Freesurfer] 答复: about functional ROIs

[Thomas Yeo]

Hi Jintao,

The difference comes from the fact that the MNI template I used is 256 x
256 x 256, which was obtained by passing the FSL MNI152 template through
the FreeSurfer recon-all pipeline. Therefore even though the header
information are different, they are still in the same space.

You can convince yourself by using freesurfer's freeview to load both the
MNI template I provide and the MNI template from FSL:

>> freeview FSL_MNI152_FreeSurferConformed_1mm.nii.gz
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

You should observe they are in perfect alignment (although the values have
been altered by recon-all intensity normalization process). If the
different headers bother you, what you can do is to use freesurfer's
function mri_vol2vol to re-interpolate the volume. For example:

>> mri_vol2vol --mov FSL_MNI152_FreeSurferConformed_1mm.nii.gz --targ
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --regheader --o
new_volume.nii.gz --no-save-reg

Regards,
Thomas



On Thu, Dec 31, 2015 at 2:59 PM, <shengjt2...@163.com> wrote:

> Hello Professor Thomas，
>
>
>
> Thank you for your reply so quickly.
>
>
>
> I download the zip files on the webside you gave me, and the images look
> like normal, but when I checked the header information, I found some
> differences with common MNI images.
>
>
>
> Could you see the following pictures and notice the regions with blue
> lines circled.
>
>
>
>
>
>
>
> Excuse me to bother you again.
>
> Best wishes,
>
> Jintao
>
>
>
>
>
>
> *发件人: *Thomas Yeo <ytho...@csail.mit.edu>
> *发送时间: *2015年12月31日 11:46
> *收件人: *shengjt2...@163.com
> *抄送: *freesurfer <freesurfer@nmr.mgh.harvard.edu>
> *主题: *Re: about functional ROIs
>
>
>
> Hi Jintao,
>
>
>
> This might be a header error in the original files. The error is not
> apparent in the FreeSurfer or FSL environment, but might be problematic
> with mricron (completely my fault).
>
>
>
> Can you try the files from this zip file instead:
> https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo2011MNIParcellation_MICRON.zip
> (courtesy of Chris Rorden).
>
>
>
> Please let me know if this resolves your issues.
>
>
>
> Regards,
>
> Thomas
>
>
>
> On Thu, Dec 31, 2015 at 10:23 AM, <shengjt2...@163.com> wrote:
>
>
>
> Dear Professor Yeo,
>
>
>
> My name is Sheng Jintao, and I am a master in China.
>
> Recently, I download the ‘Resting State Cortical Parcellation in
> nonlinear MNI152 space’ in
> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
> But when I opened images and found they are very stange. Just like this
> sectional drawing. And I don’t know why, therefore, I would love to
> consult you.
>
> Thank you, and I look forward to hearing from you.
>
>
>
> Best wishes,
>
> Jintao
>
>
>
>
>
>
>
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Re: [Freesurfer] about functional ROIs

[Thomas Yeo]

Hi Jintao,

This might be a header error in the original files. The error is not
apparent in the FreeSurfer or FSL environment, but might be problematic
with mricron (completely my fault).

Can you try the files from this zip file instead:
https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo2011MNIParcellation_MICRON.zip
(courtesy of Chris Rorden).

Please let me know if this resolves your issues.

Regards,
Thomas

On Thu, Dec 31, 2015 at 10:23 AM,  wrote:

>
>
> Dear Professor Yeo,
>
>
>
> My name is Sheng Jintao, and I am a master in China.
>
> Recently, I download the ‘Resting State Cortical Parcellation in nonlinear
> MNI152 space’ in
> https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011,
> But when I opened images and found they are very stange. Just like this
> sectional drawing. And I don’t know why, therefore, I would love to consult
> you.
>
> Thank you, and I look forward to hearing from you.
>
>
>
> Best wishes,
>
> Jintao
>
>
>
>
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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Richard,

This occurs because the gaps exist in the original fsaverage5
split_component parcellation. As explained in the documentation text
file (Yeo_JNeurophysiol11_SplitLabels_README which should also be
included in the zip file), one of the steps taken to generate
*.split_components.annot involved removing vertices at the boundaries
between parcels. This is to reduce the mixing of signals across
parcels, e.g., due to spatial smoothing.

You can see these gaps if you plot the fsaverage5 annot on the
fsaverage5 subject. Therefore when the parcellation is upsampled from
fsaverage5 to fsaverage, the gaps are propagated. I admit the gaps do
not look very visually pleasing because going from fsaverage5 to
fsaverage involved an upsampling factor of 4. However, I think the
gaps should not be detrimental to your analysis.

How does the parcellation look when you transfer the (upsampled)
fsaverage parcellation to the individual subject's surface?

Regards,
Thomas

On Mon, Dec 14, 2015 at 6:43 PM, Parker, Richard
 wrote:
> Hi Prof,
>
>
> Thanks for the speedy reply,
>
>
> When you specify fsaverage5 as -srcsubject and your own subject as
> -trgsubject, the code executes but the resulting .annot file looks like a
> mess.
>
>
> Your proposed two-step call to mri_surf2surf seems more promising. If I run
> the following:
>
>
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject fsaverage --hemi lh
> --sval-annot
> fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval
> ./lh.YeoUpsample.annot
>
> I end up with a .annot file in the same space as fsaverage, but there seem
> to be large gaps between the labels. Here's a screenshot of what I mean:
>
>
> http://imgur.com/VvqYEWx
>
>
> Do you have any suggestions on how to account for this? Is there some
> unresolved mismatch between the number of vertices following upsampling,
> perhaps?
>
>
> Best wishes,
>
>
> Richard
>
>
>
>
>
>
>
>
>
>
> Hi Richard,
>
> Sorry. My original reply was rejected by the list. Resending.
>
> In the mri_surf2surf command, Instead of the srcsubject being
> fsaverage, can you try using the srcsubject as fsaverage5 instead?
>
> Alternatively, you can try running mri_surf2surf twice. Once to
> upsample the fsaverage5 annot to fsaverage and then run the
> mri_surf2surf command from your email. (This might actually work
> better).
>
> Thanks,
> Thomas
>
> On Fri, Dec 11, 2015 at 12:51 AM, Parker, Richard
>  wrote:
>> Hi Professor Yeo,
>>
>>
>>
>> Thanks for providing a link to your split region MNI space files.
>>
>>
>>
>> Could you please advise on how to get these labels into subject native
>> space?
>>
>>
>>
>> If using the standard version of the network labels that comes packaged
>> with
>> Freesurfer 5.3.0, I can get the annotation file into native space quite
>> easily with the following command:
>>
>>
>>
>>
>>
>> mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh
>> --sval-annot
>>
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot
>> --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot
>>
>>
>>
>> However, in the dropbox link you posted, it doesn’t seem that there is a
>> .annot file compatible with fsaverage. The fsaverage5 version is present,
>> but if I try slotting the fsaverage5 .annot file into the above call to
>> mri_surf2surf, I get disastrous results.
>>
>>
>>
>> Do you perhaps have a .annot file for the upsampled (and split) network
>> labels? Or perhaps there’s an easier way to achieve what I’m after. I
>> notice
>> that you have provided a .nii file for the network ROIs that is in the
>> same
>> space as fsaverage, perhaps this file can be warped to native space
>> somehow?
>>
>>
>>
>> Best wishes,
>>
>>
>>
>> Richard Parker
>>
>> King’s College London
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Hi Erica,
>>
>>
>>
>> You can try this link:
>>
>>
>> https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip
>>
>>
>>
>> Regards,
>>
>> Thomas
>>
>>
>>
>> On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung 
>> wrote:
>>
>>> Dear Prof. Yeo,
>>
>>>
>>
>>> I would like to extract the brain regions of the functional canonical
>>
>>> network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you
>>> have
>>
>>> provided the split regions of 7&17 Network in previous discussion string.
>>
>>>
>>>
>>> (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html
>>
>>>  )
>>
>>>
>>
>>> However, the dropbox download link you offered has expired.
>>
>>> Would you mind uploading it again?
>>
>>>
>>
>>> Thank you very much.
>>
>>>
>>
>>> Erica
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe 

Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Richard,

Sorry. My original reply was rejected by the list. Resending.

In the mri_surf2surf command, Instead of the srcsubject being
fsaverage, can you try using the srcsubject as fsaverage5 instead?

Alternatively, you can try running mri_surf2surf twice. Once to
upsample the fsaverage5 annot to fsaverage and then run the
mri_surf2surf command from your email. (This might actually work
better).

