[Freesurfer] Recon-all Ending Fast

2021-03-16 Thread A.R. Sekar 
External Email - Use Caution

Hello,

I am trying to run the recon-all function and the whole process is completing 
within a minute or so. I was told that the whole process would take between 
6-24 hours. This is the output I am getting after entering the command:

Akilas-MacBook-Air:Sub01 akilasekar$ recon-all -s sub_01 -i sub1.fspgr.nii

Subject Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551

Current Stamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551

INFO: SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects

Actual FREESURFER_HOME /Applications/freesurfer/7.1.1

Darwin Akilas-MacBook-Air.local 20.3.0 Darwin Kernel Version 20.3.0: Thu Jan 21 
00:07:06 PST 2021; root:xnu-7195.81.3~1/RELEASE_X86_64 x86_64

/Applications/freesurfer/7.1.1/subjects/sub_01

\n mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii 
/Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz \n

mri_convert /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii 
/Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz

reading from /Users/akilasekar/Desktop/Cambridge/Data/Sub01/sub1.fspgr.nii...

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

i_ras = (0, -1, 0)

j_ras = (0, 0, 1)

k_ras = (1, 0, 0)

writing to /Applications/freesurfer/7.1.1/subjects/sub_01/mri/orig/001.mgz...

/Applications/freesurfer/7.1.1/subjects/sub_01/mri/transforms 
/Applications/freesurfer/7.1.1/subjects/sub_01

/Applications/freesurfer/7.1.1/subjects/sub_01



Started at Tue Mar 16 14:41:43 EAT 2021

Ended   at Tue Mar 16 14:41:49 EAT 2021

#@#%# recon-all-run-time-hours 0.002

recon-all -s sub_01 finished without error at Tue Mar 16 14:41:49 EAT 2021

done

It would great if you can help me out! Thank you!

Akila
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[Freesurfer] Cerebellum Segementation

2021-05-14 Thread A.R. Sekar 
External Email - Use Caution

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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Re: [Freesurfer] Cerebellum Segementation

2021-05-14 Thread A.R. Sekar 
External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Friday, 14 May 2021 at 16:44
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Cerebellum Segementation
Hi Akila,
Have you run recon_all on your structural data?
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

External Email - Use Caution

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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[Freesurfer] Cerebellum Segmentation

2021-05-15 Thread A.R. Sekar 
External Email - Use Caution

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. I have also ran recon all on my structural data. 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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Re: [Freesurfer] Cerebellum Segementation

2021-05-16 Thread A.R. Sekar 
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Hi Lilla,

That would be ideal!

Thanks

Akila

Get Outlook for 
iOS<https://secure-web.cisco.com/1cP38p3NqbaspVGxxeEr4rhQGxZJ8gpVNyuSJ6DTK4iNVFYJTbU3DX-Dp-UOJfR9rPfk9x5OIa2nOqZn-IehgsL7vBNsYlBs6xsZhWHJoueKg6-gthg033xmWkAHQ85F1RO-OPRwb32nNFYDNJpatSX3s90fjR6TPAjpfdDtn_1S_H3zWayg0NK_fKnVRNzsVCb9Dl0PC_R8FMvQNsor0DzMnfM6QSIB2FuP5gC7Cb8Qet9BZq3gA5o81ESrWP80eRG5cGbv309lilbk9cPFM_w/https%3A%2F%2Faka.ms%2Fo0ukef>

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Sunday, May 16, 2021 5:22:08 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation

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

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 12:13 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation


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Hey,



Thanks for your message. Yes I have!



Akila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Friday, 14 May 2021 at 16:44
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Cerebellum Segementation

Hi Akila,

Have you run recon_all on your structural data?

Lilla



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

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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Re: [Freesurfer] Cerebellum Segementation

2021-05-16 Thread A.R. Sekar 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Sunday, 16 May 2021 at 22:25
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 4:34 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

External Email - Use Caution
Hi Lilla,

That would be ideal!

