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

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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

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

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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

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

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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.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

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?

Get Outlook for iOS

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

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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-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

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.

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

Get Outlook for iOS

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

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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

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