Thanks,
Thomas

On Fri, Dec 11, 2015 at 12:51 AM, Parker, Richard
 wrote:
> Hi Professor Yeo,
>
>
>
> Thanks for providing a link to your split region MNI space files.
>
>
>
> Could you please advise on how to get these labels into subject native
> space?
>
>
>
> If using the standard version of the network labels that comes packaged with
> Freesurfer 5.3.0, I can get the annotation file into native space quite
> easily with the following command:
>
>
>
>
>
> mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh
> --sval-annot
> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot
>
>
>
> However, in the dropbox link you posted, it doesn’t seem that there is a
> .annot file compatible with fsaverage. The fsaverage5 version is present,
> but if I try slotting the fsaverage5 .annot file into the above call to
> mri_surf2surf, I get disastrous results.
>
>
>
> Do you perhaps have a .annot file for the upsampled (and split) network
> labels? Or perhaps there’s an easier way to achieve what I’m after. I notice
> that you have provided a .nii file for the network ROIs that is in the same
> space as fsaverage, perhaps this file can be warped to native space somehow?
>
>
>
> Best wishes,
>
>
>
> Richard Parker
>
> King’s College London
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hi Erica,
>
>
>
> You can try this link:
>
> https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip
>
>
>
> Regards,
>
> Thomas
>
>
>
> On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung 
> wrote:
>
>> Dear Prof. Yeo,
>
>>
>
>> I would like to extract the brain regions of the functional canonical
>
>> network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you
>> have
>
>> provided the split regions of 7&17 Network in previous discussion string.
>
>>
>> (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html
>
>>  )
>
>>
>
>> However, the dropbox download link you offered has expired.
>
>> Would you mind uploading it again?
>
>>
>
>> Thank you very much.
>
>>
>
>> Erica
>
>
>
>
> ___
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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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[Freesurfer] OHBM white paper on best practices in Data Analytics and Sharing

[Thomas Yeo]

Dear FreeSurfer List,

In 2014 OHBM Council created the Committee on Best Practices in Data
Analysis and Sharing (COBIDAS) to identify best practices of data
analysis and data sharing in the brain mapping community.

The COBIDAS committee has prepared a white paper organizing these
practices and seek input from the OHBM community before ultimately
publishing these recommendations.

You can find the whitepaper here:
http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3668.
Feedback can be provided here: http://cobidas.wordpress.com/

Regards,
Thomas
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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Erica,

You can try this link:
https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_SplitLabels.zip

Regards,
Thomas

On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung  wrote:
> Dear Prof. Yeo,
>
> I would like to extract the brain regions of the functional canonical
> network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have
> provided the split regions of 7&17 Network in previous discussion string.
> (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html
>  )
>
> However, the dropbox download link you offered has expired.
> Would you mind uploading it again?
>
> Thank you very much.
>
> Erica
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[Freesurfer] Postdoctoral Fellow in Machine Learning in Neuroimaging

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop machine learning algorithms for fMRI.

Topics are flexible. Example topics include dynamic functional
connectivity, meta-analysis, neural mass modeling, monkey-human
homologies, mental disorder subtypes, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ytho...@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.
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Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Thomas Yeo]

Hi Ali,

It should work with the old processed data.

--Thomas

On Sun, Sep 20, 2015 at 12:00 AM, Ali Radaideh <ali.radai...@hu.edu.jo> wrote:
> Dear Thomas,
>
> Many thanks for your detailed explanation. I will try it and let you know.
>
> One more question please, last year, I processed another set of subjects
> using an older version of FreeSurfer 5.0. Now the old version has been
> replaced with its new one (5.3.0) on the same PC. In other words, my PC has
> the new version of freesurfer 5.3.0 and two sets of processed T1 images. One
> set was processed using the old version of freesurfer which is no longer
> there. The other set was processed using the new version. So, can I
> transform the network atlases to the set of subjects spaces processed last
> year using the old version of freesurfe 5.0.0r? or or I have to re-run the
> recon-all again?
>
> Many thanks in advance and my apology for keeping you busy with my
> questions.
>
> Ali
>
>
> On Sat, Sep 19, 2015 at 3:14 PM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
>>
>> Hi Ali,
>>
>> Sorry, I wasn't clear. The 7 and 17 network atlases are released with
>> FreeSurfer 5.3. In particular, the "annot" files are found in
>> $FREESURFER_HOME/subjects/fsaverage/label/. Therefore since you have
>> already run recon-all using FreeSurfer, then this means that you do
>> not need to "save" the new atlas anywhere.
>>
>> The 7 and 17 network atlases are in fsaverage space. You can run the
>> following commands to transform the atlases to your individual
>> subjects' surfaces. Suppose your subject is called 100306_QD95CU_FS
>> and the recon-all of this subject is located in
>> /share/users/imganalysis/yeolab/data/GSP/.
>>
>> 1) The first step is to set the variable SUBJECTS_DIR to point to
>> where your subject is:
>>
>> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>>
>> 2) The second step is to create a symbolic link so that the FreeSurfer
>> "fsaverage" subject appears to be in your SUBJECTS_DIR
>>
>> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>>
>> 3) The final step is to run mri_surf2surf to transform the 7 network
>> atlas to your subject's native surfaces.
>>
>> >> mri_surf2surf --srcsubject fsaverage --trgsubject 100306_QD95CU_FS
>> >> --hemi lh --sval-annot
>> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
>> >> --tval 
>> >> $SUBJECTS_DIR/100306_QD95CU_FS/label/lh.Yeo2011_7Networks_N1000.annot
>>
>> Note that the above is only for the left hemisphere. You can replace
>> all the "lh" with "rh" to transform the right hemisphere instead.
>>
>> Note that the above is for the 7 networks. You can replace all the "7"
>> with "17" to transform the 17-network atlas instead.
>>
>> I hope the above is clearer. Let me know if you have other questions.
>>
>> --Thomas
>>
>> On Sat, Sep 19, 2015 at 4:16 PM, Ali Radaideh <ali.radai...@hu.edu.jo>
>> wrote:
>> > Also, could you please direct me in which directory I should save the
>> > new
>> > atlas?
>> >
>> > Thanks,
>> > Ali
>> >
>> > On Sat, Sep 19, 2015 at 9:47 AM, Thomas Yeo <ytho...@csail.mit.edu>
>> > wrote:
>> >>
>> >> Hi Ali,
>> >>
>> >> May I confirm that your data is T1 and not functional data? Here's
>> >> what you can do to transfer the parcellation to your individual
>> >> subject's surface mesh. After that you can use the usual commands to
>> >> extract thickness, etc.
>> >>
>> >> In your shell (assuming you are using c shell)
>> >>
>> >> # First set variable s to be subject id
>> >> >> set s = 100306_QD95CU_FS
>> >>
>> >> # set freesurfer environmental variable SUBJECTS_DIR to point to where
>> >> the data is
>> >> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>> >>
>> >> # use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
>> >> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>> >>
>> >> # use "-sval-annot" option to transfer annotation
>> >> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
>> >> >> --sval-annot
>> >> >>
>> >> >> $FREESURFER_HOME/subjects

Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Thomas Yeo]

Hi Ali,

May I confirm that your data is T1 and not functional data? Here's
what you can do to transfer the parcellation to your individual
subject's surface mesh. After that you can use the usual commands to
extract thickness, etc.

In your shell (assuming you are using c shell)

# First set variable s to be subject id
>> set s = 100306_QD95CU_FS

# set freesurfer environmental variable SUBJECTS_DIR to point to where
the data is
>> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/

# use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
>> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage

# use "-sval-annot" option to transfer annotation
>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval-annot 
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot 
>> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot

# use "sval" option to transfer confidence map.
>> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval 
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>>  --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz

Cheers,
Thomas

On Sat, Sep 19, 2015 at 3:12 PM, Ali Radaideh  wrote:
> Dear FreeSurfer experts,
>
> I have finished processing a group of brains MR images collected at 7T
> scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine).
>
> However, we need to get the cortical parcellation based on functional
> network connectivity. So I have downloaded the Atlas data
> (Yeo_JNeurophysiol11_FreeSurfer) to use it for the parcellation but I have
> few questions which I hope you will be able to help me on.
>
> 1- Do I need to repeat the "recon-all" process?
> 2- If yes, how can I change the default Atlas that freesurfer uses?
> 3- If no, what can I do to get the cortical parcellation based on finctional
> networks from our processed data?
> 4- At the end, shall I use the usual commands to extract the volumes,
> thicknesses ...etc?
>
>
> Many thanks for your help in advance.
>
> Ali
>
>
> --
> Ali M. Al-Radaideh. PhD
> Head of Department of Medical Imaging
> Vice Dean of the Faculty of Allied Health Sciences
> The Hashemite University,
> Zarqa, Jordan
> W.phone +962 5 390 ext.5422, 5355, 5364
> Email: ali.radai...@hu.edu.jo
> webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
>
>
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>
>
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> 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
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Re: [Freesurfer] Cortical Parcellation_Yeo_networks

[Thomas Yeo]

Hi Ali,

Sorry, I wasn't clear. The 7 and 17 network atlases are released with
FreeSurfer 5.3. In particular, the "annot" files are found in
$FREESURFER_HOME/subjects/fsaverage/label/. Therefore since you have
already run recon-all using FreeSurfer, then this means that you do
not need to "save" the new atlas anywhere.