Thanks

Akila

Get Outlook for 
iOS<https://secure-web.cisco.com/1cP38p3NqbaspVGxxeEr4rhQGxZJ8gpVNyuSJ6DTK4iNVFYJTbU3DX-Dp-UOJfR9rPfk9x5OIa2nOqZn-IehgsL7vBNsYlBs6xsZhWHJoueKg6-gthg033xmWkAHQ85F1RO-OPRwb32nNFYDNJpatSX3s90fjR6TPAjpfdDtn_1S_H3zWayg0NK_fKnVRNzsVCb9Dl0PC_R8FMvQNsor0DzMnfM6QSIB2FuP5gC7Cb8Qet9BZq3gA5o81ESrWP80eRG5cGbv309lilbk9cPFM_w/https%3A%2F%2Faka.ms%2Fo0ukef>

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Sunday, May 16, 2021 5:22:08 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation

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

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 12:13 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

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Hey,



Thanks for your message. Yes I have!



Akila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Friday, 14 May 2021 at 16:44
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Cerebellum Segementation

Hi Akila,

Have you run recon_all on your structural data?

Lilla



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

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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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Cerebellum Segementation

2021-05-16 Thread A.R. Sekar 
External Email - Use Caution

Sorry for another message,

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

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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 10:37:04 PM
To: Freesurfer support list 
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



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Sunday, 16 May 2021 at 22:25
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 4:34 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

Hi Lilla,



That would be ideal!



Thanks



Akila



Get Outlook for 
iOS<https://secure-web.cisco.com/1cP38p3NqbaspVGxxeEr4rhQGxZJ8gpVNyuSJ6DTK4iNVFYJTbU3DX-Dp-UOJfR9rPfk9x5OIa2nOqZn-IehgsL7vBNsYlBs6xsZhWHJoueKg6-gthg033xmWkAHQ85F1RO-OPRwb32nNFYDNJpatSX3s90fjR6TPAjpfdDtn_1S_H3zWayg0NK_fKnVRNzsVCb9Dl0PC_R8FMvQNsor0DzMnfM6QSIB2FuP5gC7Cb8Qet9BZq3gA5o81ESrWP80eRG5cGbv309lilbk9cPFM_w/https%3A%2F%2Faka.ms%2Fo0ukef>



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Sunday, May 16, 2021 5:22:08 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



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

Lila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 12:13 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

Hey,



Thanks for your message. Yes I have!



Akila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Friday, 14 May 2021 at 16:44
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Cerebellum Segementation

Hi Akila,

Have you run recon_all on your structural data?

Lilla



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

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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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Cerebellum Segementation

2021-05-16 Thread A.R. Sekar 
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 
iOS<https://secure-web.cisco.com/1gqN3EUycQThQVGuEVVLF26HprGoX4yNvtzkB7mw66mArVWqe1ua47g4eK6B2ZnKZ78e3qDdGU2KBt2rnm5gXHyuA7KwCMae-5WV4Dll9B8G1aMcJceC1Bwtd6_JsxXHKf1x2rHHgx04v5i02K7SZ3weUKjlhLLnKj6LTiz91ZRV0e6ii4Cz8Ns9Ht61DrxIi55Rto1bA6VBLaeMT8WN1cd5Pylob6TDmz5o79f3Ln2M7U2HHiY_UjrRlO_nO0sL26L_-mEtR_7gjouG9l8_Ihg/https%3A%2F%2Faka.ms%2Fo0ukef>

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Sunday, May 16, 2021 10:49:04 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation

Yes, you can use that one as well.
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 5:41 PM
To: Freesurfer support list 
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?

