Cerebellum Segementation

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A.R. Sekar

14 May 2021 14 May '21

10:35 a.m.

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Hello Experts!

This is the first time I am doing tractography and my aim is to do it specifically for the cerebellum. I saw online that FreeSurfurer can segment the cerebellum, to create the ROI but I’m not entirely sure how to go about this. So far I have done the pre-processing, co-registration onto diffusion space and created FOD. It would be great if you could give me advice and any feedback about the pipeline.

Thanks for your help!

Regards, Akila

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Zollei, Lilla,Ph.D.

14 May 14 May

11:44 a.m.

Hi Akila, Have you run recon_all on your structural data? Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Friday, May 14, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cerebellum Segementation

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Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

12:13 p.m.

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Hey,

Thanks for your message. Yes I have!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@MGH.HARVARD.EDU Date: Friday, 14 May 2021 at 16:44 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation Hi Akila, Have you run recon_all on your structural data? Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Friday, May 14, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cerebellum Segementation

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Hello Experts!

Thanks for your help!

Regards,

Akila

Zollei, Lilla,Ph.D.

16 May 16 May

12:22 a.m.

Is your question then how to isolate the cerebellar WM/GM labels from aseg? Lila ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Friday, May 14, 2021 12:13 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Friday, May 14, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cerebellum Segementation

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Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

4:34 a.m.

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Hi Lilla,

That would be ideal!

Thanks

Akila

Get Outlook for iOShttps://secure-web.cisco.com/1cP38p3NqbaspVGxxeEr4rhQGxZJ8gpVNyuSJ6DTK4iNVFYJTbU3DX-Dp-UOJfR9rPfk9x5OIa2nOqZn-IehgsL7vBNsYlBs6xsZhWHJoueKg6-gthg033xmWkAHQ85F1RO-OPRwb32nNFYDNJpatSX3s90fjR6TPAjpfdDtn_1S_H3zWayg0NK_fKnVRNzsVCb9Dl0PC_R8FMvQNsor0DzMnfM6QSIB2FuP5gC7Cb8Qet9BZq3gA5o81ESrWP80eRG5cGbv309lilbk9cPFM_w/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Sent: Sunday, May 16, 2021 5:22:08 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

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Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

Zollei, Lilla,Ph.D.

5:23 p.m.

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 4:34 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

That would be ideal!

Thanks

Akila

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

5:37 p.m.

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards, Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@MGH.HARVARD.EDU Date: Sunday, 16 May 2021 at 22:25 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

External Email - Use Caution

External Email - Use Caution Hi Lilla,

That would be ideal!

Thanks

Akila

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

5:41 p.m.

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

Get Outlook for iOShttps://secure-web.cisco.com/147PXKkFY6kebtynYSivzZJLuEDgG0lD53ixLapqXi0ddfjq_-5ccN6Kg5Wwbh15wUijedAouXUMgGYryi4GHuciIvz68lHI1JoaAryp25P5kc0NwjRirPjUBwXey23W6cB3O3nUbpamWt3Y6DtncsUND9EObf74KTxYhBSOafqKtk8eu4pugY6OP0PlcFad1dZ-raNEpBJXFiFy2B1pAqqZ2_ctY8SO8pNA4cnh38yGH7-J_z-1QoQ9NNgFUWqI7p4HVyTHhyEJ3Na_bEv3TDw/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 10:37:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 4:34 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@mgh.harvard.edu Sent: Sunday, May 16, 2021 5:22:08 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Friday, May 14, 2021 12:13 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

Zollei, Lilla,Ph.D.

5:49 p.m.

Yes, you can use that one as well. Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 5:41 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

5:53 p.m.

