External Email - Use Caution
Thanks so much for the help!
-Colleen
________________________________
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: Wednesday, May 12, 2021 2:16 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Infant Freesurfer exiting without error
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER
<ccpletc...@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
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER
<ccpletc...@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
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER
<ccpletc...@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
External Email - Use Caution
Hi,
Just checking in about this question. Please let me know if you need anything
else from me!
Thanks,
Colleen
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER
<ccpletc...@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
External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D.
<lzol...@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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of COLLEEN PLETCHER
<ccpletc...@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
External Email - Use Caution
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
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