Get Outlook for 
iOS<https://secure-web.cisco.com/147PXKkFY6kebtynYSivzZJLuEDgG0lD53ixLapqXi0ddfjq_-5ccN6Kg5Wwbh15wUijedAouXUMgGYryi4GHuciIvz68lHI1JoaAryp25P5kc0NwjRirPjUBwXey23W6cB3O3nUbpamWt3Y6DtncsUND9EObf74KTxYhBSOafqKtk8eu4pugY6OP0PlcFad1dZ-raNEpBJXFiFy2B1pAqqZ2_ctY8SO8pNA4cnh38yGH7-J_z-1QoQ9NNgFUWqI7p4HVyTHhyEJ3Na_bEv3TDw/https%3A%2F%2Faka.ms%2Fo0ukef>

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 10:37:04 PM
To: Freesurfer support list 
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



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Sunday, 16 May 2021 at 22:25
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 4:34 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

Hi Lilla,



That would be ideal!



Thanks



Akila



Get Outlook for 
iOS<https://secure-web.cisco.com/1cP38p3NqbaspVGxxeEr4rhQGxZJ8gpVNyuSJ6DTK4iNVFYJTbU3DX-Dp-UOJfR9rPfk9x5OIa2nOqZn-IehgsL7vBNsYlBs6xsZhWHJoueKg6-gthg033xmWkAHQ85F1RO-OPRwb32nNFYDNJpatSX3s90fjR6TPAjpfdDtn_1S_H3zWayg0NK_fKnVRNzsVCb9Dl0PC_R8FMvQNsor0DzMnfM6QSIB2FuP5gC7Cb8Qet9BZq3gA5o81ESrWP80eRG5cGbv309lilbk9cPFM_w/https%3A%2F%2Faka.ms%2Fo0ukef>



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Sunday, May 16, 2021 5:22:08 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



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

Lila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 12:13 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

Hey,



Thanks for your message. Yes I have!



Akila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Friday, 14 May 2021 at 16:44
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Cerebellum Segementation

Hi Akila,

Have you run recon_all on your structural data?

Lilla



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

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 entir

Re: [Freesurfer] Cerebellum Segementation

2021-05-16 Thread A.R. Sekar 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Sunday, 16 May 2021 at 22:54
To: Freesurfer support list 
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?

Get Outlook for 
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Sunday, May 16, 2021 10:49:04 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation

Yes, you can use that one as well.
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 5:41 PM
To: Freesurfer support list 
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?

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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 10:37:04 PM
To: Freesurfer support list 
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



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Sunday, 16 May 2021 at 22:25
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 4:34 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



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Hi Lilla,



That would be ideal!



Thanks



Akila



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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Sunday, May 16, 2021 5:22:08 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



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

Lila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 12:13 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

Hey,



Thanks for your m

[Freesurfer] Expression Syntax Error

2021-05-17 Thread A.R. Sekar 
External Email - Use Caution

Hello experts,

I am doing cerebellar segmentation from one of my previous posts using the 
command:
isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L 
$label 7,8,46,47

Following the command I am getting an expression syntax error:


Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz 
--outprefix aparc+aseg_labels --L $label 7,8,46,47

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:  7,8,46,47

@: Expression Syntax.

It would be great if you can help me solve this. Thanks!

Akila
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Re: [Freesurfer] Cerebellum Segementation

2021-05-18 Thread A.R. Sekar 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Tuesday, 18 May 2021 at 04:55
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 7:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Sunday, 16 May 2021 at 22:54
To: Freesurfer support list 
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?



Get Outlook for 
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Sunday, May 16, 2021 10:49:04 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



Yes, you can use that one as well.

Lilla



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 5:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



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?



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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 10:37:04 PM
To: Freesurfer support list 
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



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Sunday, 16 May 2021 at 22:25
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16,

Re: [Freesurfer] Cerebellum Segementation

2021-05-18 Thread A.R. Sekar 
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, 40673.00mm^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
 047
binval1
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 40672.00 16777216 0.242424
mri_binarize done
Akilas-MacBook-Air:SB301001 akilasekar$

Thanks!