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Get Outlook for iOShttps://secure-web.cisco.com/1gqN3EUycQThQVGuEVVLF26HprGoX4yNvtzkB7mw66mArVWqe1ua47g4eK6B2ZnKZ78e3qDdGU2KBt2rnm5gXHyuA7KwCMae-5WV4Dll9B8G1aMcJceC1Bwtd6_JsxXHKf1x2rHHgx04v5i02K7SZ3weUKjlhLLnKj6LTiz91ZRV0e6ii4Cz8Ns9Ht61DrxIi55Rto1bA6VBLaeMT8WN1cd5Pylob6TDmz5o79f3Ln2M7U2HHiY_UjrRlO_nO0sL26L_-mEtR_7gjouG9l8_Ihg/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@MGH.HARVARD.EDU Sent: Sunday, May 16, 2021 10:49:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

7:05 p.m.

External Email - Use Caution

I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards, Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Date: Sunday, 16 May 2021 at 22:54 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

External Email - Use Caution

External Email - Use Caution Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

Zollei, Lilla,Ph.D.

17 May 17 May

11:52 p.m.

Hi Sekar,

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 7:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@MGH.HARVARD.EDU Sent: Sunday, May 16, 2021 10:49:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

Yes, you can use that one as well.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 5:41 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 10:37:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

18 May 18 May

4:02 a.m.

External Email - Use Caution

Hi Lilla,

Thanks for your message, even if I put one label I am still getting the same error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

@: Expression Syntax.

Thanks for your help!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@MGH.HARVARD.EDU Date: Tuesday, 18 May 2021 at 04:55 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation Hi Sekar,

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 7:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

Yes, you can use that one as well.

Lilla

________________________________

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

5:56 a.m.

External Email - Use Caution

Hi Lilla,

I completed the process and got my 4 ROI files: Is there a way I can quality check the ROIs and just to see if the files are correct?

Akilas-MacBook-Air:SB301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 47 Input file: aparc+aseg.mgz Output prefix: aparc+aseg_labels mri_convert aparc+aseg.mgz aparc+aseg.nii.gz reading from aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to aparc+aseg.nii.gz... Label of interest: 47 Number of voxels and volume for label 47 is = (40673, 40673.000000mm^3) mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

7.1.1 cwd /Users/akilasekar/Desktop/SB301001 cmdline mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz sysname Darwin hostname Akilas-MacBook-Air.local machine x86_64 user akilasekar

input aparc+aseg.nii.gz frame 0 nErode3d 0 nErode2d 0 output aparc+aseg_labels_label47.mgz Binarizing based on matching values nMatch 1 0 47 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 40673 values in range Counting number of voxels in first frame Found 40672 voxels in final mask Count: 40672 40672.000000 16777216 0.242424 mri_binarize done Akilas-MacBook-Air:SB301001 akilasekar$

Thanks!

Regards, Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Date: Tuesday, 18 May 2021 at 09:04 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution Hi Lilla,

Thanks for your message, even if I put one label I am still getting the same error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

@: Expression Syntax.

Thanks for your help!

Akila

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 7:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

Yes, you can use that one as well.

Lilla

________________________________

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

Zollei, Lilla,Ph.D.

9:43 a.m.

You can use freeview and overlay them over norm.mgz Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Tuesday, May 18, 2021 5:56 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Hi Lilla,

I completed the process and got my 4 ROI files:

Is there a way I can quality check the ROIs and just to see if the files are correct?

Akilas-MacBook-Air:SB301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 47

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 47

Number of voxels and volume for label 47 is = (40673, 40673.000000mm^3)

mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

7.1.1

cwd /Users/akilasekar/Desktop/SB301001

cmdline mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

sysname Darwin

hostname Akilas-MacBook-Air.local

machine x86_64

user akilasekar

input aparc+aseg.nii.gz

frame 0

nErode3d 0

nErode2d 0

output aparc+aseg_labels_label47.mgz

Binarizing based on matching values

nMatch 1

0 47

binval 1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 40673 values in range

Counting number of voxels in first frame

Found 40672 voxels in final mask

Count: 40672 40672.000000 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$

Thanks!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks for your message, even if I put one label I am still getting the same error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

@: Expression Syntax.

Thanks for your help!

Akila

Hi Sekar,

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Sunday, May 16, 2021 7:05 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

Yes, you can use that one as well.