The 7 and 17 network atlases are in fsaverage space. You can run the
following commands to transform the atlases to your individual
subjects' surfaces. Suppose your subject is called 100306_QD95CU_FS
and the recon-all of this subject is located in
/share/users/imganalysis/yeolab/data/GSP/.

1) The first step is to set the variable SUBJECTS_DIR to point to
where your subject is:

>> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/

2) The second step is to create a symbolic link so that the FreeSurfer
"fsaverage" subject appears to be in your SUBJECTS_DIR

>> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage

3) The final step is to run mri_surf2surf to transform the 7 network
atlas to your subject's native surfaces.

>> mri_surf2surf --srcsubject fsaverage --trgsubject 100306_QD95CU_FS --hemi lh 
>> --sval-annot 
>> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot 
>> --tval $SUBJECTS_DIR/100306_QD95CU_FS/label/lh.Yeo2011_7Networks_N1000.annot

Note that the above is only for the left hemisphere. You can replace
all the "lh" with "rh" to transform the right hemisphere instead.

Note that the above is for the 7 networks. You can replace all the "7"
with "17" to transform the 17-network atlas instead.

I hope the above is clearer. Let me know if you have other questions.

--Thomas

On Sat, Sep 19, 2015 at 4:16 PM, Ali Radaideh <ali.radai...@hu.edu.jo> wrote:
> Also, could you please direct me in which directory I should save the new
> atlas?
>
> Thanks,
> Ali
>
> On Sat, Sep 19, 2015 at 9:47 AM, Thomas Yeo <ytho...@csail.mit.edu> wrote:
>>
>> Hi Ali,
>>
>> May I confirm that your data is T1 and not functional data? Here's
>> what you can do to transfer the parcellation to your individual
>> subject's surface mesh. After that you can use the usual commands to
>> extract thickness, etc.
>>
>> In your shell (assuming you are using c shell)
>>
>> # First set variable s to be subject id
>> >> set s = 100306_QD95CU_FS
>>
>> # set freesurfer environmental variable SUBJECTS_DIR to point to where
>> the data is
>> >> setenv SUBJECTS_DIR /share/users/imganalysis/yeolab/data/GSP/
>>
>> # use symbolic link so fsaverage "appears" to be in SUBJECTS_DIR
>> >> ln -s $FREESURFER_HOME/subjects/fsaverage/ $SUBJECTS_DIR/fsaverage
>>
>> # use "-sval-annot" option to transfer annotation
>> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
>> >> --sval-annot
>> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
>> >> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
>>
>> # use "sval" option to transfer confidence map.
>> >> mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh --sval
>> >> $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>> >> --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz
>>
>> Cheers,
>> Thomas
>>
>> On Sat, Sep 19, 2015 at 3:12 PM, Ali Radaideh <ali.radai...@hu.edu.jo>
>> wrote:
>> > Dear FreeSurfer experts,
>> >
>> > I have finished processing a group of brains MR images collected at 7T
>> > scanner using freesurfer 5.3.0 (Ubuntu 64 bits machine).
>> >
>> > However, we need to get the cortical parcellation based on functional
>> > network connectivity. So I have downloaded the Atlas data
>> > (Yeo_JNeurophysiol11_FreeSurfer) to use it for the parcellation but I
>> > have
>> > few questions which I hope you will be able to help me on.
>> >
>> > 1- Do I need to repeat the "recon-all" process?
>> > 2- If yes, how can I change the default Atlas that freesurfer uses?
>> > 3- If no, what can I do to get the cortical parcellation based on
>> > finctional
>> > networks from our processed data?
>> > 4- At the end, shall I use the usual commands to extract the volumes,
>> > thicknesses ...etc?
>> >
>> >
>> > Many thanks for your help in advance.
>> >
>> > Ali
>> >
>> >
>> > --
>> > Ali M. Al-Radaideh. PhD
>> > Head of D

Re: [Freesurfer] question on Cortical Parcellation Estimated by Intrinsic Functional Connectivity

[Thomas Yeo]

Hi Hong Xin,

Yes. fslview will complain. After you install freesurfer. You can use
freeview to display my parcellation and the fsl template. You should
verify that they align perfectly well. So my parcellation and FSL mni
template are in alignment, but the header information are not the
same.

Since the parcellations are released as part of freesurfer, I am
cc-ing the freesurfer list so other users might benefit from your
question.

Cheers,
Thomas

On Sun, Aug 23, 2015 at 10:30 AM, Hong Xin (SBIC)
hong_...@sbic.a-star.edu.sg wrote:
 Thanks you very much for the quick response. We use FSL for processing, which 
 displays the parcellations and template/our images in different orientations 
 and we were not able to overlay them due to the different matrix size. I'll 
 install freesurfer and try mri_vol2vol.
 Thanks again.

 
 From: Thomas Yeo [thomas@nus.edu.sg]
 Sent: Friday, August 21, 2015 5:36 PM
 To: Hong Xin (SBIC)
 Subject: Re: question on Cortical Parcellation Estimated by Intrinsic 
 Functional Connectivity

 Hi Xin,

 Actually, the 256x256x256 and 182x218x182 volumes are already in
 alignment. It's just that their header information are different.
 Therefore you do not need to perform an image registration. I suggest
 you use mri_vol2vol, which is a freesurfer function:

 mri_vol2vol --mov my256x256x256_parcellation.nii.gz --targ
 182x182x182_brain.nii.gz --o output.nii.gz --regheader --interp
 nearest

 The above command should work. Let me know if you have other issues.

 Cheers,
 Thomas

 On Fri, Aug 21, 2015 at 5:32 PM, Hong Xin (SBIC)
 hong_...@sbic.a-star.edu.sg wrote:
 Hi Prof Yeo,



 We would like to apply the cortical parcellations to our study. Our images
 are in the MNI space (matrix size 182x218x182), though the 'parcellations in
 Nonlinear MNI152 Volume Space' match the MNI template (MNI152_T1_1mm_brain),
 the labeled image has a different matrix size (256x256x256) and orientation.
 Since we are not familiar with freesurfer, we wondered if there is a version
 of the parcellations in the MNI space (with same matrix size and
 orientation) available? Or we need to make it by ourselves? If so, could you
 help to check if the following proposed steps are correct: 1. run a rigid
 body transformation, bring FSL_MNI152_FreeSurferConformed_1mm to
 MNI152_T1_1mm_brain. 2. apply the transformation to the labeled images (eg,
 Yeo2011_7Networks_MNI152_FreeSurferConformed1mm).



 Your input is highly appreciated.



 Best,

 Xin

 

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Re: [Freesurfer] assigning 74 Destrieux parcellations into lobes, networks, sensory-motor modalities

[Thomas Yeo]

As mentioned by Chris, (2) and (3) are not super clear cut, but you
can perhaps use my resting-state networks (available in FreeSurfer;
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011)
as a basic reference. Roughly speaking, for the 7-network
parcellation, the blue cluster corresponds to
somatosensory,motor,auditory, while the purple cluster corresponds to
visual. The remaining networks can be considered
association/heteromodal. The cream network can be considered
limbic/paralimbic.

--Thomas


On Fri, Jul 24, 2015 at 12:24 AM, Watson, Christopher
christopher.wat...@childrens.harvard.edu wrote:
 I have tools in R that can do #1, and network/graph theory analysis on top
 of that. I plan to work on things like #2-3 but haven't yet (e.g. there is
 possibly less consensus if region X is limbic vs. para-limbic, as opposed to
 temporal vs. parietal).
 I can send you something in a few days/a week.

 Although, If you read the Destrieux 2010 paper, you will see the regions (in
 the text) separated by lobe, at the least.

 
 From: freesurfer-boun...@nmr.mgh.harvard.edu
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Julie Evans
 [julie.evans.st...@gmail.com]
 Sent: Thursday, July 23, 2015 11:39 AM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: [Freesurfer] assigning 74 Destrieux parcellations into lobes,
 networks, sensory-motor modalities

 Dear FreeSurfer community,

 I am a statistician who knows shamefully little about brain anatomy and I am
 writing with a request.