Regards,
Akila

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Tuesday, 18 May 2021 at 09:04
To: Freesurfer support list 
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

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Tuesday, 18 May 2021 at 04:55
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 7:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Sunday, 16 May 2021 at 22:54
To: Freesurfer support list 
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?



Get Outlook for 
iOS<https://secure-web.cisco.com/1gqN3EUycQThQVGuEVVLF26HprGoX4yNvtzkB7mw66mArVWqe1ua47g4eK6B2ZnKZ78e3qDdGU2KBt2rnm5gXHyuA7KwCMae-5WV4Dll9B8G1aMcJceC1Bwtd6_JsxXHKf1x2rHHgx04v5i02K7SZ3weUKjlhLLnKj6LTiz91ZRV0e6ii4Cz8Ns9Ht61DrxIi55Rto1bA6VBLaeMT8WN1cd5Pylob6TDmz5o79f3Ln2M7U2HHiY_UjrRlO_nO0sL26L_-mEtR_7gjouG9l8_Ihg/https%3A%2F%2Faka.ms%2Fo0ukef>



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Sent: Sunday, May 16, 2021 10:49:04 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



Yes, you can use that one as well.

Lilla



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 5:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

External Email - Use Caution

Sorry for another message,



I have the

Re: [Freesurfer] Cerebellum Segementation

2021-05-18 Thread A.R. Sekar 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Tuesday, 18 May 2021 at 14:45
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation
You can use freeview and overlay them over norm.mgz
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Tuesday, May 18, 2021 5:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

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, 40673.00mm^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

 047

binval1

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 40672.00 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$



Thanks!



Regards,

Akila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Tuesday, 18 May 2021 at 09:04
To: Freesurfer support list 
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



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Tuesday, 18 May 2021 at 04:55
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 7:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Sunday, 16 May 2021 at 22:54
To: Freesurfer support list 
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?



Get Outlook for 
iOS<https://secure-web.cisco.

Re: [Freesurfer] Cerebellum Segementation

2021-05-19 Thread A.R. Sekar 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Tuesday, 18 May 2021 at 17:58
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Tuesday, 18 May 2021 at 14:45
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation
You can use freeview and overlay them over norm.mgz
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Tuesday, May 18, 2021 5:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

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, 40673.00mm^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

 047

binval1

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 40672.00 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$



Thanks!



Regards,

Akila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Tuesday, 18 May 2021 at 09:04
To: Freesurfer support list 
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



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Tuesday, 18 May 2021 at 04:55
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Sunday, May 16, 2021 7:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Sunday, 16 May 2021 at 22:54
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation

External Email - Use Caution

Hi Lilla,



Thanks a lot for your

Re: [Freesurfer] Cerebellum Segementation

2021-05-19 Thread A.R. Sekar 
External Email - Use Caution

Thanks a lot for your help!

Get Outlook for 
iOS<https://secure-web.cisco.com/1x46MFro4vLJ3DVuLFKn6_WMVcQch2a_JjAncVJCQbEYtCkEQ8o6e5mGARFx3oU_eSBvaEMJV8bG0BbAWcOmpf6whnM1j44bfDB2ozMZ3BuJ_Pl8UhnQDPukOItPHYFkbAIhuBXvOK1elVks0Q0z41Mh3Fiz0mki3ILUybhJAry2jxQoO6Afc3EsSvzrEVCLfiTlDk_ZAWhQHhVtfLkm7eYuakl2_NN1jfiV8EfhY-j2PfRsvD2_j27EptLifQ9wXmvKeyn1g1h1-us_olhIbqw/https%3A%2F%2Faka.ms%2Fo0ukef>

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Wednesday, May 19, 2021 3:56:58 PM
To: Freesurfer support list 
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



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of A.R. Sekar
Sent: Wednesday, May 19, 2021 7:12 AM
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of A.R. Sekar mailto:ar...@cam.ac.uk>>
Date: Tuesday, 18 May 2021 at 17:58
To: Freesurfer support list 
mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Zollei, Lilla,Ph.D. 
mailto:lzol...@mgh.harvard.edu>>
Date: Tuesday, 18 May 2021 at 14:45
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Cerebellum Segementation

You can use freeview and overlay them over norm.mgz

Lilla



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



External Email - Use Caution

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, 40673.00mm^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

 047

binval1

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 40672.00 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$



Thanks!