Lilla

________________________________

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

12:57 p.m.

External Email - Use Caution

Hi Lilla,

Thanks for your help, sorry to be asking so many questions! I’m not entirely sure what the norm.mgz file is? Is this one of the output files from the recon-all?

Secondly, do I use the load DTI function in Freeview?

Thanks! Akila From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@MGH.HARVARD.EDU Date: Tuesday, 18 May 2021 at 14:45 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation You can use freeview and overlay them over norm.mgz Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Tuesday, May 18, 2021 5:56 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Hi Lilla,

I completed the process and got my 4 ROI files:

Is there a way I can quality check the ROIs and just to see if the files are correct?

Akilas-MacBook-Air:SB301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 47

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 47

Number of voxels and volume for label 47 is = (40673, 40673.000000mm^3)

mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

7.1.1

cwd /Users/akilasekar/Desktop/SB301001

cmdline mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

sysname Darwin

hostname Akilas-MacBook-Air.local

machine x86_64

user akilasekar

input aparc+aseg.nii.gz

frame 0

nErode3d 0

nErode2d 0

output aparc+aseg_labels_label47.mgz

Binarizing based on matching values

nMatch 1

0 47

binval 1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 40673 values in range

Counting number of voxels in first frame

Found 40672 voxels in final mask

Count: 40672 40672.000000 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$

Thanks!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks for your message, even if I put one label I am still getting the same error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

@: Expression Syntax.

Thanks for your help!

Akila

Hi Sekar,

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla

________________________________

External Email - Use Caution

I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

Yes, you can use that one as well.

Lilla

________________________________

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

19 May 19 May

7:11 a.m.

External Email - Use Caution

Hello,

Just a follow up question: can I run the isolate function on 1. Co-registered nii files? Or do they have to be mgz files?

Thanks!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Date: Tuesday, 18 May 2021 at 17:58 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution Hi Lilla,

Thanks for your help, sorry to be asking so many questions! I’m not entirely sure what the norm.mgz file is? Is this one of the output files from the recon-all?

Secondly, do I use the load DTI function in Freeview?

External Email - Use Caution

Hi Lilla,

I completed the process and got my 4 ROI files:

Is there a way I can quality check the ROIs and just to see if the files are correct?

Akilas-MacBook-Air:SB301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 47

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 47

Number of voxels and volume for label 47 is = (40673, 40673.000000mm^3)

mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

7.1.1

cwd /Users/akilasekar/Desktop/SB301001

cmdline mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

sysname Darwin

hostname Akilas-MacBook-Air.local

machine x86_64

user akilasekar

input aparc+aseg.nii.gz

frame 0

nErode3d 0

nErode2d 0

output aparc+aseg_labels_label47.mgz

Binarizing based on matching values

nMatch 1

0 47

binval 1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 40673 values in range

Counting number of voxels in first frame

Found 40672 voxels in final mask

Count: 40672 40672.000000 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$

Thanks!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks for your message, even if I put one label I am still getting the same error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

@: Expression Syntax.

Thanks for your help!

Akila

Hi Sekar,

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla

________________________________

External Email - Use Caution

I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

Yes, you can use that one as well.

Lilla

________________________________

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

Fischl, Bruce

10:56 a.m.

All of our binaries read any of our supported formats, so that should be fine as like as the direction cosines are correct

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of A.R. Sekar Sent: Wednesday, May 19, 2021 7:12 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

External Email - Use Caution Hello,

Just a follow up question: can I run the isolate function on 1. Co-registered nii files? Or do they have to be mgz files?

Thanks!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Date: Tuesday, 18 May 2021 at 17:58 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution Hi Lilla,

Thanks for your help, sorry to be asking so many questions! I'm not entirely sure what the norm.mgz file is? Is this one of the output files from the recon-all?

Secondly, do I use the load DTI function in Freeview?

Thanks! Akila From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Date: Tuesday, 18 May 2021 at 14:45 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation You can use freeview and overlay them over norm.mgz Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Tuesday, May 18, 2021 5:56 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

I completed the process and got my 4 ROI files:

Is there a way I can quality check the ROIs and just to see if the files are correct?