 I don’t have easy access to Freesurfer and the original data but have the
 final text output i.e., the /stats folder, from a large cohort, which
 including *h.aparc.a2009s.stats.



 I have been attempting to assign higher-order labels to the 74 Destrieux
 parcellations.



 1) Categorizing uniquely into the 4 lobes: frontal, occipital, parietal,
 temporal;



 2) Categorizing uniquely into “types of networks”: limbic, paralimbic,
 unimodal, heteromodal, subcortical, primary;



 3) sensory-motor modality: somatosensory, visual, auditory, motor



 As far as I understand these higher-order assignments of the 74
 parcellations are not uncommon although not all cases are clear-cut so some
 knowledge of anatomy is needed (assuming that I am indeed looking at the
 correct level – gyri and sulci in the aparc.a2009s.stats file).



 If so, would anyone mind sharing a text file with the correspondence between
 the 74 parcellations and lobes, network types, and/or modality?



 I’d be very grateful for any guidance and help.



 Thank you kindly,


 J Evans


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Re: [Freesurfer] Repost: Make liberal ROI masks

[Thomas Yeo]

Hi Martin,

I am a little confused. Can you explain a little more about what you
need? Do you want the freesurfer cortical ROIs dilated into the
surrounding regions like white matter and CSF or something? If so,
then Doug's suggestion sounds reasonable.

In the case of my parcellation, I ran the MNI152 template through
recon-all, which unfortunately resulted in an overly conservative
estimate of gray matter (i.e., the tight mask in
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011).
Therefore I went through a rather complicated way of generating the
liberal mask by registering the recon-all of 1000 subjects to MNI
space.

Since you appear to be working on an individual subject, the
freesurfer estimate of the cortical ROIs is likely to be quite
accurate. Why might you want to dilate them into CSF or white matter?

Regards,
Thomas

On Wed, Jul 15, 2015 at 12:38 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
 There is not an easy way to do that, though Thomas might want to chime
 in. I would probably use the code that generates the wmparc
 (mri_aparc2aseg --labelwm) to create labels in the adjacent WM out to a
 few mm (--wmparc-dmax 2), then merge the WM labels with the GM labels

 On 07/14/2015 08:18 AM, Martin Hebart wrote:
 Dear Freesurfer users,

 I would be really happy if someone could help me out on the issue I
 mentioned below.

 What I want to do is create non-overlapping anatomical ROI masks that
 are not restricted to grey matter only.

 Thanks a lot in advance!
 Martin

 -

 Dear all,

 I've created non-overlapping ROI masks using

 mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader orig.mgz --o
 rois.nii --temp sub.nii --subject 01

 Now these ROI masks are actually quite conservative concerning grey
 matter vs. other structures, i.e. they are only on the grey matter.
 I've seen more liberal masks e.g. here:
 https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011

 I would like to create similarly liberal non-overlapping ROI masks for
 all ROIs in the voxel size defined by the image in --temp, but
 excluding specific tissue types such as white matter, CSF, and other
 non-grey matter tissue. What would be the best way to do so?

 Cheers,
 Martin



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 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

Can you share with us how you resolved the issue, so that other people
who might search the email list for similar issues might benefit?

Thanks,
Thomas

On Mon, May 18, 2015 at 3:39 PM, 陳昱潔 poohann1...@gmail.com wrote:
 Hi Dr. Yeo:

 Thank you very much we already solved the problem!

 Very appreciate for your kindness!

 Best wishes,
 Annie

 2015-05-18 2:16 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:

 Hi Annie,

 I am a little unsure why this might happen. Did you inspect if
 $SUBJECTS_DIR/5204/label/lh.Yeo2011_17Networks_N1000.annot is correct?

 Cheers,
 Thomas

 On Mon, May 18, 2015 at 1:52 PM, 陳昱潔 poohann1...@gmail.com wrote:
  Hi Dr. Yeo :
 
  Thank you very much for helping us a lot!
  I ran the command this below:
  mri_surf2surf --srcsubject fsaverage5 --trgsubject 5204 --hemi lh \
 --sval-annot
  $SUBJECTS_DIR/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot \
 --tval
  $SUBJECTS_DIR/5204/label/lh.Yeo2011_17Networks_N1000.annot
  and after I ran this command:
  mris_anatomical_stats -a
  5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot  -b 5202
  rh
  All turned out
  MRISreadAnnotationIntoArray: vertex index out of range: 892219914
  i=352E320A, in_array_size=153173
  annot file:
  5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
  MRISreadAnnotationIntoArray: vertex index out of range: 892219914
  i=352E320A, in_array_size=153173
  annot file:
  5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
  MRISreadAnnotationIntoArray: vertex index out of range: 892219914
  i=352E320A, in_array_size=153173
  annot file:
  5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
  MRISreadAnnotationIntoArray: vertex index out of range: 892219914
  i=352E320A, in_array_size=153173
  annot file:
  5202/label/rh.Yeo2011_17Networks_N1000.split_components.annot
  MRISreadAnnotationIntoArray: vertex index out of range: 892219914
  i=352E320A, in_array_size=153173
 
  Best wishes,
  Annie
 
  2015-05-15 8:15 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:
 
  Hi Annie,
 
  Can you tell us the exact mri_surf2surf command you use?
 
  Cheers,
  Thomas
 
  On Fri, May 15, 2015 at 5:24 PM, 陳昱潔 poohann1...@gmail.com wrote:
   Hi Dr. Yeo,
  
   Thank you very much for your help! It is the exactly we need!
   Only a little question that when we ran mris_surf2surf
   Something seems wrong , but I can't figure out.
   annot file:
  
  
   /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
   MRISreadAnnotationIntoArray: vertex index out of range: 152420
   i=00A4F8DC,
   in_array_size=10242
   annot file:
  
  
   /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
   MRISreadAnnotationIntoArray: vertex index out of range: 152421
   i=00A4F8DC,
   in_array_size=10242
   annot file:
  
  
   /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
   MRISreadAnnotationIntoArray: vertex index out of range: 152422
   i=00010101,
   in_array_size=10242
   annot file:
  
  
   /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot\
   reading colortable from annotation file...
   colortable with 18 entries read (originally MyColorLUT)
   Reading target surface reg
   /home/annie/test_run_allindex/5204/surf/lh.sphere.reg
   Done
   Mapping Source Volume onto Source Subject Surface
   surf2surf_nnfr: building source hash (res=16).
   Surf2Surf: Forward Loop (160564)
  
   Surf2Surf: Dividing by number of hits (160564)
   INFO: nSrcLost = 0
   nTrg121 = 160564, nTrgMulti = 0, MnTrgMultiHits = 0
   nSrc121 = 0, nSrcLost = 0, nSrcMulti = 10242, MnSrcMultiHits
   =
   15.677
   Saving target data
   Converting to target annot
   Saving to target annot
  
  
   /home/annie/test_run_allindex/5204/label/lh.Yeo2011_17Networks_N1000.annot
  
  
   Sorry for giving such long code. But it seems the vertex number
   didn't
   match.
   Or just something goes wrong while I proceed.
  
   Best,
   Annie
  
   2015-05-14 4:54 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:
  
   Hi Annie,
  
   I have previously extracted individual regions from the 7 and 17
   networks. You can download them here
  
  
  
   (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0).
   Please see the README in the folder for more explanations. There
   should be a precuneus DMN region.
  
   The 17 networks consist of 114 regions that have been previously
   published:
  
   1) Krienen et al., Reconfigurable state-dependent functional
   coupling
   modes cluster around a core functional architecture. Philosophical
   Transactions of the Royal Society B, 369:20130526, 2014
  
   2) Yeo et al., Functional connectivity during rested wakefulness
   predicts vulnerability to sleep deprivation. Neuroimage 111:147-158,
   2015
  
   Hope this helps.
  
   Cheers,
   Thomas
  
   On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 poohann1

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

Can you tell us the exact mri_surf2surf command you use?

