[Contact]: ribbon.mgz

[johnerichards]

I have followed the pipeline on https://prime-re.github.io/structural/surfaces_and_flatmaps_notebook/Surfaces_and_Flatmaps.html. It was extremely helpful, thanks.

I am trying to create the gm ribbon on a subject, and the thickness. I used the makesurf to vol, and it asks for the ribbon.mgz. However, the ribbon was not created in the pipeline. Is there a "simple" way to create the ribbon? The code is below

Thanks, John

mri_surf2vol --subject fsSurf --o thickness-in-volume.nii.gz --so lh.white lh.thickness --so rh.white rh.thickness
Loading /work/jerlab/JERLab_MRI/S16001//fsSurf/mri/ribbon.mgz
error: mghRead(/work/jerlab/JERLab_MRI/S16001//fsSurf/mri/ribbon.mgz, -1): could not open file

[pcklink]

Hi John, I do not know from the top of my head, but I'd start with looking at the detailed table of (sub)procedures that are normally hidden in the recon-all pipeline for Freesurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. It specifies where and how certain outputs are generated. Hopefully it will put you on track to getting the robbon.mgz file.

[johnerichards]

Thanks Sent via the Samsung Galaxy S20+ 5G, an AT&T 5G smartphone Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Chris Klink ***@***.***> Sent: Sunday, January 2, 2022 5:06:52 PM To: PRIME-RE/prime-re.github.io ***@***.***> Cc: Richards, John ***@***.***>; Author ***@***.***> Subject: Re: [PRIME-RE/prime-re.github.io] [Contact]: ribbon.mgz (Issue #60) Hi John, I do not know from the top of my head, but I'd start with looking at the detailed table of (sub)procedures that are normally hidden in the recon-all pipeline for Freesurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-01678d8a56fbc1b8&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable>. It specifies where and how certain outputs are generated. Hopefully it will put you on track to getting the robbon.mgz file. — Reply to this email directly, view it on GitHub<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-5b2e1c12f6e53a49&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fgithub.com%2FPRIME-RE%2Fprime-re.github.io%2Fissues%2F60%23issuecomment-1003782738>, or unsubscribe<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-d839cf96d76439a5&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FANUC5LNVHINKGRGBEMBPKW3UUDD7ZANCNFSM5LEDQ5IQ>. Triage notifications on the go with GitHub Mobile for iOS<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-7045840aacf1c8ac&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675> or Android<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-ddc2c2d26099be72&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[johnerichards]

So.... The procedure for the ribbon requires the aseg.mgz. This is a segmented "subcortical" ROI + cortex + ... To get this it is required to go through several of the steps, most which require the Talairach registration to the MNI. I'm pretty sure this will not work with macaques, especially infant macaques. The procedure in FS to do sphere-to-sphere registration requires not only aseg but aparc. Both of these require good registration to the MNI, not possible with macaque? I would think that sphere-to-sphere registration would be the rationale for the macaque surface piplines, and/or/ thickness or the ribbon. But none of these can be done in FS without aseg. Any thoughts on this? John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: ***@***.******@***.***> https://jerlab.sc.edu ************************************************* From: Richards, John ***@***.***> Sent: Sunday, January 2, 2022 5:58 PM To: PRIME-RE/prime-re.github.io ***@***.***>; PRIME-RE/prime-re.github.io ***@***.***> Cc: Author ***@***.***> Subject: Re: [PRIME-RE/prime-re.github.io] [Contact]: ribbon.mgz (Issue #60) Thanks Sent via the Samsung Galaxy S20+ 5G, an AT&T 5G smartphone Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Chris Klink ***@***.******@***.***>> Sent: Sunday, January 2, 2022 5:06:52 PM To: PRIME-RE/prime-re.github.io ***@***.******@***.***>> Cc: Richards, John ***@***.******@***.***>>; Author ***@***.******@***.***>> Subject: Re: [PRIME-RE/prime-re.github.io] [Contact]: ribbon.mgz (Issue #60) Hi John, I do not know from the top of my head, but I'd start with looking at the detailed table of (sub)procedures that are normally hidden in the recon-all pipeline for Freesurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-01678d8a56fbc1b8&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReconAllDevTable>. It specifies where and how certain outputs are generated. Hopefully it will put you on track to getting the robbon.mgz file. - Reply to this email directly, view it on GitHub<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-5b2e1c12f6e53a49&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fgithub.com%2FPRIME-RE%2Fprime-re.github.io%2Fissues%2F60%23issuecomment-1003782738>, or unsubscribe<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-d839cf96d76439a5&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FANUC5LNVHINKGRGBEMBPKW3UUDD7ZANCNFSM5LEDQ5IQ>. Triage notifications on the go with GitHub Mobile for iOS<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-7045840aacf1c8ac&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675> or Android<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-ddc2c2d26099be72&q=1&e=20f0f682-bef3-477c-905b-8622f58d361f&u=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[pcklink]