Akilas-MacBook-Air:SB301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 47

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 47

Number of voxels and volume for label 47 is = (40673, 40673.000000mm^3)

mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

7.1.1

cwd /Users/akilasekar/Desktop/SB301001

cmdline mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

sysname Darwin

hostname Akilas-MacBook-Air.local

machine x86_64

user akilasekar

input aparc+aseg.nii.gz

frame 0

nErode3d 0

nErode2d 0

output aparc+aseg_labels_label47.mgz

Binarizing based on matching values

nMatch 1

0 47

binval 1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 40673 values in range

Counting number of voxels in first frame

Found 40672 voxels in final mask

Count: 40672 40672.000000 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$

Thanks!

Regards,

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Date: Tuesday, 18 May 2021 at 09:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

Thanks for your message, even if I put one label I am still getting the same error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

@: Expression Syntax.

Thanks for your help!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Date: Tuesday, 18 May 2021 at 04:55 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

Hi Sekar,

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Sunday, May 16, 2021 7:05 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Date: Sunday, 16 May 2021 at 22:54 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Sent: Sunday, May 16, 2021 10:49:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

Yes, you can use that one as well.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Sunday, May 16, 2021 5:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Sunday, May 16, 2021 10:37:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Date: Sunday, 16 May 2021 at 22:25 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Sunday, May 16, 2021 4:34 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu> Sent: Sunday, May 16, 2021 5:22:08 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Friday, May 14, 2021 12:13 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hey,

Thanks for your message. Yes I have!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Date: Friday, 14 May 2021 at 16:44 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Friday, May 14, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Cerebellum Segementation

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Hello Experts!

This is the first time I am doing tractography and my aim is to do it specifically for the cerebellum. I saw online that FreeSurfurer can segment the cerebellum, to create the ROI but I'm not entirely sure how to go about this. So far I have done the pre-processing, co-registration onto diffusion space and created FOD. It would be great if you could give me advice and any feedback about the pipeline.

Thanks for your help!

Regards,

Akila

A.R. Sekar

11 a.m.

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Thanks a lot for your help!

Get Outlook for iOShttps://secure-web.cisco.com/1x46MFro4vLJ3DVuLFKn6_WMVcQch2a_JjAncVJCQbEYtCkEQ8o6e5mGARFx3oU_eSBvaEMJV8bG0BbAWcOmpf6whnM1j44bfDB2ozMZ3BuJ_Pl8UhnQDPukOItPHYFkbAIhuBXvOK1elVks0Q0z41Mh3Fiz0mki3ILUybhJAry2jxQoO6Afc3EsSvzrEVCLfiTlDk_ZAWhQHhVtfLkm7eYuakl2_NN1jfiV8EfhY-j2PfRsvD2_j27EptLifQ9wXmvKeyn1g1h1-us_olhIbqw/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@MGH.HARVARD.EDU Sent: Wednesday, May 19, 2021 3:56:58 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

All of our binaries read any of our supported formats, so that should be fine as like as the direction cosines are correct

Cheers

Bruce

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Hello,

Just a follow up question: can I run the isolate function on 1. Co-registered nii files? Or do they have to be mgz files?

Thanks!

Akila

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Hi Lilla,

Thanks for your help, sorry to be asking so many questions!

I’m not entirely sure what the norm.mgz file is? Is this one of the output files from the recon-all?

Secondly, do I use the load DTI function in Freeview?

Thanks!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Date: Tuesday, 18 May 2021 at 14:45 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

You can use freeview and overlay them over norm.mgz

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Tuesday, May 18, 2021 5:56 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

I completed the process and got my 4 ROI files:

Is there a way I can quality check the ROIs and just to see if the files are correct?