Cheers,
Thomas

On Fri, May 15, 2015 at 5:24 PM, 陳昱潔 poohann1...@gmail.com wrote:
 Hi Dr. Yeo,

 Thank you very much for your help! It is the exactly we need!
 Only a little question that when we ran mris_surf2surf
 Something seems wrong , but I can't figure out.
 annot file:
 /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
 MRISreadAnnotationIntoArray: vertex index out of range: 152420 i=00A4F8DC,
 in_array_size=10242
 annot file:
 /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
 MRISreadAnnotationIntoArray: vertex index out of range: 152421 i=00A4F8DC,
 in_array_size=10242
 annot file:
 /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
 MRISreadAnnotationIntoArray: vertex index out of range: 152422 i=00010101,
 in_array_size=10242
 annot file:
 /home/annie/test_run_allindex/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot\
 reading colortable from annotation file...
 colortable with 18 entries read (originally MyColorLUT)
 Reading target surface reg
 /home/annie/test_run_allindex/5204/surf/lh.sphere.reg
 Done
 Mapping Source Volume onto Source Subject Surface
 surf2surf_nnfr: building source hash (res=16).
 Surf2Surf: Forward Loop (160564)

 Surf2Surf: Dividing by number of hits (160564)
 INFO: nSrcLost = 0
 nTrg121 = 160564, nTrgMulti = 0, MnTrgMultiHits = 0
 nSrc121 = 0, nSrcLost = 0, nSrcMulti = 10242, MnSrcMultiHits =
 15.677
 Saving target data
 Converting to target annot
 Saving to target annot
 /home/annie/test_run_allindex/5204/label/lh.Yeo2011_17Networks_N1000.annot


 Sorry for giving such long code. But it seems the vertex number didn't
 match.
 Or just something goes wrong while I proceed.

 Best,
 Annie

 2015-05-14 4:54 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:

 Hi Annie,

 I have previously extracted individual regions from the 7 and 17
 networks. You can download them here

 (https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0).
 Please see the README in the folder for more explanations. There
 should be a precuneus DMN region.

 The 17 networks consist of 114 regions that have been previously
 published:

 1) Krienen et al., Reconfigurable state-dependent functional coupling
 modes cluster around a core functional architecture. Philosophical
 Transactions of the Royal Society B, 369:20130526, 2014

 2) Yeo et al., Functional connectivity during rested wakefulness
 predicts vulnerability to sleep deprivation. Neuroimage 111:147-158,
 2015

 Hope this helps.

 Cheers,
 Thomas

 On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 poohann1...@gmail.com wrote:
  Hello Dr. Yeo,
 
  Thank you for your previous help and reply. We've worked out the way to
  switch the resolution of parcellation and successfully extracted the
  anatomical information using your mask derived from iFC work.
 
  However, we came across a new problem to apply the cortical mask and
  need
  your kind help again. We aim to conduct a seed-based analysis to
  investigate
  structural covariance based on the network defined by iFC, and find your
  work of cortical parcellation conceptually perfectly suit our research
  question. Based on the current approach, however, it seemed that we
  could
  only extract the anatomical information from the whole well-defined
  network,
  but not the specific hub within the network (e.g., the anatomical
  information of the precuneus from the DMN). We wonder if you have any
  suggestion to resolve our problem, ie, to be specific, is there any way
  to
  only extract the discrete hub information rather than the whole network?
 
  We really appreciate your generous help. Thank you very much.
 
  p.s. This email would also forward to my senior colleague, Dr.
  Hsiang-Yuan
  Lin, who is a child and adolescent psychiatrist doing imaging research
  in
  Taiwan.
 
 
  2015-05-13 19:15 GMT+08:00 陳昱潔 poohann1...@gmail.com:
 
  Hi Professor Yeo :
 
  Thank you for helping us so much!
  After mris_anatomical_stat I tried aparcstats2table to extract the
  table.
  But I failed with generating the table.
 
 
  Best wishes,
  Annie
 
  2015-05-12 8:29 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:
 
  Hi Annie,
 
  I assume this means 5202 is your subject ID? Maybe you should check if
 
  /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot
  exist?
 
  If so, you can run mris_anatomical_stats to generate statistics for
  the parcellation.
 
  Cheers,
  Thomas
 
  On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 poohann1...@gmail.com wrote:
   Hi Professor Yeo :
   After I rechecked the directory and run again mri_surf2surf
   I got the result:
   Saving target data
   Converting to target annot
   Saving to target annot
  
  
   /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot
   The file of 5202/label didn't come out with
   lh.Yeo2011_7Networks_N1000

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

I have previously extracted individual regions from the 7 and 17
networks. You can download them here
(https://www.dropbox.com/s/u23nn3ov18tlhfs/Yeo_JNeurophysiol11_SplitLabels.zip?dl=0).
Please see the README in the folder for more explanations. There
should be a precuneus DMN region.

The 17 networks consist of 114 regions that have been previously published:

1) Krienen et al., Reconfigurable state-dependent functional coupling
modes cluster around a core functional architecture. Philosophical
Transactions of the Royal Society B, 369:20130526, 2014

2) Yeo et al., Functional connectivity during rested wakefulness
predicts vulnerability to sleep deprivation. Neuroimage 111:147-158,
2015

Hope this helps.

Cheers,
Thomas

On Thu, May 14, 2015 at 3:08 PM, 陳昱潔 poohann1...@gmail.com wrote:
 Hello Dr. Yeo,

 Thank you for your previous help and reply. We've worked out the way to
 switch the resolution of parcellation and successfully extracted the
 anatomical information using your mask derived from iFC work.

 However, we came across a new problem to apply the cortical mask and need
 your kind help again. We aim to conduct a seed-based analysis to investigate
 structural covariance based on the network defined by iFC, and find your
 work of cortical parcellation conceptually perfectly suit our research
 question. Based on the current approach, however, it seemed that we could
 only extract the anatomical information from the whole well-defined network,
 but not the specific hub within the network (e.g., the anatomical
 information of the precuneus from the DMN). We wonder if you have any
 suggestion to resolve our problem, ie, to be specific, is there any way to
 only extract the discrete hub information rather than the whole network?

 We really appreciate your generous help. Thank you very much.

 p.s. This email would also forward to my senior colleague, Dr. Hsiang-Yuan
 Lin, who is a child and adolescent psychiatrist doing imaging research in
 Taiwan.


 2015-05-13 19:15 GMT+08:00 陳昱潔 poohann1...@gmail.com:

 Hi Professor Yeo :

 Thank you for helping us so much!
 After mris_anatomical_stat I tried aparcstats2table to extract the table.
 But I failed with generating the table.


 Best wishes,
 Annie

 2015-05-12 8:29 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:

 Hi Annie,

 I assume this means 5202 is your subject ID? Maybe you should check if
 /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot
 exist?

 If so, you can run mris_anatomical_stats to generate statistics for
 the parcellation.

 Cheers,
 Thomas

 On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 poohann1...@gmail.com wrote:
  Hi Professor Yeo :
  After I rechecked the directory and run again mri_surf2surf
  I got the result:
  Saving target data
  Converting to target annot
  Saving to target annot
 
  /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot
  The file of 5202/label didn't come out with
  lh.Yeo2011_7Networks_N1000.annot
  But it seems succeed, right?
  How can I get the stat of this parcellation ?
 
  Thank you very much!
 
  Best wishes,
  Annie
 
  2015-05-12 6:06 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:
 
  Hi Annie,
 
  mri_surf2surf is complaining that it cannot write out the annotation.
 
  Just to clarify, is your subject called test_run_allindex? In other
  words, is the variable s equal to test_run_allindex?
 
  Does the directory /home/annie/test_run_allindex/label/ exist? If
  not, then you first need to create the directory first, and then
  mri_surf2surf can write the resulting annotation file into the
  directory.
 
  Cheers,
  Thomas
 
  On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 poohann1...@gmail.com wrote:
   Hi Professor Yeo :
  
  We tried the code
   mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
   --sval-annot
  
  
  
   $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
   --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
   However there came an error of could not write annot file
   /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot
   No such file or directory
   And we checked our individual subject's label there isn't
   lh.Yeo2011_7Networks_N1000.annot
   Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into
   our
   subjects/label first?
   What can we do ?
   Thank you very much!
  
   Best wishes,
   Annie
  
  
   2015-05-05 8:36 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:
  
   Hi Annie,
  
   Please cc the freesurfer list when you reply because there might be
   other people more qualified to answer your question.
  
   Based on what you are saying, I think you can first use
   mri_surf2surf
   (with the sval-annot flag) to transform the 2011 functional
   networks
   .annot file from fsaverage space to the subject's native surface
   space. Type mri_surf2surf --help to see examples.
  
   You can then use mris_anatomical_stats to compute thickness
   statistics

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

mri_surf2surf is complaining that it cannot write out the annotation.

Just to clarify, is your subject called test_run_allindex? In other
words, is the variable s equal to test_run_allindex?

Does the directory /home/annie/test_run_allindex/label/ exist? If
not, then you first need to create the directory first, and then
mri_surf2surf can write the resulting annotation file into the
directory.

Cheers,
Thomas

On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 poohann1...@gmail.com wrote:
 Hi Professor Yeo :

We tried the code
 mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
 --sval-annot

 $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
 --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
 However there came an error of could not write annot file
 /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot
 No such file or directory
 And we checked our individual subject's label there isn't
 lh.Yeo2011_7Networks_N1000.annot
 Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into our
 subjects/label first?
 What can we do ?
 Thank you very much!

