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-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

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-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

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

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-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

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-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

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-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

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

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-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

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-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

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-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

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-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

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

External Email - Use Caution

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: 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-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

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-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

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-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

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-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

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-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

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