I included the list of FS labels with their IDs. When you know the correspondences, you should be able to use scripts / FS commands to change the labels automatically.
Lila
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER <ccpletcher@medicine.wisc.edu>
Sent: Tuesday, May 11, 2021 4:28 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
 

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Hello, 

Getting a list of the labels would be fantastic! Also, when relabeling the segmentations, do you normally just do that by hand? 

Thanks so much, 

Colleen
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: Thursday, May 6, 2021 4:14 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
 
Hi Colleen,
The segmentations just need to be relabled in order to match the labels that are produced by the infantFS pipeline. I am happy to send you a list of lables that get generated by our tool and then you can match those up with the ones that you get with FSL.
Best, Lilla
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER <ccpletcher@medicine.wisc.edu>
Sent: Tuesday, April 27, 2021 4:11 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
 

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Hi,

I was using FSL anat in order to do the initial segmentation for the --segfile input. I am not sure how to put FS aseg labels in something that is not a freesurfer aseg file. Can you offer any advice on how to do this? 

Thanks so much for the help!

-Colleen 
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: Saturday, April 24, 2021 2:14 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
 
Hi Colleen,
Do you have all the FS aseg lables in your input segmentation file?
Lilla
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER <ccpletcher@medicine.wisc.edu>
Sent: Friday, April 23, 2021 3:01 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
 

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Hi, 

Just checking in about this question. Please let me know if you need anything else from me!

Thanks, 

Colleen
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER <ccpletcher@medicine.wisc.edu>
Sent: Tuesday, April 13, 2021 12:48 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
 

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Hello, 

I have attached the log file and the command used is the first line, please let me know if you need anything else.

-Colleen
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: Tuesday, April 13, 2021 12:33 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
 
Hi Colleen,

 Can you send the exact command that you used and also the log file for more information?

Best, Lilla
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER <ccpletcher@medicine.wisc.edu>
Sent: Tuesday, April 13, 2021 1:29 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Infant Freesurfer exiting without error
 

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Hi, 

I am trying to run infant freesurfer using the --segfile and --masked options. When I attempt to run it, it runs for a bit and then I get this: 

USAGE: mri_or  <options> fname1 fname2 .. 



After this, the program exits. I am not getting any error, so I am confused about why it is exiting suddenly? 


Thank you very much!


-Colleen