 Best wishes,
 Annie


 2015-05-05 8:36 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:

 Hi Annie,

 Please cc the freesurfer list when you reply because there might be
 other people more qualified to answer your question.

 Based on what you are saying, I think you can first use mri_surf2surf
 (with the sval-annot flag) to transform the 2011 functional networks
 .annot file from fsaverage space to the subject's native surface
 space. Type mri_surf2surf --help to see examples.

 You can then use mris_anatomical_stats to compute thickness statistics.

 Cheers,
 Thomas

 On Tue, May 5, 2015 at 3:21 PM, 陳昱潔 poohann1...@gmail.com wrote:
  Dear Pro. Yeo:
 
   Very appreciate for your reply !
 
  We are trying to use your definition of the functional network regions
  to
  re-parcellate our images
  and get the regions of volume or cortical thickness for our study
  interest
  of structural network.
  However, we did not want to re-run the first recon-all again due to it's
  spending to much time.
  And we are still can't find the way to solve this problem.
  Thank you very much for helping us!
 
  Best wishes,
  Annie Chen
 
  2015-05-02 8:25 GMT+08:00 Thomas Yeo ytho...@csail.mit.edu:
 
  Hi Yu-Chieh,
 
  I am cc-ing the freesurfer list who may help you with your issues.
 
  Can you explain what exactly you are trying do? The parcellation is
  released in different resolutions including fsaverage5. Why can't you
  just use the fsaverage5 parcellation?
 
  Cheers,
  Thomas
 
  On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 poohann1...@gmail.com wrote:
   Dear professor Yeo :
  
  My name is Yu-chieh Chen , I am a graduated student from National
   Taiwan
   University of medical school, and my supervisor is professor Susan
   Shur-Fen
   Gau from department of psychiatry, National Taiwan University
   Hospital 
   College of Medicine. We are very interesting about your paper
   published
   in
   2011 which using resting MRI to separate brain regions to functional
   networks. We'd like to use your percellation to re-separate the brain
   regions based on your released data in Freesurfer(
   http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011).
   And
   use
   these volume of brain regions for our study, however, there comes the
   problem that we assumed that we can change the fsaverage into
   fsaverage5,
   thus we may get the new volume of the parcellation_Yeo. But it is not
   work.
   So I send this email for help. Last , I am very appreciate your
   kindness
   and
   very sorry for my inappropriate and rough.
   Thank you very much for read this email and sorry for occupied your
   time.
  
   Best wishes,
   Yu-chieh Chen
  
 
 



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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.

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

I assume this means 5202 is your subject ID? Maybe you should check if
/home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot
exist?

If so, you can run mris_anatomical_stats to generate statistics for
the parcellation.

Cheers,
Thomas

On Tue, May 12, 2015 at 6:29 PM, 陳昱潔 poohann1...@gmail.com wrote:
 Hi Professor Yeo :
 After I rechecked the directory and run again mri_surf2surf
 I got the result:
 Saving target data
 Converting to target annot
 Saving to target annot
 /home/annie/test_run_allindex/5202/label/lh.Yeo2011_7Networks_N1000.annot
 The file of 5202/label didn't come out with lh.Yeo2011_7Networks_N1000.annot
 But it seems succeed, right?
 How can I get the stat of this parcellation ?

 Thank you very much!

 Best wishes,
 Annie

 2015-05-12 6:06 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:

 Hi Annie,

 mri_surf2surf is complaining that it cannot write out the annotation.

 Just to clarify, is your subject called test_run_allindex? In other
 words, is the variable s equal to test_run_allindex?

 Does the directory /home/annie/test_run_allindex/label/ exist? If
 not, then you first need to create the directory first, and then
 mri_surf2surf can write the resulting annotation file into the
 directory.

 Cheers,
 Thomas

 On Tue, May 12, 2015 at 5:46 PM, 陳昱潔 poohann1...@gmail.com wrote:
  Hi Professor Yeo :
 
 We tried the code
  mri_surf2surf --srcsubject fsaverage --trgsubject $s --hemi lh
  --sval-annot
 
 
  $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot
  --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot
  However there came an error of could not write annot file
  /home/annie/test_run_allindex/label/lh.Yeo2011_7Networks_N1000.annot
  No such file or directory
  And we checked our individual subject's label there isn't
  lh.Yeo2011_7Networks_N1000.annot
  Should we generate/import the lh.Yeo2011_7Networks_N1000.annot into our
  subjects/label first?
  What can we do ?
  Thank you very much!
 
  Best wishes,
  Annie
 
 
  2015-05-05 8:36 GMT-04:00 Thomas Yeo ytho...@csail.mit.edu:
 
  Hi Annie,
 
  Please cc the freesurfer list when you reply because there might be
  other people more qualified to answer your question.
 
  Based on what you are saying, I think you can first use mri_surf2surf
  (with the sval-annot flag) to transform the 2011 functional networks
  .annot file from fsaverage space to the subject's native surface
  space. Type mri_surf2surf --help to see examples.
 
  You can then use mris_anatomical_stats to compute thickness statistics.
 
  Cheers,
  Thomas
 
  On Tue, May 5, 2015 at 3:21 PM, 陳昱潔 poohann1...@gmail.com wrote:
   Dear Pro. Yeo:
  
Very appreciate for your reply !
  
   We are trying to use your definition of the functional network
   regions
   to
   re-parcellate our images
   and get the regions of volume or cortical thickness for our study
   interest
   of structural network.
   However, we did not want to re-run the first recon-all again due to
   it's
   spending to much time.
   And we are still can't find the way to solve this problem.
   Thank you very much for helping us!
  
   Best wishes,
   Annie Chen
  
   2015-05-02 8:25 GMT+08:00 Thomas Yeo ytho...@csail.mit.edu:
  
   Hi Yu-Chieh,
  
   I am cc-ing the freesurfer list who may help you with your issues.
  
   Can you explain what exactly you are trying do? The parcellation is
   released in different resolutions including fsaverage5. Why can't
   you
   just use the fsaverage5 parcellation?
  
   Cheers,
   Thomas
  
   On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 poohann1...@gmail.com wrote:
Dear professor Yeo :
   
   My name is Yu-chieh Chen , I am a graduated student from
National
Taiwan
University of medical school, and my supervisor is professor Susan
Shur-Fen
Gau from department of psychiatry, National Taiwan University
Hospital 
College of Medicine. We are very interesting about your paper
published
in
2011 which using resting MRI to separate brain regions to
functional
networks. We'd like to use your percellation to re-separate the
brain
regions based on your released data in Freesurfer(
   
http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011).
And
use
these volume of brain regions for our study, however, there comes
the
problem that we assumed that we can change the fsaverage into
fsaverage5,
thus we may get the new volume of the parcellation_Yeo. But it is
not
work.
So I send this email for help. Last , I am very appreciate your
kindness
and
very sorry for my inappropriate and rough.
Thank you very much for read this email and sorry for occupied
your
time.
   
Best wishes,
Yu-chieh Chen
   
  
  
 
 



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Annie,

Please cc the freesurfer list when you reply because there might be
other people more qualified to answer your question.

Based on what you are saying, I think you can first use mri_surf2surf
(with the sval-annot flag) to transform the 2011 functional networks
.annot file from fsaverage space to the subject's native surface
space. Type mri_surf2surf --help to see examples.

You can then use mris_anatomical_stats to compute thickness statistics.

Cheers,
Thomas

On Tue, May 5, 2015 at 3:21 PM, 陳昱潔 poohann1...@gmail.com wrote:
 Dear Pro. Yeo:

  Very appreciate for your reply !

 We are trying to use your definition of the functional network regions to
 re-parcellate our images
 and get the regions of volume or cortical thickness for our study interest
 of structural network.
 However, we did not want to re-run the first recon-all again due to it's
 spending to much time.
 And we are still can't find the way to solve this problem.
 Thank you very much for helping us!

 Best wishes,
 Annie Chen

 2015-05-02 8:25 GMT+08:00 Thomas Yeo ytho...@csail.mit.edu:

 Hi Yu-Chieh,

 I am cc-ing the freesurfer list who may help you with your issues.

 Can you explain what exactly you are trying do? The parcellation is
 released in different resolutions including fsaverage5. Why can't you
 just use the fsaverage5 parcellation?