Hm, that sounds like a typical 'not-a-human-brain' problem indeed. I created the NHP-Freesurfer for surface visualisation and never used these steps. Perhaps the precon-all (https://github.com/neurabenn/precon_all) or PREEMACS (https://github.com/pGarciaS/PREEMACS) pipelines could be helpful?

[johnerichards]

Thanks. I’ll look into those. I’m also looking at the afni surface registration, which could aid in the surface-to-surface registration issue. Not sure about the ribbon. John *********************************************** John E. Richards Carolina Distinguished Professor Department of Psychology University of South Carolina Columbia, SC 29208 Dept Phone: 803 777 2079 Fax: 803 777 9558 Email: ***@***.******@***.***> https://jerlab.sc.edu ************************************************* From: Chris Klink ***@***.***> Sent: Monday, January 3, 2022 10:53 AM To: PRIME-RE/prime-re.github.io ***@***.***> Cc: Richards, John ***@***.***>; Author ***@***.***> Subject: Re: [PRIME-RE/prime-re.github.io] [Contact]: ribbon.mgz (Issue #60) Hm, that sounds like a typical 'not-a-human-brain' problem indeed. I created the NHP-Freesurfer for surface visualisation and never used these steps. Perhaps the precon-all (https://github.com/neurabenn/precon_all<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-1f44bd93c3bd4472&q=1&e=4bdd2487-ce60-4b4a-a7f7-c5df2bd7f899&u=https%3A%2F%2Fgithub.com%2Fneurabenn%2Fprecon_all>) or PREEMACS (https://github.com/pGarciaS/PREEMACS<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-dd85563156b7d6d4&q=1&e=4bdd2487-ce60-4b4a-a7f7-c5df2bd7f899&u=https%3A%2F%2Fgithub.com%2FpGarciaS%2FPREEMACS>) pipelines could be helpful? — Reply to this email directly, view it on GitHub<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-483955fcbe8e523a&q=1&e=4bdd2487-ce60-4b4a-a7f7-c5df2bd7f899&u=https%3A%2F%2Fgithub.com%2FPRIME-RE%2Fprime-re.github.io%2Fissues%2F60%23issuecomment-1004184340>, or unsubscribe<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-49f19c115d93872d&q=1&e=4bdd2487-ce60-4b4a-a7f7-c5df2bd7f899&u=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FANUC5LK7FVVHYCA3WWWHWOTUUHA6JANCNFSM5LEDQ5IQ>. Triage notifications on the go with GitHub Mobile for iOS<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-7045840aacf1c8ac&q=1&e=4bdd2487-ce60-4b4a-a7f7-c5df2bd7f899&u=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675> or Android<https://protect2.fireeye.com/v1/url?k=31323334-501d2dca-31327df5-454455534531-ddc2c2d26099be72&q=1&e=4bdd2487-ce60-4b4a-a7f7-c5df2bd7f899&u=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.******@***.***>>

[pcklink]

I find the AFNI developers extremely responsive and helpful, so that might be a good route.