Akilas-MacBook-Air:SB301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 47

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 47

Number of voxels and volume for label 47 is = (40673, 40673.000000mm^3)

mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

7.1.1

cwd /Users/akilasekar/Desktop/SB301001

cmdline mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

sysname Darwin

hostname Akilas-MacBook-Air.local

machine x86_64

user akilasekar

input aparc+aseg.nii.gz

frame 0

nErode3d 0

nErode2d 0

output aparc+aseg_labels_label47.mgz

Binarizing based on matching values

nMatch 1

0 47

binval 1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 40673 values in range

Counting number of voxels in first frame

Found 40672 voxels in final mask

Count: 40672 40672.000000 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$

Thanks!

Regards,

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Date: Tuesday, 18 May 2021 at 09:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

Thanks for your message, even if I put one label I am still getting the same error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

@: Expression Syntax.

Thanks for your help!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Date: Tuesday, 18 May 2021 at 04:55 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

Hi Sekar,

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Sunday, May 16, 2021 7:05 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Date: Sunday, 16 May 2021 at 22:54 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Sent: Sunday, May 16, 2021 10:49:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

Yes, you can use that one as well.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Sunday, May 16, 2021 5:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Sunday, May 16, 2021 10:37:04 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Date: Sunday, 16 May 2021 at 22:25 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Sunday, May 16, 2021 4:34 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edumailto:LZOLLEI@mgh.harvard.edu> Sent: Sunday, May 16, 2021 5:22:08 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Friday, May 14, 2021 12:13 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

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Hey,

Thanks for your message. Yes I have!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDUmailto:LZOLLEI@MGH.HARVARD.EDU> Date: Friday, 14 May 2021 at 16:44 To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Cerebellum Segementation

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.ukmailto:ars66@cam.ac.uk> Sent: Friday, May 14, 2021 10:35 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Cerebellum Segementation

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Hello Experts!

Thanks for your help!

Regards,

Akila

Zollei, Lilla,Ph.D.

21 May 21 May

12:34 p.m.

Hi Akila, Yes, the norm file should be in the mri folder of the recon output. To look at the ROI files you just need to load volumes in freeview or call it as freeview -v $volname from the command line. Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Tuesday, May 18, 2021 12:57 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

Thanks for your help, sorry to be asking so many questions!

I’m not entirely sure what the norm.mgz file is? Is this one of the output files from the recon-all?

Secondly, do I use the load DTI function in Freeview?

Thanks!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@MGH.HARVARD.EDU Date: Tuesday, 18 May 2021 at 14:45 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

You can use freeview and overlay them over norm.mgz

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Tuesday, May 18, 2021 5:56 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

I completed the process and got my 4 ROI files:

Is there a way I can quality check the ROIs and just to see if the files are correct?

Akilas-MacBook-Air:SB301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 47

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 47

Number of voxels and volume for label 47 is = (40673, 40673.000000mm^3)

mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

7.1.1

cwd /Users/akilasekar/Desktop/SB301001

cmdline mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

sysname Darwin

hostname Akilas-MacBook-Air.local

machine x86_64

user akilasekar

input aparc+aseg.nii.gz

frame 0

nErode3d 0

nErode2d 0

output aparc+aseg_labels_label47.mgz

Binarizing based on matching values

nMatch 1

0 47

binval 1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 40673 values in range

Counting number of voxels in first frame

Found 40672 voxels in final mask

Count: 40672 40672.000000 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$

Thanks!

Regards,

Akila

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Hi Lilla,

Thanks for your message, even if I put one label I am still getting the same error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

@: Expression Syntax.

Thanks for your help!

Akila

Hi Sekar,

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla

________________________________

External Email - Use Caution

I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

Yes, you can use that one as well.

Lilla

________________________________

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

A.R. Sekar

4 Jun 4 Jun

3:30 p.m.

External Email - Use Caution

Hi Lilla,

I was looking to use the labels 601 – 628 for cerebellar segmentation but I am getting the following output:

Any idea what is wrong here?

Thanks for your help!