 Cheers,
 Thomas

 On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 poohann1...@gmail.com wrote:
  Dear professor Yeo :
 
 My name is Yu-chieh Chen , I am a graduated student from National
  Taiwan
  University of medical school, and my supervisor is professor Susan
  Shur-Fen
  Gau from department of psychiatry, National Taiwan University Hospital 
  College of Medicine. We are very interesting about your paper published
  in
  2011 which using resting MRI to separate brain regions to functional
  networks. We'd like to use your percellation to re-separate the brain
  regions based on your released data in Freesurfer(
  http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). And
  use
  these volume of brain regions for our study, however, there comes the
  problem that we assumed that we can change the fsaverage into
  fsaverage5,
  thus we may get the new volume of the parcellation_Yeo. But it is not
  work.
  So I send this email for help. Last , I am very appreciate your kindness
  and
  very sorry for my inappropriate and rough.
  Thank you very much for read this email and sorry for occupied your
  time.
 
  Best wishes,
  Yu-chieh Chen
 



___
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.

Re: [Freesurfer] Data interest of the CorticalParcellation_Yeo2011

[Thomas Yeo]

Hi Yu-Chieh,

I am cc-ing the freesurfer list who may help you with your issues.

Can you explain what exactly you are trying do? The parcellation is
released in different resolutions including fsaverage5. Why can't you
just use the fsaverage5 parcellation?

Cheers,
Thomas

On Fri, May 1, 2015 at 6:14 PM, 陳昱潔 poohann1...@gmail.com wrote:
 Dear professor Yeo :

My name is Yu-chieh Chen , I am a graduated student from National Taiwan
 University of medical school, and my supervisor is professor Susan Shur-Fen
 Gau from department of psychiatry, National Taiwan University Hospital 
 College of Medicine. We are very interesting about your paper published in
 2011 which using resting MRI to separate brain regions to functional
 networks. We'd like to use your percellation to re-separate the brain
 regions based on your released data in Freesurfer(
 http://ftp.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011). And use
 these volume of brain regions for our study, however, there comes the
 problem that we assumed that we can change the fsaverage into fsaverage5,
 thus we may get the new volume of the parcellation_Yeo. But it is not work.
 So I send this email for help. Last , I am very appreciate your kindness and
 very sorry for my inappropriate and rough.
 Thank you very much for read this email and sorry for occupied your time.

 Best wishes,
 Yu-chieh Chen


___
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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.

Re: [Freesurfer] problem of regist MNI .nifti volume to fsaverage space

[Thomas Yeo]

Hi Amy,

Good point. You can first use mri_vol2vol to upsample to 1mm:

mri_vol2vol --mov yourROIs.nii --targ
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz --regheader --o
yourROIs_1mm.nii --interp nearest

then

mri_vol2surf --mov yourROIs_1mm.nii --mni152reg --hemi rh --surf white
--o rh.ROIs.mgh

You can then visualize with freeview:

freeview -f 
$FREESURFER_HOME/subjects/fsaverage/surf/rh.inflated:overlay=rh.ROIs.mgh

By default it uses a heatmap, so you have to adjust the overlay accordingly.

Cheers,
Thomas

On Mon, Mar 2, 2015 at 7:39 PM, Amy Lin amylin0...@gmail.com wrote:
 hi, of course. The result look strange too. Please see the attached file
 with -mni152reg command and this transformation matrix is not for the 2mm
 resolution image. lets me know if you have any other suggestion. thanks.

 Amy


 On Mon, Mar 2, 2015 at 12:26 PM, Thomas Yeo ytho...@csail.mit.edu wrote:

 Hi Amy,

 Have you tried the --mni152reg flag instead of --reg
 /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat. Is the
 attached picture from your original command or mni152reg flag?

 p.s. Can you please reply all to the freesurfer list?

 Cheers,
 Thomas

 On Mon, Mar 2, 2015 at 6:54 PM, Amy Lin amylin0...@gmail.com wrote:
  Hello Thomas, thanks for the tips but the result still look strange.
  please
  help me to take a look as the attached picture. Another question is how
  to
  adjust the color bar and assign by my define look up table.
 
  This is my command:
 
  amy@ubuntu:~/Downloads$ mri_vol2surf --mov my_MNI_ROIs.nii --reg
  /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --hemi lh
  --inflated --o lh.ROIs.mgh
  srcvol = my_MNI_ROIs.nii
  srcreg = /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat
  srcregold = 0
  srcwarp unspecified
  surf = inflated
  hemi = lh
  reshape = 0
  interp = nearest
  float2int = round
  GetProjMax = 0
  INFO: float2int code = 0
  Done loading volume
  Reading surface
  /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated
  Done reading source surface
  Mapping Source Volume onto Source Subject Surface
   1 0 0 0
  using old
  Done mapping volume to surface
  Number of source voxels hit = 18019
  Writing to lh.ROIs.mgh
  Dim: 163842 1 1
  amy@ubuntu:~/Downloads$ tksurfer fsaverage lh inflated -overlay
  lh.ROIs.mgh
  subject is fsaverage
  hemiis lh
  surface is inflated
  surfer: current subjects dir: /usr/local/freesurfer/subjects
  surfer: not in scripts dir == using cwd for session root
  surfer: session root data dir ($session) set to:
  surfer: /home/amy/Downloads
  checking for nofix files in 'inflated'
  Reading image info (/usr/local/freesurfer/subjects/fsaverage)
  Reading /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz
  surfer: Reading header info from
  /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz
  surfer: vertices=163842, faces=327680
  tkmedit: Trying to open lh.ROIs.dat
  surfer: Interpreting overlay volume lh.ROIs.mgh as encoded scalar
  volume.
  surfer: curvature read: min=-0.673989 max=0.540227
  surfer: single buffered window
  surfer: tkoInitWindow(fsaverage)
  surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl
  Reading /usr/local/freesurfer/tktools/tkm_common.tcl
  Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
  Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
  Reading /usr/local/freesurfer/tktools/tkUtils.tcl
  Successfully parsed tksurfer.tcl
  reading white matter vertex locations...
 
  On Mon, Mar 2, 2015 at 1:15 AM, Thomas Yeo ytho...@csail.mit.edu
  wrote:
 
  Hi Amy,
 
  What exactly is the command you use?
 
  The command should be something like for the right hemisphere:
  mri_vol2surf --mov youROIs.nii.gz --mni152reg --hemi rh --surf
  inflated --o rh.ROIs.mgh
 
  You need to repeat for the left hemisphere. I am cc-ing the freesurfer
  list to keep our conversation on the list.
 
  Cheers,
  Thomas
 
 
  On Mon, Mar 2, 2015 at 3:38 AM, Amy Lin amylin0...@gmail.com wrote:
   hi, thanks for reply the email. i use command mri_vol2surf try to map
   my
   define ROI (.nii) to inflated brain. the command work but not so good
   in
   my
   case.  My question is how to generate the inflated brain similar as
   the
   attached picture with my define ROIs.
  
   Amy
  
   On Feb 28, 2015 1:02 AM, Thomas Yeo thomas@nus.edu.sg wrote:
  
   Hi Amy,
  
   I am confused. Are you trying to run recon-all? From what you said,
   you have some ROIs in MNI space, which you want to map to fsaverage
   space?
  
   p.s. Can you post your question to the freesurfer list instead of
   directly emailing me?
  
   Cheers,
   Thomas
  
   On Sat, Feb 28, 2015 at 12:02 AM, Amy Lin amylin0...@gmail.com
   wrote:
Hello Thomas,
   
I have one quick question for the registration issue from the MNI
volume
to
the freesurfer fsaverage sphere and inflated space. I can not
generate
the
correct .gcs or the .annot file from the my MNI .nifti file

Re: [Freesurfer] problem of regist MNI .nifti volume to fsaverage space

[Thomas Yeo]

Hi Amy,

Have you tried the --mni152reg flag instead of --reg
/usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat. Is the
attached picture from your original command or mni152reg flag?

p.s. Can you please reply all to the freesurfer list?

Cheers,
Thomas

On Mon, Mar 2, 2015 at 6:54 PM, Amy Lin amylin0...@gmail.com wrote:
 Hello Thomas, thanks for the tips but the result still look strange. please
 help me to take a look as the attached picture. Another question is how to
 adjust the color bar and assign by my define look up table.

