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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@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 $label 7
Input file: aparc+aseg.mgz
Output prefix: aparc+aseg_labels
mri_convert aparc+aseg.mgz aparc+aseg.nii.gz
reading from aparc+aseg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to aparc+aseg.nii.gz...
Label of interest: 7
@: Expression Syntax.
Thanks for your help!
Akila
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@mgh.harvard.edu>
Date: Tuesday, 18 May 2021 at 04:55
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation
Hi Sekar,
Just use one label at a time.
Then you will need to move all of these into diffusion space before using them
for tractography.
Lilla
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@cam.ac.uk>
Sent: Sunday, May 16, 2021 7:05 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation
External Email - Use Caution
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I followed the command and got the following expression:
Akilas-MacBook-Air:B301001 akilasekar$ 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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@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?
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________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@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
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________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@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
External Email - Use Caution
Hey,
Thanks for your message. Yes I have!
Akila
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@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!
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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