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol raparc+aseg.nii --outprefix raparc+aseg_labels --L $label 601 Input file: raparc+aseg.nii Output prefix: raparc+aseg_labels mri_convert raparc+aseg.nii raparc+aseg.nii.gz reading from raparc+aseg.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to raparc+aseg.nii.gz... Label of interest: 601 Number of voxels and volume for label 601 is = (0, 0.000000mm^3) mri_binarize --i raparc+aseg.nii.gz --match 601 --o raparc+aseg_labels_label601.mgz 7.1.1 cwd /Users/akilasekar/Desktop/B301001 cmdline mri_binarize --i raparc+aseg.nii.gz --match 601 --o raparc+aseg_labels_label601.mgz sysname Darwin hostname Akilas-MacBook-Air.local machine x86_64 user akilasekar

input raparc+aseg.nii.gz frame 0 nErode3d 0 nErode2d 0 output raparc+aseg_labels_label601.mgz Binarizing based on matching values nMatch 1 0 601 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found -1 voxels in final mask Count: -1 -1.642760 5242880 -0.000019 mri_binarize done

Regards, Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@MGH.HARVARD.EDU Date: Friday, 21 May 2021 at 17:35 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation Hi Akila, Yes, the norm file should be in the mri folder of the recon output. To look at the ROI files you just need to load volumes in freeview or call it as freeview -v $volname from the command line. Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of A.R. Sekar ars66@cam.ac.uk Sent: Tuesday, May 18, 2021 12:57 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

Thanks for your help, sorry to be asking so many questions!

I’m not entirely sure what the norm.mgz file is? Is this one of the output files from the recon-all?

Secondly, do I use the load DTI function in Freeview?

Thanks!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zollei, Lilla,Ph.D. LZOLLEI@MGH.HARVARD.EDU Date: Tuesday, 18 May 2021 at 14:45 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum Segementation

You can use freeview and overlay them over norm.mgz

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

I completed the process and got my 4 ROI files:

Is there a way I can quality check the ROIs and just to see if the files are correct?

Akilas-MacBook-Air:SB301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 47

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 47

Number of voxels and volume for label 47 is = (40673, 40673.000000mm^3)

mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

7.1.1

cwd /Users/akilasekar/Desktop/SB301001

cmdline mri_binarize --i aparc+aseg.nii.gz --match 47 --o aparc+aseg_labels_label47.mgz

sysname Darwin

hostname Akilas-MacBook-Air.local

machine x86_64

user akilasekar

input aparc+aseg.nii.gz

frame 0

nErode3d 0

nErode2d 0

output aparc+aseg_labels_label47.mgz

Binarizing based on matching values

nMatch 1

0 47

binval 1

binvalnot 0

fstart = 0, fend = 0, nframes = 1

Found 40673 values in range

Counting number of voxels in first frame

Found 40672 voxels in final mask

Count: 40672 40672.000000 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$

Thanks!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks for your message, even if I put one label I am still getting the same error:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest: 7

@: Expression Syntax.

Thanks for your help!

Akila

Hi Sekar,

Just use one label at a time.

Then you will need to move all of these into diffusion space before using them for tractography.

Lilla

________________________________

External Email - Use Caution

I followed the command and got the following expression:

Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label

Input file: aparc+aseg.mgz

Output prefix: aparc+aseg_labels

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

reading from aparc+aseg.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to aparc+aseg.nii.gz...

Label of interest:

@: Expression Syntax.

After I put the label number in, it says command not found.

Thanks for your help!

Regards,

Akila

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

________________________________

Yes, you can use that one as well.

Lilla

________________________________

External Email - Use Caution

Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

________________________________

External Email - Use Caution

Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

________________________________

External Email - Use Caution

Hi Lilla,

That would be ideal!

Thanks

Akila

________________________________

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

________________________________

External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

Hi Akila,

Have you run recon_all on your structural data?

Lilla

________________________________

External Email - Use Caution

Hello Experts!

Thanks for your help!

Regards,

Akila

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freesurfer@nmr.mgh.harvard.edu

20 comments

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participants (3)

A.R. Sekar
Fischl, Bruce
Zollei, Lilla,Ph.D.