Regards,

Akila



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of A.R. Sekar mailto:ar...@cam.ac.uk>>
Date: Tuesday, 18 May 2021 at 09:04
To: Freesurfer support list 
mailto: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 a

[Freesurfer] Labels #601-#628

2021-06-03 Thread A.R. Sekar 
External Email - Use Caution

Hello Experts,

I am trying to isolate ROIs using labels #601-#628 however I am getting the 
following output and it is the same for each label. 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, 0.00mm^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

binval1

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 -0.19

mri_binarize done

Regards,
Akila
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Re: [Freesurfer] Cerebellum Segementation

2021-06-04 Thread A.R. Sekar 
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, 0.00mm^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
binval1
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 -0.19
mri_binarize done

Regards,
Akila


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Friday, 21 May 2021 at 17:35
To: Freesurfer support list 
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-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Tuesday, May 18, 2021 12:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

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-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Tuesday, 18 May 2021 at 14:45
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation

You can use freeview and overlay them over norm.mgz

Lilla



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Tuesday, May 18, 2021 5:56 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Cerebellum Segementation



External Email - Use Caution

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, 40673.00mm^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

 047

binval1

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 40672.00 16777216 0.242424

mri_binarize done

Akilas-MacBook-Air:SB301001 akilasekar$



Thanks!



Regards,

Akila



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Date: Tuesday, 18 May 2021 at 09:04
To: Freesurfer support list 
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

[Freesurfer] Tracula Anlsysis

2021-06-16 Thread A.R. Sekar 
External Email - Use Caution

Hello Experts,

I am using Tracula to analyse the white matter tracts of the cerebellum. I saw 
that the atlas has the Middle cerebellar 
peduncle,
 does it also have the other 2 major white matter tracts of the cerebellum: 
inferior (ICP), and superior cerebellar peduncles (SCP)? If not how can I go 
about using tracula for the analysis of these white matter tracts?

Thanks for your help!

Regards,
Akila


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[Freesurfer] Isolate Function Error

2021-08-26 Thread A.R. Sekar 
External Email - Use Caution

Hello Experts,

Hope you are well! I am trying to extract ROIs from the aparc+aseg file after 
running recon all however, I am getting the following result for all my images:


ciddrg@CIDDRGs-MacBook-Air C961060 % cd /Volumes/Akila/Cambridge/C961022

ciddrg@CIDDRGs-MacBook-Air C961022 % isolate_labels.csh --vol aparc+aseg.nii 
--outprefix aparc+aseg_labels --L $label 7

Input file: aparc+aseg.nii

Output prefix: aparc+aseg_labels

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

reading from aparc+aseg.nii...

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

Number of voxels and volume for label 7 is = (0, 0.00mm^3)

mri_binarize --i aparc+aseg.nii.gz --match 7 --o aparc+aseg_labels_label7.mgz



7.1.1

cwd /Volumes/Akila/Cambridge/C961022

cmdline mri_binarize --i aparc+aseg.nii.gz --match 7 --o 
aparc+aseg_labels_label7.mgz

sysname  Darwin

hostname CIDDRGs-MacBook-Air.local

machine  x86_64

user ciddrg



input  aparc+aseg.nii.gz

frame  0

nErode3d   0

nErode2d   0

output aparc+aseg_labels_label7.mgz

Binarizing based on matching values

nMatch 1

 0 7

binval1

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 -1.00 16777216 -0.06

mri_binarize done

ciddrg@CIDDRGs-MacBook-Air C961022 %

Could you help me with where the error might be? I would really appreciate your 
help, thank you!

Regards,
Akila


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