 This is my command:

 amy@ubuntu:~/Downloads$ mri_vol2surf --mov my_MNI_ROIs.nii --reg
 /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --hemi lh
 --inflated --o lh.ROIs.mgh
 srcvol = my_MNI_ROIs.nii
 srcreg = /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat
 srcregold = 0
 srcwarp unspecified
 surf = inflated
 hemi = lh
 reshape = 0
 interp = nearest
 float2int = round
 GetProjMax = 0
 INFO: float2int code = 0
 Done loading volume
 Reading surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated
 Done reading source surface
 Mapping Source Volume onto Source Subject Surface
  1 0 0 0
 using old
 Done mapping volume to surface
 Number of source voxels hit = 18019
 Writing to lh.ROIs.mgh
 Dim: 163842 1 1
 amy@ubuntu:~/Downloads$ tksurfer fsaverage lh inflated -overlay lh.ROIs.mgh
 subject is fsaverage
 hemiis lh
 surface is inflated
 surfer: current subjects dir: /usr/local/freesurfer/subjects
 surfer: not in scripts dir == using cwd for session root
 surfer: session root data dir ($session) set to:
 surfer: /home/amy/Downloads
 checking for nofix files in 'inflated'
 Reading image info (/usr/local/freesurfer/subjects/fsaverage)
 Reading /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz
 surfer: Reading header info from
 /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz
 surfer: vertices=163842, faces=327680
 tkmedit: Trying to open lh.ROIs.dat
 surfer: Interpreting overlay volume lh.ROIs.mgh as encoded scalar volume.
 surfer: curvature read: min=-0.673989 max=0.540227
 surfer: single buffered window
 surfer: tkoInitWindow(fsaverage)
 surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl
 Reading /usr/local/freesurfer/tktools/tkm_common.tcl
 Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
 Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
 Reading /usr/local/freesurfer/tktools/tkUtils.tcl
 Successfully parsed tksurfer.tcl
 reading white matter vertex locations...

 On Mon, Mar 2, 2015 at 1:15 AM, Thomas Yeo ytho...@csail.mit.edu wrote:

 Hi Amy,

 What exactly is the command you use?

 The command should be something like for the right hemisphere:
 mri_vol2surf --mov youROIs.nii.gz --mni152reg --hemi rh --surf
 inflated --o rh.ROIs.mgh

 You need to repeat for the left hemisphere. I am cc-ing the freesurfer
 list to keep our conversation on the list.

 Cheers,
 Thomas


 On Mon, Mar 2, 2015 at 3:38 AM, Amy Lin amylin0...@gmail.com wrote:
  hi, thanks for reply the email. i use command mri_vol2surf try to map my
  define ROI (.nii) to inflated brain. the command work but not so good in
  my
  case.  My question is how to generate the inflated brain similar as the
  attached picture with my define ROIs.
 
  Amy
 
  On Feb 28, 2015 1:02 AM, Thomas Yeo thomas@nus.edu.sg wrote:
 
  Hi Amy,
 
  I am confused. Are you trying to run recon-all? From what you said,
  you have some ROIs in MNI space, which you want to map to fsaverage
  space?
 
  p.s. Can you post your question to the freesurfer list instead of
  directly emailing me?
 
  Cheers,
  Thomas
 
  On Sat, Feb 28, 2015 at 12:02 AM, Amy Lin amylin0...@gmail.com wrote:
   Hello Thomas,
  
   I have one quick question for the registration issue from the MNI
   volume
   to
   the freesurfer fsaverage sphere and inflated space. I can not
   generate
   the
   correct .gcs or the .annot file from the my MNI .nifti file .
  
   -MNI volume contain several ROIs (see the attached file and the
   follows
   link
   (https://www.dropbox.com/s/f84tm4rwuovyr8p/my_MNI_ROIs.nii?dl=0)
  
   Do you have any tips for this?
   Thanks for the time.
  
   Best,
   Amy Lin
  
  


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Re: [Freesurfer] resampling method to transform EPI vol to surf

[Thomas Yeo]

Hi Ri,

The command you provide just register (align) the EPI data with the T1
image. It doesn't actually tell us how you sample your data onto the
surface. Presumably you must have used mri_vol2surf (at least
implicitly) to use the resultant registration to sample your data onto
the surface. What is the exact command you use?

Cheers,
Thomas


On Tue, Dec 23, 2014 at 7:26 PM, Ritobrato Datta
rida...@mail.med.upenn.edu wrote:
 Hi All,

 For a reviewer, I need the following ASAP:

 Comments from Reviewer: Please provide a brief description of the resampling 
 method by which volume data were transformed to surface data. Was the data 
 averaged between the white and pial boundaries? Or was a constant normal 
 average taken?

 I used bbregister as follows to register the epi image to freesurfer anatomy

 bbregister --s $Subject --bold --mov Functional-FS.nii --init-fsl --reg 
 FS-register.dat

 Can someone comment on the resampling method as the reviewer asked ?

 Thanks

 Ri
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Re: [Freesurfer] Resample the surface mesh

[Thomas Yeo]

Hi Ting,

What I usually do is to project my functional data to fsaverage space
and then smooth and downsample to whatever resolution I want. There
are different fsaverage resolution meshes, like fsaverage5 (~20k
vertices) and fsaverage6 (~80k vertices). This can be achieved using
standard freesurfer tools like mri_vol2surf and mri_surf2surf. Note
that in this scenario, even though the data is in fsaverage space,
this does not preclude individual subject analysis. The advantage of
the above approach is that we can still easily perform a group
analysis if we want to in the future.

The disadvantage is that we lose a little bit of the subject's native
cortical geometry, which is not an issue for your proposed approach.
However, I am not aware of freesurfer tools that will let you
downsample an arbitrary mesh. Perhaps someone who is more intimately
aware of freesurfer's tools can jump in on this.

Cheers,
Thomas

On Mon, Nov 24, 2014 at 5:10 AM, ting xu xutin...@gmail.com wrote:
 Hi Thomas,

 I want to analyze the data in native surface space. The functional volume
 data could be register to native surface with bbregister, however, the
 resolution of the native surface is quite high, too much nodes for
 computational capacity to me. Any ideas?

 Thanks,

 Ting


 On Fri, Nov 21, 2014 at 10:37 PM, Thomas Yeo ytho...@csail.mit.edu wrote:

 Hi Ting,

 I am not an expert, but why do you want to downsample the native
 surface mesh? The usual way of doing this is to register the full
 surface mesh with the functional volume data using Doug's bbregister.

 Cheers,
 Thomas

 On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutin...@gmail.com wrote:
  Dear freesurfer experts,
 
  Is there any way to down resample the native surface mesh and register
  the
  functional volume data to the down resampled surface in freesurfer?
 
  Many thanks,
 
  Ting
 
 
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Re: [Freesurfer] Resample the surface mesh

[Thomas Yeo]

Hi Ting,

I am not an expert, but why do you want to downsample the native
surface mesh? The usual way of doing this is to register the full
surface mesh with the functional volume data using Doug's bbregister.

Cheers,
Thomas

On Fri, Nov 21, 2014 at 4:08 AM, ting xu xutin...@gmail.com wrote:
 Dear freesurfer experts,

 Is there any way to down resample the native surface mesh and register the
 functional volume data to the down resampled surface in freesurfer?

 Many thanks,

 Ting


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[Freesurfer] Postdoctoral Fellow in Analysis of Cross-Species fMRI and/or Neurophysiology

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc to develop novel tools for fMRI and/or
neurophysiology analysis. Details below.

Cheers,
Thomas

Project: Develop computational tools for discovering (1) homologies
and divergences between macaque and human brain organization using
resting-fMRI and/or (2) relationship between macaque brain network
organization revealed by fMRI versus neurophysiological recordings.

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (thomas@nus.edu.sg) with your CV.

Deadline: Whenever the position is filled.
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[Freesurfer] Postdoctoral Fellow in Human-Macaque Brain Network Organization

[Thomas Yeo]

Dear All,

I am looking to hire a postdoc in human-macaque brain organization.
Details below.

Cheers,
Thomas

Project: (1) Discover homologies and divergences between macaque and
human brain organization using resting-fMRI and/or (2) Elucidate
relationship between macaque brain network organization revealed by
fMRI versus neurophysiological recordings.

Requirements: PhD in neuroscience, psychology, cognitive science or
related fields. The successful applicant will work with an
interdisciplinary team of computer scientists and neuroscientists, and
must be willing to do some programming.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: The National University of Singapore (NUS) boasts one of
the few primate neurophysiology labs in the world. Perform
ground-breaking research at NUS, while enjoying the beautiful
sceneries and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world 
(http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (thomas@nus.edu.sg) with your CV.

Deadline: Whenever the position is filled.
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[Freesurfer] Brainmap Ontology

[Thomas Yeo]

Dear FreeSurfer List,

I like to introduce you to a new set of reference brain networks
(cognitive components) estimated from 10,449 experiments and 83
behavioral tasks from the BrainMap database, which can be downloaded
here: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainmapOntology_Yeo2015.
The networks will be incorporated in some future version of
FreeSurfer.

Since these networks are estimated from (meta-analytic) task data,
they are meant to complement (not replace) the current resting-state
networks in FreeSurfer
(https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011)

Cheers,
Thomas
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