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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@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 $volname
from the command line.
Lilla
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@cam.ac.uk>
Sent: Tuesday, May 18, 2021 12:57 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation
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Hi Lilla,
Thanks for your help, sorry to be asking so many questions!
I’m not entirely sure what the norm.mgz file is? Is this one of the output
files from the recon-all?
Secondly, do I use the load DTI function in Freeview?
Thanks!
Akila
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@mgh.harvard.edu>
Date: Tuesday, 18 May 2021 at 14:45
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation
You can use freeview and overlay them over norm.mgz
Lilla
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of A.R. Sekar
<ar...@cam.ac.uk>
Sent: Tuesday, May 18, 2021 5:56 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation
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Hi Lilla,
I completed the process and got my 4 ROI files:
Is there a way I can quality check the ROIs and just to see if the files are
correct?
Akilas-MacBook-Air:SB301001 akilasekar$ 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
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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
External Email - Use Caution
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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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